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Laver TW, Wakeling MN, Caswell RC, Bunce B, Yau D, Männistö JME, Houghton JAL, Hopkins JJ, Weedon MN, Saraff V, Kershaw M, Honey EM, Murphy N, Giri D, Nath S, Tangari Saredo A, Banerjee I, Hussain K, Owens NDL, Flanagan SE. Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements. Eur J Hum Genet 2024:10.1038/s41431-024-01593-z. [PMID: 38605124 DOI: 10.1038/s41431-024-01593-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Persistent congenital hyperinsulinism (HI) is a rare genetically heterogeneous condition characterised by dysregulated insulin secretion leading to life-threatening hypoglycaemia. For up to 50% of affected individuals screening of the known HI genes does not identify a disease-causing variant. Large deletions have previously been used to identify novel regulatory regions causing HI. Here, we used genome sequencing to search for novel large (>1 Mb) deletions in 180 probands with HI of unknown cause and replicated our findings in a large cohort of 883 genetically unsolved individuals with HI using off-target copy number variant calling from targeted gene panels. We identified overlapping heterozygous deletions in five individuals (range 3-8 Mb) spanning chromosome 20p11.2. The pancreatic beta-cell transcription factor gene, FOXA2, a known cause of HI was deleted in two of the five individuals. In the remaining three, we found a minimal deleted region of 2.4 Mb adjacent to FOXA2 that encompasses multiple non-coding regulatory elements that are in conformational contact with FOXA2. Our data suggests that the deletions in these three children may cause disease through the dysregulation of FOXA2 expression. These findings provide new insights into the regulation of FOXA2 in the beta-cell and confirm an aetiological role for chromosome 20p11.2 deletions in syndromic HI.
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Affiliation(s)
- Thomas W Laver
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Matthew N Wakeling
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Richard C Caswell
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Benjamin Bunce
- The Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Daphne Yau
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Jonna M E Männistö
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
- Department of Health Sciences, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jayne A L Houghton
- The Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jasmin J Hopkins
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Vrinda Saraff
- Department of Paediatric Endocrinology and Diabetes, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Melanie Kershaw
- Department of Paediatric Endocrinology and Diabetes, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Nuala Murphy
- Department of Paediatric Endocrinology, Children's University Hospital, Dublin, Ireland
| | - Dinesh Giri
- Department of Paediatric Endocrinology, Bristol Royal Hospital for Children, Bristol, UK
| | | | | | - Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Khalid Hussain
- Department of Paediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Nick D L Owens
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK.
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2
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Russ-Silsby J, Patel KA, Laver TW, Hawkes G, Johnson MB, Wakeling MN, Patil PP, Hattersley AT, Flanagan SE, Weedon MN, De Franco E. The Role of ONECUT1 Variants in Monogenic and Type 2 Diabetes Mellitus. Diabetes 2023; 72:1729-1734. [PMID: 37639628 DOI: 10.2337/db23-0498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
ONECUT1 (also known as HNF6) is a transcription factor involved in pancreatic development and β-cell function. Recently, biallelic variants in ONECUT1 were reported as a cause of neonatal diabetes mellitus (NDM) in two subjects, and missense monoallelic variants were associated with type 2 diabetes and possibly maturity-onset diabetes of the young (MODY). Here we examine the role of ONECUT1 variants in NDM, MODY, and type 2 diabetes in large international cohorts of subjects with monogenic diabetes and >400,000 subjects from UK Biobank. We identified a biallelic frameshift ONECUT1 variant as the cause of NDM in one individual. However, we found no enrichment of missense or null ONECUT1 variants among 484 individuals clinically suspected of MODY, in whom all known genes had been excluded. Finally, using a rare variant burden test in the UK Biobank European cohort, we identified a significant association between heterozygous ONECUT1 null variants and type 2 diabetes (P = 0.006) but did not find an association between missense variants and type 2 diabetes. Our results confirm biallelic ONECUT1 variants as a cause of NDM and highlight monoallelic null variants as a risk factor for type 2 diabetes. These findings confirm the critical role of ONECUT1 in human β-cell function. ARTICLE HIGHLIGHTS
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Affiliation(s)
- James Russ-Silsby
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Kashyap A Patel
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Thomas W Laver
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Gareth Hawkes
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Matthew B Johnson
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Matthew N Wakeling
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Prashant P Patil
- The Society for the Rehabilitation of Crippled Children Narayana Health Children's Hospital, Mumbai, India
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
| | - Elisa De Franco
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, U.K
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Hopkins JJ, Childs AJ, Houghton JAL, Hewat TI, Atapattu N, Johnson MB, Patel KA, Laver TW, Flanagan SE. Hyperinsulinemic Hypoglycemia Diagnosed in Childhood Can Be Monogenic. J Clin Endocrinol Metab 2023; 108:680-687. [PMID: 36239000 PMCID: PMC9931180 DOI: 10.1210/clinem/dgac604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/05/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Congenital hyperinsulinism (HI) is characterized by inappropriate insulin secretion despite low blood glucose. Persistent HI is often monogenic, with the majority of cases diagnosed in infancy. Less is known about the contribution of monogenic forms of disease in those presenting in childhood. OBJECTIVE We investigated the likelihood of finding a genetic cause in childhood-onset HI and explored potential factors leading to later age at presentation of disease. METHODS We screened known disease-causing genes in 1848 individuals with HI, referred for genetic testing as part of routine clinical care. Individuals were classified as infancy-onset (diagnosed with HI < 12 months of age) or childhood-onset (diagnosed at age 1-16 years). We assessed clinical characteristics and the genotypes of individuals with monogenic HI diagnosed in childhood to gain insights into the later age at diagnosis of HI in these children. RESULTS We identified the monogenic cause in 24% (n = 42/173) of the childhood-onset HI cohort; this was significantly lower than the proportion of genetic diagnoses in infancy-onset cases (74.5% [n = 1248/1675], P < 0.00001). Most (75%) individuals with genetically confirmed childhood-onset HI were diagnosed before 2.7 years, suggesting these cases represent the tail end of the normal distribution in age at diagnosis. This is supported by the finding that 81% of the variants identified in the childhood-onset cohort were detected in those diagnosed in infancy. CONCLUSION We have shown that monogenic HI is an important cause of hyperinsulinism presenting outside of infancy. Genetic testing should be considered in children with persistent hyperinsulinism, regardless of age at diagnosis.
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Affiliation(s)
| | | | - Jayne A L Houghton
- The Genomics Laboratory, Royal Devon University Healthcare NHS foundation Trust, Exeter EX2 5DW, UK
| | - Thomas I Hewat
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Navoda Atapattu
- Paediatric Endocrinology, Lady Ridgeway Hospital, Colombo 00800, Sri Lanka
| | - Matthew B Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
- The Genomics Laboratory, Royal Devon University Healthcare NHS foundation Trust, Exeter EX2 5DW, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Sarah E Flanagan
- Correspondence: Dr. Sarah E. Flanagan, Associate Professor in Genomic Medicine, RILD Building, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK.
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Mirshahi UL, Colclough K, Wright CF, Wood AR, Beaumont RN, Tyrrell J, Laver TW, Stahl R, Golden A, Goehringer JM, Frayling TF, Hattersley AT, Carey DJ, Weedon MN, Patel KA. Reduced penetrance of MODY-associated HNF1A/HNF4A variants but not GCK variants in clinically unselected cohorts. Am J Hum Genet 2022; 109:2018-2028. [PMID: 36257325 PMCID: PMC9674944 DOI: 10.1016/j.ajhg.2022.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/28/2022] [Indexed: 01/26/2023] Open
Abstract
The true prevalence and penetrance of monogenic disease variants are often not known because of clinical-referral ascertainment bias. We comprehensively assess the penetrance and prevalence of pathogenic variants in HNF1A, HNF4A, and GCK that account for >80% of monogenic diabetes. We analyzed clinical and genetic data from 1,742 clinically referred probands, 2,194 family members, clinically unselected individuals from a US health system-based cohort (n = 132,194), and a UK population-based cohort (n = 198,748). We show that one in 1,500 individuals harbor a pathogenic variant in one of these genes. The penetrance of diabetes for HNF1A and HNF4A pathogenic variants was substantially lower in the clinically unselected individuals compared to clinically referred probands and was dependent on the setting (32% in the population, 49% in the health system cohort, 86% in a family member, and 98% in probands for HNF1A). The relative risk of diabetes was similar across the clinically unselected cohorts highlighting the role of environment/other genetic factors. Surprisingly, the penetrance of pathogenic GCK variants was similar across all cohorts (89%-97%). We highlight that pathogenic variants in HNF1A, HNF4A, and GCK are not ultra-rare in the population. For HNF1A and HNF4A, we need to tailor genetic interpretation and counseling based on the setting in which a pathogenic monogenic variant was identified. GCK is an exception with near-complete penetrance in all settings. This along with the clinical implication of diagnosis makes it an excellent candidate for the American College of Medical Genetics secondary gene list.
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Affiliation(s)
| | - Kevin Colclough
- Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Richard Stahl
- Geisinger Clinic, Geisinger Health System, Danville, PA, USA
| | - Alicia Golden
- Geisinger Clinic, Geisinger Health System, Danville, PA, USA
| | | | - Timothy F Frayling
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - David J Carey
- Geisinger Clinic, Geisinger Health System, Danville, PA, USA
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK.
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK.
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5
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Hewat TI, Laver TW, Houghton JAL, Männistö JME, Alvi S, Brearey SP, Cody D, Dastamani A, De los Santos La Torre M, Murphy N, Rami‐Merhar B, Wefers B, Huopio H, Banerjee I, Johnson MB, Flanagan SE. Increased referrals for congenital hyperinsulinism genetic testing in children with trisomy 21 reflects the high burden of non-genetic risk factors in this group. Pediatr Diabetes 2022; 23:457-461. [PMID: 35294086 PMCID: PMC9310623 DOI: 10.1111/pedi.13333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Hyperinsulinism results from inappropriate insulin secretion during hypoglycaemia. Down syndrome is causally linked to a number of endocrine disorders including Type 1 diabetes and neonatal diabetes. We noted a high number of individuals with Down syndrome referred for hyperinsulinism genetic testing, and therefore aimed to investigate whether the prevalence of Down syndrome was increased in our hyperinsulinism cohort compared to the population. METHODS We identified individuals with Down syndrome referred for hyperinsulinism genetic testing to the Exeter Genomics Laboratory between 2008 and 2020. We sequenced the known hyperinsulinism genes in all individuals and investigated their clinical features. RESULTS We identified 11 individuals with Down syndrome in a cohort of 2011 patients referred for genetic testing for hyperinsulinism. This represents an increased prevalence compared to the population (2.5/2011 expected vs. 11/2011 observed, p = 6.8 × 10-5 ). A pathogenic ABCC8 mutation was identified in one of the 11 individuals. Of the remaining 10 individuals, five had non-genetic risk factors for hyperinsulinism resulting from the Down syndrome phenotype: intrauterine growth restriction, prematurity, gastric/oesophageal surgery, and asparaginase treatment for leukaemia. For five individuals no risk factors for hypoglycaemia were reported although two of these individuals had transient hyperinsulinism and one was lost to follow-up. CONCLUSIONS Down syndrome is more common in patients with hyperinsulinism than in the population. This is likely due to an increased burden of non-genetic risk factors resulting from the Down syndrome phenotype. Down syndrome should not preclude genetic testing as coincidental monogenic hyperinsulinism and Down syndrome is possible.
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Affiliation(s)
- Thomas I. Hewat
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - Thomas W. Laver
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | | | - Jonna M. E. Männistö
- Department of PediatricsUniversity of Eastern Finland and Kuopio University HospitalKuopioFinland
| | | | | | - Declan Cody
- Children's Health Ireland at CrumlinDublinIreland
| | - Antonia Dastamani
- Endocrinology DepartmentGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | | | | | - Birgit Rami‐Merhar
- Department of Pediatric and Adolescent MedicineMedical University of ViennaViennaAustria
| | | | - Hanna Huopio
- Department of PediatricsKuopio University HospitalKuopioFinland
| | - Indraneel Banerjee
- Department of Paediatric EndocrinologyRoyal Manchester Children's HospitalManchesterUK
| | - Matthew B. Johnson
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - Sarah E. Flanagan
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
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Abstract
CONTEXT PLIN1 encodes perilipin-1, which coats lipid droplets in adipocytes and is involved in droplet formation, triglyceride storage, and lipolysis. Rare PLIN1 frameshift variants that extend the translated protein have been described to cause lipodystrophy. OBJECTIVE This work aimed to test whether PLIN1 protein-truncating variants (PTVs) cause lipodystrophy in a large population-based cohort. METHODS We identified individuals with PLIN1 PTVs in individuals with exome data in the UK Biobank. We performed gene-burden testing for individuals with PLIN1 PTVs. We replicated the associations using data from the T2D Knowledge portal. We performed a phenome-wide association study using publicly available association statistics. A total of 362 791 individuals in the UK Biobank, a population-based cohort, and 43 125 individuals in the T2D Knowledge portal, a type 2 diabetes (T2D) case-control study, were included in the analyses. Main outcome measures included 22 diseases and traits relevant to lipodystrophy. RESULTS The 735 individuals with PLIN1 PTVs had a favorable metabolic profile. These individuals had increased high-density lipoprotein cholesterol (0.12 mmol/L; 95% CI, 0.09 to 0.14, P = 2 × 10-18), reduced triglycerides (-0.22 mmol/L; 95% CI, -0.29 to -0.14, P = 3 × 10-11), reduced waist-to-hip ratio (-0.02; 95% CI, -0.02 to -0.01, P = 9 × 10-12), and reduced systolic blood pressure (-1.67 mm Hg; 95% CI, -3.25 to -0.09, P = .05). These associations were consistent in the smaller T2D Knowledge portal cohort. In the UK Biobank, PLIN1 PTVs were associated with reduced risk of myocardial infarction (odds ratio [OR] = 0.59; 95% CI, 0.35 to 0.93, P = .02) and hypertension (OR = 0.85; 95% CI, 0.73 to 0.98, P = .03), but not T2D (OR = 0.99; 95% CI, 0.63-1.51, P = .99). CONCLUSION Our study suggests that PLIN1 haploinsufficiency causes a favorable metabolic profile and may protect against cardiovascular disease.
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Affiliation(s)
| | - Shivang Burman
- University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Thomas W Laver
- University of Exeter Medical School, Exeter, EX2 5DW, UK
| | | | | | - Michael N Weedon
- University of Exeter Medical School, Exeter, EX2 5DW, UK
- Correspondence: Michael N. Weedon, PhD, RILD Building, University of Exeter Medical School, Barrack Rd, Exeter, EX2 5DW, UK.
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Laver TW, Wakeling MN, Knox O, Colclough K, Wright CF, Ellard S, Hattersley AT, Weedon MN, Patel KA. Evaluation of Evidence for Pathogenicity Demonstrates That BLK, KLF11, and PAX4 Should Not Be Included in Diagnostic Testing for MODY. Diabetes 2022; 71:1128-1136. [PMID: 35108381 PMCID: PMC9044126 DOI: 10.2337/db21-0844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/30/2022] [Indexed: 12/05/2022]
Abstract
Maturity-onset diabetes of the young (MODY) is an autosomal dominant form of monogenic diabetes, reported to be caused by variants in 16 genes. Concern has been raised about whether variants in BLK (MODY11), KLF11 (MODY7), and PAX4 (MODY9) cause MODY. We examined variant-level genetic evidence (cosegregation with diabetes and frequency in population) for published putative pathogenic variants in these genes and used burden testing to test gene-level evidence in a MODY cohort (n = 1,227) compared with a control population (UK Biobank [n = 185,898]). For comparison we analyzed well-established causes of MODY, HNF1A, and HNF4A. The published variants in BLK, KLF11, and PAX4 showed poor cosegregation with diabetes (combined logarithm of the odds [LOD] scores ≤1.2), compared with HNF1A and HNF4A (LOD scores >9), and are all too common to cause MODY (minor allele frequency >4.95 × 10-5). Ultra-rare missense and protein-truncating variants (PTV) were not enriched in a MODY cohort compared with the UK Biobank population (PTV P > 0.05, missense P > 0.1 for all three genes) while HNF1A and HNF4A were enriched (P < 10-6). Findings of sensitivity analyses with different population cohorts supported our results. Variant and gene-level genetic evidence does not support BLK, KLF11, or PAX4 as a cause of MODY. They should not be included in MODY diagnostic genetic testing.
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Affiliation(s)
- Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Matthew N. Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Olivia Knox
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Caroline F. Wright
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | | | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - Kashyap A. Patel
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
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8
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Hewat TI, Yau D, Jerome JCS, Laver TW, Houghton JAL, Shields BM, Flanagan SE, Patel KA. Birth weight and diazoxide unresponsiveness strongly predict the likelihood of congenital hyperinsulinism due to a mutation in ABCC8 or KCNJ11. Eur J Endocrinol 2021; 185:813-818. [PMID: 34633981 PMCID: PMC7611977 DOI: 10.1530/eje-21-0476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Mutations in the KATP channel genes, ABCC8 and KCNJ11, are the most common cause of congenital hyperinsulinism. The diagnosis of KATP-hyperinsulinism is important for the clinical management of the condition. We aimed to determine the clinical features that help to identify KATP-hyperinsulinism at diagnosis. DESIGN We studied 761 individuals with KATP-hyperinsulinism and 862 probands with hyperinsulinism of unknown aetiology diagnosed before 6 months of age. All were referred as part of routine clinical care. METHODS We compared the clinical features of KATP-hyperinsulinism and unknown hyperinsulinism cases. We performed logistic regression and receiver operator characteristic (ROC) analysis to identify the features that predict KATP-hyperinsulinism. RESULTS Higher birth weight, diazoxide unresponsiveness and diagnosis in the first week of life were independently associated with KATP-hyperinsulinism (adjusted odds ratio: 4.5 (95% CI: 3.4-5.9), 0.09 (0.06-0.13) and 3.3 (2.0-5.0) respectively). Birth weight and diazoxide unresponsiveness were additive and highly discriminatory for identifying KATP-hyperinsulinism (ROC area under the curve for birth weight 0.80, diazoxide responsiveness 0.77, and together 0.88, 95% CI: 0.85-0.90). In this study, 86% born large for gestation and 78% born appropriate for gestation and who did not respond to diazoxide treatment had KATP-hyperinsulinism. In contrast, of those individuals born small for gestation, none who were diazoxide responsive and only 4% of those who were diazoxide unresponsive had KATP-hyperinsulinism. CONCLUSIONS Individuals with hyperinsulinism born appropriate or large for gestation and unresponsive to diazoxide treatment are most likely to have an ABCC8 or KCNJ11 mutation. These patients should be prioritised for genetic testing of KATP channel genes.
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Affiliation(s)
- Thomas I Hewat
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Daphne Yau
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Joseph C S Jerome
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Beverley M Shields
- National Institute for Health Research Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- Royal Devon and Exeter Foundation Hospital, Exeter, UK
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9
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Caswell RC, Snowsill T, Houghton JAL, Chakera AJ, Shepherd MH, Laver TW, Knight BA, Wright D, Hattersley AT, Ellard S. Noninvasive Fetal Genotyping by Droplet Digital PCR to Identify Maternally Inherited Monogenic Diabetes Variants. Clin Chem 2021; 66:958-965. [PMID: 32533152 PMCID: PMC7611030 DOI: 10.1093/clinchem/hvaa104] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Babies of women with heterozygous pathogenic glucokinase (GCK) variants causing mild fasting hyperglycemia are at risk of macrosomia if they do not inherit the variant. Conversely, babies who inherit a pathogenic hepatocyte nuclear factor 4α (HNF4A) diabetes variant are at increased risk of high birth weight. Noninvasive fetal genotyping for maternal pathogenic variants would inform pregnancy management. METHODS Droplet digital PCR was used to quantify reference and variant alleles in cell-free DNA extracted from blood from 38 pregnant women heterozygous for a GCK or HNF4A variant and to determine fetal fraction by measurement of informative maternal and paternal variants. Droplet numbers positive for the reference/alternate allele together with the fetal fraction were used in a Bayesian analysis to derive probability for the fetal genotype. The babies' genotypes were ascertained postnatally by Sanger sequencing. RESULTS Droplet digital PCR assays for GCK or HNF4A variants were validated for testing in all 38 pregnancies. Fetal fraction of ≥2% was demonstrated in at least 1 cell-free DNA sample from 33 pregnancies. A threshold of ≥0.95 for calling homozygous reference genotypes and ≤0.05 for heterozygous fetal genotypes allowed correct genotype calls for all 33 pregnancies with no false-positive results. In 30 of 33 pregnancies, a result was obtained from a single blood sample. CONCLUSIONS This assay can be used to identify pregnancies at risk of macrosomia due to maternal monogenic diabetes variants.
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Affiliation(s)
- Richard C Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Tristan Snowsill
- Institute of Health Research, University of Exeter Medical School, Exeter, UK
| | - Jayne A L Houghton
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Ali J Chakera
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Royal Sussex County Hospital, Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Maggie H Shepherd
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Bridget A Knight
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - David Wright
- Institute of Health Research, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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10
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De Franco E, Lytrivi M, Ibrahim H, Montaser H, Wakeling MN, Fantuzzi F, Patel K, Demarez C, Cai Y, Igoillo-Esteve M, Cosentino C, Lithovius V, Vihinen H, Jokitalo E, Laver TW, Johnson MB, Sawatani T, Shakeri H, Pachera N, Haliloglu B, Ozbek MN, Unal E, Yıldırım R, Godbole T, Yildiz M, Aydin B, Bilheu A, Suzuki I, Flanagan SE, Vanderhaeghen P, Senée V, Julier C, Marchetti P, Eizirik DL, Ellard S, Saarimäki-Vire J, Otonkoski T, Cnop M, Hattersley AT. YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress. J Clin Invest 2021; 130:6338-6353. [PMID: 33164986 PMCID: PMC7685733 DOI: 10.1172/jci141455] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
Neonatal diabetes is caused by single gene mutations reducing pancreatic β cell number or impairing β cell function. Understanding the genetic basis of rare diabetes subtypes highlights fundamental biological processes in β cells. We identified 6 patients from 5 families with homozygous mutations in the YIPF5 gene, which is involved in trafficking between the endoplasmic reticulum (ER) and the Golgi. All patients had neonatal/early-onset diabetes, severe microcephaly, and epilepsy. YIPF5 is expressed during human brain development, in adult brain and pancreatic islets. We used 3 human β cell models (YIPF5 silencing in EndoC-βH1 cells, YIPF5 knockout and mutation knockin in embryonic stem cells, and patient-derived induced pluripotent stem cells) to investigate the mechanism through which YIPF5 loss of function affects β cells. Loss of YIPF5 function in stem cell–derived islet cells resulted in proinsulin retention in the ER, marked ER stress, and β cell failure. Partial YIPF5 silencing in EndoC-βH1 cells and a patient mutation in stem cells increased the β cell sensitivity to ER stress–induced apoptosis. We report recessive YIPF5 mutations as the genetic cause of a congenital syndrome of microcephaly, epilepsy, and neonatal/early-onset diabetes, highlighting a critical role of YIPF5 in β cells and neurons. We believe this is the first report of mutations disrupting the ER-to-Golgi trafficking, resulting in diabetes.
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Affiliation(s)
- Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Maria Lytrivi
- ULB Center for Diabetes Research and.,Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew N Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Federica Fantuzzi
- ULB Center for Diabetes Research and.,Endocrinology and Metabolism, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Kashyap Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | | | - Ying Cai
- ULB Center for Diabetes Research and
| | | | | | - Väinö Lithovius
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Matthew B Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | | | | | | | | | | | - Edip Unal
- Dicle University, Faculty of Medicine, Department of Pediatric Endocrinology, Diyarbakır, Turkey
| | - Ruken Yıldırım
- Dicle University, Faculty of Medicine, Department of Pediatric Endocrinology, Diyarbakır, Turkey
| | | | - Melek Yildiz
- Istanbul University, Istanbul Faculty of Medicine, Department of Pediatric Endocrinology, Istanbul, Turkey
| | - Banu Aydin
- Kanuni Sultan Suleyman Training and Research Hospital, Department of Pediatric Endocrinology, Istanbul, Turkey
| | - Angeline Bilheu
- Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Ikuo Suzuki
- Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Pierre Vanderhaeghen
- Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.,Welbio, Université Libre de Bruxelles, Brussels, Belgium
| | - Valérie Senée
- Université de Paris, Faculté de Médecine Paris-Diderot, U958, Paris, France
| | - Cécile Julier
- Université de Paris, Faculté de Médecine Paris-Diderot, U958, Paris, France
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Decio L Eizirik
- ULB Center for Diabetes Research and.,Welbio, Université Libre de Bruxelles, Brussels, Belgium.,Indiana Biosciences Research Institute, Indianapolis, Indiana, USA
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Miriam Cnop
- ULB Center for Diabetes Research and.,Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
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11
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Banerjee I, Senniappan S, Laver TW, Caswell R, Zenker M, Mohnike K, Cheetham T, Wakeling MN, Ismail D, Lennerz B, Splitt M, Berberoğlu M, Empting S, Wabitsch M, Pötzsch S, Shah P, Siklar Z, Verge CF, Weedon MN, Ellard S, Hussain K, Flanagan SE. Refinement of the critical genomic region for congenital hyperinsulinism in the Chromosome 9p deletion syndrome. Wellcome Open Res 2020; 4:149. [PMID: 32832699 PMCID: PMC7422856 DOI: 10.12688/wellcomeopenres.15465.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Large contiguous gene deletions at the distal end of the short arm of chromosome 9 result in the complex multi-organ condition chromosome 9p deletion syndrome. A range of clinical features can result from these deletions with the most common being facial dysmorphisms and neurological impairment. Congenital hyperinsulinism is a rarely reported feature of the syndrome with the genetic mechanism for the dysregulated insulin secretion being unknown. Methods: We studied the clinical and genetic characteristics of 12 individuals with chromosome 9p deletions who had a history of neonatal hypoglycaemia. Using off-target reads generated from targeted next-generation sequencing of the genes known to cause hyperinsulinaemic hypoglycaemia (n=9), or microarray analysis (n=3), we mapped the minimal shared deleted region on chromosome 9 in this cohort. Targeted sequencing was performed in three patients to search for a recessive mutation unmasked by the deletion. Results: In 10/12 patients with hypoglycaemia, hyperinsulinism was confirmed biochemically. A range of extra-pancreatic features were also reported in these patients consistent with the diagnosis of the Chromosome 9p deletion syndrome. The minimal deleted region was mapped to 7.2 Mb, encompassing 38 protein-coding genes. In silico analysis of these genes highlighted SMARCA2 and RFX3 as potential candidates for the hypoglycaemia. Targeted sequencing performed on three of the patients did not identify a second disease-causing variant within the minimal deleted region. Conclusions: This study identifies 9p deletions as an important cause of hyperinsulinaemic hypoglycaemia and increases the number of cases reported with 9p deletions and hypoglycaemia to 15 making this a more common feature of the syndrome than previously appreciated. Whilst the precise genetic mechanism of the dysregulated insulin secretion could not be determined in these patients, mapping the deletion breakpoints highlighted potential candidate genes for hypoglycaemia within the deleted region.
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Affiliation(s)
- Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Senthil Senniappan
- Department of Paediatric Endocrinology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Martin Zenker
- Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Klaus Mohnike
- Department of Paediatrics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Tim Cheetham
- Department of Paediatric Endocrinology, Royal Victoria Infirmary, Newcastle, UK
| | - Matthew N. Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Dunia Ismail
- Department of Paediatric Endocrinology & Diabetes, Royal Alexandra Children’s Hospital, Brighton, UK
| | - Belinda Lennerz
- Department of Paediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Merih Berberoğlu
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara, Turkey
| | - Susann Empting
- Department of Paediatrics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Martin Wabitsch
- Department of Paediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Simone Pötzsch
- Department for Children and Adolescent Medicine, HELIOS Vogtland-Klinikum Plauen, Plauen, Germany
| | - Pratik Shah
- Endocrinology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Zeynep Siklar
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara, Turkey
| | - Charles F. Verge
- Department of Endocrinology, Sydney Children's Hospital, Randwick and School of Women's and Children's Health,, Sydney, New South Wales, Australia
| | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Khalid Hussain
- Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Sarah E. Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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12
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De Franco E, Saint-Martin C, Brusgaard K, Knight Johnson AE, Aguilar-Bryan L, Bowman P, Arnoux JB, Larsen AR, Sanyoura M, Greeley SAW, Calzada-León R, Harman B, Houghton JAL, Nishimura-Meguro E, Laver TW, Ellard S, Del Gaudio D, Christesen HT, Bellanné-Chantelot C, Flanagan SE. Update of variants identified in the pancreatic β-cell K ATP channel genes KCNJ11 and ABCC8 in individuals with congenital hyperinsulinism and diabetes. Hum Mutat 2020; 41:884-905. [PMID: 32027066 PMCID: PMC7187370 DOI: 10.1002/humu.23995] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/08/2020] [Accepted: 02/04/2020] [Indexed: 01/03/2023]
Abstract
The most common genetic cause of neonatal diabetes and hyperinsulinism is pathogenic variants in ABCC8 and KCNJ11. These genes encode the subunits of the β-cell ATP-sensitive potassium channel, a key component of the glucose-stimulated insulin secretion pathway. Mutations in the two genes cause dysregulated insulin secretion; inactivating mutations cause an oversecretion of insulin, leading to congenital hyperinsulinism, whereas activating mutations cause the opposing phenotype, diabetes. This review focuses on variants identified in ABCC8 and KCNJ11, the phenotypic spectrum and the treatment implications for individuals with pathogenic variants.
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Affiliation(s)
- Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Cécile Saint-Martin
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Klaus Brusgaard
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Amy E Knight Johnson
- Department of Human Genetics, University of Chicago Genetic Services Laboratory, The University of Chicago, Chicago, Illinois
| | | | - Pamela Bowman
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jean-Baptiste Arnoux
- Reference Center for Inherited Metabolic Diseases, Necker-Enfants Malades Hospital, Paris, France
| | - Annette Rønholt Larsen
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - May Sanyoura
- Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, Kovler Diabetes Center, University of Chicago, Chicago, Illinois
| | - Siri Atma W Greeley
- Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, Kovler Diabetes Center, University of Chicago, Chicago, Illinois
| | - Raúl Calzada-León
- Pediatric Endocrinology, Endocrine Service, National Institute for Pediatrics, Mexico City, Mexico
| | - Bradley Harman
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jayne A L Houghton
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Elisa Nishimura-Meguro
- Department of Pediatric Endocrinology, Children's Hospital, National Medical Center XXI Century, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Daniela Del Gaudio
- Department of Human Genetics, University of Chicago Genetic Services Laboratory, The University of Chicago, Chicago, Illinois
| | - Henrik Thybo Christesen
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center, Odense University Hospital, Odense, Denmark
| | | | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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13
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Yau D, Laver TW, Dastamani A, Senniappan S, Houghton JAL, Shaikh G, Cheetham T, Mushtaq T, Kapoor RR, Randell T, Ellard S, Shah P, Banerjee I, Flanagan SE. Using referral rates for genetic testing to determine the incidence of a rare disease: The minimal incidence of congenital hyperinsulinism in the UK is 1 in 28,389. PLoS One 2020; 15:e0228417. [PMID: 32027664 PMCID: PMC7004321 DOI: 10.1371/journal.pone.0228417] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital hyperinsulinism (CHI) is a significant cause of hypoglycaemia in neonates and infants with the potential for permanent neurologic injury. Accurate calculations of the incidence of rare diseases such as CHI are important as they inform health care planning and can aid interpretation of genetic testing results when assessing the frequency of variants in large-scale, unselected sequencing databases. Whilst minimal incidence rates have been calculated for four European countries, the incidence of CHI in the UK is not known. In this study we have used referral rates to a central laboratory for genetic testing and annual birth rates from census data to calculate the minimal incidence of CHI within the UK from 2007 to 2016. CHI was diagnosed in 278 individuals based on inappropriately detectable insulin and/or C-peptide measurements at the time of hypoglycaemia which persisted beyond 6 months of age. From these data, we have calculated a minimum incidence of 1 in 28,389 live births for CHI in the UK. This is comparable to estimates from other outbred populations and provides an accurate estimate that will aid both health care provision and interpretation of genetic results, which will help advance our understanding of CHI.
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Affiliation(s)
- Daphne Yau
- Department of Paediatric Endocrinology, Royal Manchester Children’s Hospital, Manchester, United Kingdom
| | - Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Antonia Dastamani
- Department of Paediatric Endocrinology, Great Ormond Street Hospital, London, United Kingdom
| | - Senthil Senniappan
- Department of Paediatric Endocrinology, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Jayne A. L. Houghton
- Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Guftar Shaikh
- Department of Paediatric Endocrinology, Royal Hospital for Children, Glasgow, United Kingdom
| | - Tim Cheetham
- Department of Paediatric Endocrinology, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Talat Mushtaq
- Department of Paediatric Endocrinology, Leeds Children’s Hospital, Leeds, United Kingdom
| | - Ritika R. Kapoor
- Department of Paediatric Endocrinology, King’s College London, London, United Kingdom
| | - Tabitha Randell
- Department of Paediatric Endocrinology, Nottingham Children’s Hospital, Nottingham, United Kingdom
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
- Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Pratik Shah
- Department of Paediatric Endocrinology, Great Ormond Street Hospital, London, United Kingdom
| | - Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children’s Hospital, Manchester, United Kingdom
| | - Sarah E. Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
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14
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Houghton JA, Banerjee I, Shaikh G, Jabbar S, Laver TW, Cheesman E, Chinnoy A, Yau D, Salomon-Estebanez M, Dunne MJ, Flanagan SE. Unravelling the genetic causes of mosaic islet morphology in congenital hyperinsulinism. J Pathol Clin Res 2019; 6:12-16. [PMID: 31577849 PMCID: PMC6966704 DOI: 10.1002/cjp2.144] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/29/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022]
Abstract
Congenital hyperinsulinism (CHI) causes dysregulated insulin secretion which can lead to life‐threatening hypoglycaemia if not effectively managed. CHI can be sub‐classified into three distinct groups: diffuse, focal and mosaic pancreatic disease. Whilst the underlying causes of diffuse and focal disease have been widely characterised, the genetic basis of mosaic pancreatic disease is not known. To gain new insights into the underlying disease processes of mosaic‐CHI we studied the islet tissue histopathology derived from limited surgical resection from the tail of the pancreas in a patient with CHI. The underlying genetic aetiology was investigated using a combination of high depth next‐generation sequencing, microsatellite analysis and p57kip2 immunostaining. Histopathology of the pancreatic tissue confirmed the presence of a defined area associated with marked islet hypertrophy and a cytoarchitecture distinct from focal CHI but compatible with mosaic CHI localised to a discrete region within the pancreas. Analysis of DNA extracted from the lesion identified a de novo mosaic ABCC8 mutation and mosaic paternal uniparental disomy which were not present in leukocyte DNA or the surrounding unaffected pancreatic tissue. This study provides the first description of two independent disease‐causing somatic genetic events occurring within the pancreas of an individual with localised mosaic CHI. Our findings increase knowledge of the genetic causes of islet disease and provide further insights into the underlying developmental changes associated with β‐cell expansion in CHI.
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Affiliation(s)
- Jayne Al Houghton
- The Genomics Laboratory, Royal Devon and Exeter Foundation Hospital, Exeter, UK.,Molecular Genetics, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK.,Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Guftar Shaikh
- Department of Paediatric Endocrinology, Royal Hospital for Children, Glasgow, UK
| | - Shamila Jabbar
- Department of Paediatric Pathology, Royal Manchester Children's Hospital, Manchester, UK
| | - Thomas W Laver
- Molecular Genetics, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Edmund Cheesman
- Department of Paediatric Pathology, Royal Manchester Children's Hospital, Manchester, UK
| | - Amish Chinnoy
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Daphne Yau
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Maria Salomon-Estebanez
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Mark J Dunne
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Sarah E Flanagan
- Molecular Genetics, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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15
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Banerjee I, Senniappan S, Laver TW, Caswell R, Zenker M, Mohnike K, Cheetham T, Wakeling MN, Ismail D, Lennerz B, Splitt M, Berberoğlu M, Empting S, Wabitsch M, Pötzsch S, Shah P, Siklar Z, Verge CF, Weedon MN, Ellard S, Hussain K, Flanagan SE. Refinement of the critical genomic region for hypoglycaemia in the Chromosome 9p deletion syndrome. Wellcome Open Res 2019; 4:149. [PMID: 32832699 PMCID: PMC7422856 DOI: 10.12688/wellcomeopenres.15465.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2019] [Indexed: 11/23/2023] Open
Abstract
Background: Large contiguous gene deletions at the distal end of the short arm of chromosome 9 result in the complex multi-organ condition chromosome 9p deletion syndrome. A range of clinical features can result from these deletions with the most common being facial dysmorphisms and neurological impairment. Congenital hyperinsulinism is a rarely reported feature of the syndrome with the genetic mechanism for the dysregulated insulin secretion being unknown. Methods: We studied the clinical and genetic characteristics of 12 individuals with chromosome 9p deletions who had a history of neonatal hypoglycaemia. Using off-target reads generated from targeted next-generation sequencing of the genes known to cause hyperinsulinaemic hypoglycaemia (n=9), or microarray analysis (n=3), we mapped the minimal shared deleted region on chromosome 9 in this cohort. Targeted sequencing was performed in three patients to search for a recessive mutation unmasked by the deletion. Results: In 10/12 patients with hypoglycaemia, hyperinsulinism was confirmed biochemically. A range of extra-pancreatic features were also reported in these patients consistent with the diagnosis of the Chromosome 9p deletion syndrome. The minimal deleted region was mapped to 7.2 Mb, encompassing 38 protein-coding genes. In silico analysis of these genes highlighted SMARCA2 and RFX3 as potential candidates for the hypoglycaemia. Targeted sequencing performed on three of the patients did not identify a second disease-causing variant within the minimal deleted region. Conclusions: This study identifies 9p deletions as an important cause of hyperinsulinaemic hypoglycaemia and increases the number of cases reported with 9p deletions and hypoglycaemia to 15 making this a more common feature of the syndrome than previously appreciated. Whilst the precise genetic mechanism of the dysregulated insulin secretion could not be determined in these patients, mapping the deletion breakpoints highlighted potential candidate genes for hypoglycaemia within the deleted region.
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Affiliation(s)
- Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Senthil Senniappan
- Department of Paediatric Endocrinology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Martin Zenker
- Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Klaus Mohnike
- Department of Paediatrics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Tim Cheetham
- Department of Paediatric Endocrinology, Royal Victoria Infirmary, Newcastle, UK
| | - Matthew N. Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Dunia Ismail
- Department of Paediatric Endocrinology & Diabetes, Royal Alexandra Children’s Hospital, Brighton, UK
| | - Belinda Lennerz
- Department of Paediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Merih Berberoğlu
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara, Turkey
| | - Susann Empting
- Department of Paediatrics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Martin Wabitsch
- Department of Paediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Simone Pötzsch
- Department for Children and Adolescent Medicine, HELIOS Vogtland-Klinikum Plauen, Plauen, Germany
| | - Pratik Shah
- Endocrinology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Zeynep Siklar
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara, Turkey
| | - Charles F. Verge
- Department of Endocrinology, Sydney Children's Hospital, Randwick and School of Women's and Children's Health,, Sydney, New South Wales, Australia
| | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Khalid Hussain
- Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Sarah E. Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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16
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Abstract
Multiple Nucleotide Variants (MNVs) are miscalled by the most widely utilised next generation sequencing analysis (NGS) pipelines, presenting the potential for missing diagnoses that would previously have been made by standard Sanger (dideoxy) sequencing. These variants, which should be treated as a single insertion-deletion mutation event, are commonly called as separate single nucleotide variants. This can result in misannotation, incorrect amino acid predictions and potentially false positive and false negative diagnostic results. This risk will be increased as confirmatory Sanger sequencing of Single Nucleotide variants (SNVs) ceases to be standard practice. Using simulated data and re-analysis of sequencing data from a diagnostic targeted gene panel, we demonstrate that the widely adopted pipeline, GATK best practices, results in miscalling of MNVs and that alternative tools can call these variants correctly. The adoption of calling methods that annotate MNVs correctly would present a solution for individual laboratories, however GATK best practices are the basis for important public resources such as the gnomAD database. We suggest integrating a solution into these guidelines would be the optimal approach.
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Affiliation(s)
- Matthew N Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Kevin Colclough
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew Parish
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.,Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Emma L Baple
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.,Clinical Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
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17
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Wakeling MN, Laver TW, Colclough K, Parish A, Ellard S, Baple EL. Misannotation of multiple-nucleotide variants risks misdiagnosis. Wellcome Open Res 2019; 4:145. [PMID: 31976378 PMCID: PMC6957021 DOI: 10.12688/wellcomeopenres.15420.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2019] [Indexed: 11/20/2022] Open
Abstract
Multiple Nucleotide Variants (MNVs) are miscalled by the most widely utilised next generation sequencing analysis (NGS) pipelines, presenting the potential for missing diagnoses that would previously have been made by standard Sanger (dideoxy) sequencing. These variants, which should be treated as a single insertion-deletion mutation event, are commonly called as separate single nucleotide variants. This can result in misannotation, incorrect amino acid predictions and potentially false positive and false negative diagnostic results. This risk will be increased as confirmatory Sanger sequencing of Single Nucleotide variants (SNVs) ceases to be standard practice. Using simulated data and re-analysis of sequencing data from a diagnostic targeted gene panel, we demonstrate that the widely adopted pipeline, GATK best practices, results in miscalling of MNVs and that alternative tools can call these variants correctly. The adoption of calling methods that annotate MNVs correctly would present a solution for individual laboratories, however GATK best practices are the basis for important public resources such as the gnomAD database. We suggest integrating a solution into these guidelines would be the optimal approach.
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Affiliation(s)
- Matthew N. Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Thomas W. Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Kevin Colclough
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew Parish
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Emma L. Baple
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
- Clinical Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
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18
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Wright CF, West B, Tuke M, Jones SE, Patel K, Laver TW, Beaumont RN, Tyrrell J, Wood AR, Frayling TM, Hattersley AT, Weedon MN. Assessing the Pathogenicity, Penetrance, and Expressivity of Putative Disease-Causing Variants in a Population Setting. Am J Hum Genet 2019; 104:275-286. [PMID: 30665703 PMCID: PMC6369448 DOI: 10.1016/j.ajhg.2018.12.015] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022] Open
Abstract
More than 100,000 genetic variants are classified as disease causing in public databases. However, the true penetrance of many of these rare alleles is uncertain and might be over-estimated by clinical ascertainment. Here, we use data from 379,768 UK Biobank (UKB) participants of European ancestry to assess the pathogenicity and penetrance of putatively clinically important rare variants. Although rare variants are harder to genotype accurately than common variants, we were able to classify as high quality 1,244 of 4,585 (27%) putatively clinically relevant rare (MAF < 1%) variants genotyped on the UKB microarray. We defined as "clinically relevant" variants that were classified as either pathogenic or likely pathogenic in ClinVar or are in genes known to cause two specific monogenic diseases: maturity-onset diabetes of the young (MODY) and severe developmental disorders (DDs). We assessed the penetrance and pathogenicity of these high-quality variants by testing their association with 401 clinically relevant traits. 27 of the variants were associated with a UKB trait, and we were able to refine the penetrance estimate for some of the variants. For example, the HNF4A c.340C>T (p.Arg114Trp) (GenBank: NM_175914.4) variant associated with diabetes is <10% penetrant by the time an individual is 40 years old. We also observed associations with relevant traits for heterozygous carriers of some rare recessive conditions, e.g., heterozygous carriers of the ERCC4 c.2395C>T (p.Arg799Trp) variant that causes Xeroderma pigmentosum were more susceptible to sunburn. Finally, we refute the previous disease association of RNF135 in developmental disorders. In conclusion, this study shows that very large population-based studies will help refine our understanding of the pathogenicity of rare genetic variants.
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Affiliation(s)
- Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
| | - Ben West
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Samuel E Jones
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Kashyap Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Research, Innovation, Learning and Development building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
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19
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Laver TW, Wakeling MN, Hua JHY, Houghton JAL, Hussain K, Ellard S, Flanagan SE. Comprehensive screening shows that mutations in the known syndromic genes are rare in infants presenting with hyperinsulinaemic hypoglycaemia. Clin Endocrinol (Oxf) 2018; 89:621-627. [PMID: 30238501 PMCID: PMC6283248 DOI: 10.1111/cen.13841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Hyperinsulinaemic hypoglycaemia (HH) can occur in isolation or more rarely feature as part of a syndrome. Screening for mutations in the "syndromic" HH genes is guided by phenotype with genetic testing used to confirm the clinical diagnosis. As HH can be the presenting feature of a syndrome, it is possible that mutations will be missed as these genes are not routinely screened in all newly diagnosed individuals. We investigated the frequency of pathogenic variants in syndromic genes in infants with HH who had not been clinically diagnosed with a syndromic disorder at referral for genetic testing. DESIGN We used genome sequencing data to assess the prevalence of mutations in syndromic HH genes in an international cohort of patients with HH of unknown genetic cause. PATIENTS We undertook genome sequencing in 82 infants with HH without a clinical diagnosis of a known syndrome at referral for genetic testing. MEASUREMENTS Within this cohort, we searched for the genetic aetiologies causing 20 different syndromes where HH had been reported as a feature. RESULTS We identified a pathogenic KMT2D variant in a patient with HH diagnosed at birth, confirming a genetic diagnosis of Kabuki syndrome. Clinical data received following the identification of the mutation highlighted additional features consistent with the genetic diagnosis. Pathogenic variants were not identified in the remainder of the cohort. CONCLUSIONS Pathogenic variants in the syndromic HH genes are rare; thus, routine testing of these genes by molecular genetics laboratories is unlikely to be justified in patients without syndromic phenotypes.
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Affiliation(s)
- Thomas W. Laver
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - Matthew N. Wakeling
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | | | - Jayne A. L. Houghton
- Department of Molecular GeneticsRoyal Devon and Exeter NHS Foundation TrustExeterUK
| | - Khalid Hussain
- Department of Pediatric MedicineDivision of EndocrinologySidra MedicineDohaQatar
| | - Sian Ellard
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - Sarah E. Flanagan
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
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20
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Locke JM, Saint-Martin C, Laver TW, Patel KA, Wood AR, Sharp SA, Ellard S, Bellanné-Chantelot C, Hattersley AT, Harries LW, Weedon MN. The Common HNF1A Variant I27L Is a Modifier of Age at Diabetes Diagnosis in Individuals With HNF1A-MODY. Diabetes 2018; 67:1903-1907. [PMID: 29895593 PMCID: PMC6109380 DOI: 10.2337/db18-0133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/05/2018] [Indexed: 01/03/2023]
Abstract
There is wide variation in the age at diagnosis of diabetes in individuals with maturity-onset diabetes of the young (MODY) due to a mutation in the HNF1A gene. We hypothesized that common variants at the HNF1A locus (rs1169288 [I27L], rs1800574 [A98V]), which are associated with type 2 diabetes susceptibility, may modify age at diabetes diagnosis in individuals with HNF1A-MODY. Meta-analysis of two independent cohorts, comprising 781 individuals with HNF1A-MODY, found no significant associations between genotype and age at diagnosis. However after stratifying according to type of mutation (protein-truncating variant [PTV] or missense), we found each 27L allele to be associated with a 1.6-year decrease (95% CI -2.6, -0.7) in age at diagnosis, specifically in the subset (n = 444) of individuals with a PTV. The effect size was similar and significant across the two independent cohorts of individuals with HNF1A-MODY. We report a robust genetic modifier of HNF1A-MODY age at diagnosis that further illustrates the strong effect of genetic variation within HNF1A upon diabetes phenotype.
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Affiliation(s)
- Jonathan M Locke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K.
| | - Cécile Saint-Martin
- Department of Genetics, Pitié-Salpétrière Hospital, Assistance Publique-Hôpitaux de Paris, and Pierre et Marie Curie University, Paris, France
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Seth A Sharp
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Christine Bellanné-Chantelot
- Department of Genetics, Pitié-Salpétrière Hospital, Assistance Publique-Hôpitaux de Paris, and Pierre et Marie Curie University, Paris, France
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Lorna W Harries
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
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21
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Laver TW, Patel KA, Colclough K, Curran J, Dale J, Davis N, Savage DB, Flanagan SE, Ellard S, Hattersley AT, Weedon MN. PLIN1 Haploinsufficiency Is Not Associated With Lipodystrophy. J Clin Endocrinol Metab 2018; 103:3225-3230. [PMID: 30020498 PMCID: PMC6126890 DOI: 10.1210/jc.2017-02662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/12/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT Monogenic partial lipodystrophy is a genetically heterogeneous disease where only variants with specific genetic mechanisms are causative. Three heterozygous protein extending frameshift variants in PLIN1 have been reported to cause a phenotype of partial lipodystrophy and insulin resistance. OBJECTIVE We investigated if null variants in PLIN1 cause lipodystrophy. METHODS As part of a targeted sequencing panel test, we sequenced PLIN1 in 2208 individuals. We also investigated the frequency of PLIN1 variants in the gnomAD database, and the type 2 diabetes knowledge portal. RESULTS We identified 6/2208 (1 in 368) individuals with a PLIN1 null variant. None of these individuals had clinical or biochemical evidence of overt lipodystrophy. Additionally, 14/17,000 (1 in 1214) individuals with PLIN1 null variants in the type 2 diabetes knowledge portal showed no association with biomarkers of lipodystrophy. PLIN1 null variants occur too frequently in gnomAD (126/138,632; 1 in 1100) to be a cause of rare overt monogenic partial lipodystrophy. CONCLUSIONS Our study suggests that heterozygous variants that are predicted to result in PLIN1 haploinsufficiency are not a cause of familial partial lipodystrophy and should not be reported as disease-causing variants by diagnostic genetic testing laboratories. This finding is in keeping with other known monogenic causes of lipodystrophy, such as PPARG and LMNA, where only variants with specific genetic mechanisms cause lipodystrophy.
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Affiliation(s)
- Thomas W Laver
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
- Correspondence and Reprint Requests: Thomas W. Laver, PhD, Institute of Biomedical & Clinical Science, RILD Building Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, United Kingdom. E-mail:
| | - Kashyap A Patel
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
| | - Kevin Colclough
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Jacqueline Curran
- Department of Endocrinology, Princess Margaret Hospital, Perth, Western Australia, Australia
| | - Jane Dale
- The Dudley Group NHS Foundation Trust, Dudley, United Kingdom
| | - Nikki Davis
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - David B Savage
- The University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, United Kingdom
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Sarah E Flanagan
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
| | - Sian Ellard
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Andrew T Hattersley
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
| | - Michael N Weedon
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
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22
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Patel KA, Kettunen J, Laakso M, Stančáková A, Laver TW, Colclough K, Johnson MB, Abramowicz M, Groop L, Miettinen PJ, Shepherd MH, Flanagan SE, Ellard S, Inagaki N, Hattersley AT, Tuomi T, Cnop M, Weedon MN. Heterozygous RFX6 protein truncating variants are associated with MODY with reduced penetrance. Nat Commun 2017; 8:888. [PMID: 29026101 PMCID: PMC5638866 DOI: 10.1038/s41467-017-00895-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 08/04/2017] [Indexed: 12/20/2022] Open
Abstract
Finding new causes of monogenic diabetes helps understand glycaemic regulation in humans. To find novel genetic causes of maturity-onset diabetes of the young (MODY), we sequenced MODY cases with unknown aetiology and compared variant frequencies to large public databases. From 36 European patients, we identify two probands with novel RFX6 heterozygous nonsense variants. RFX6 protein truncating variants are enriched in the MODY discovery cohort compared to the European control population within ExAC (odds ratio = 131, P = 1 × 10-4). We find similar results in non-Finnish European (n = 348, odds ratio = 43, P = 5 × 10-5) and Finnish (n = 80, odds ratio = 22, P = 1 × 10-6) replication cohorts. RFX6 heterozygotes have reduced penetrance of diabetes compared to common HNF1A and HNF4A-MODY mutations (27, 70 and 55% at 25 years of age, respectively). The hyperglycaemia results from beta-cell dysfunction and is associated with lower fasting and stimulated gastric inhibitory polypeptide (GIP) levels. Our study demonstrates that heterozygous RFX6 protein truncating variants are associated with MODY with reduced penetrance.Maturity-onset diabetes of the young (MODY) is the most common subtype of familial diabetes. Here, Patel et al. use targeted DNA sequencing of MODY patients and large-scale publically available data to show that RFX6 heterozygous protein truncating variants cause reduced penetrance MODY.
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Affiliation(s)
- Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Jarno Kettunen
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, 00029, Finland
- Folkhalsan Research Center, University of Helsinki, Helsinki, 00014, Finland
- Research Program of Diabetes and Obesity, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Markku Laakso
- Department of Medicine, Kuopio University Hospital, Kuopio, 70029, Finland
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70029, Finland
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70029, Finland
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Kevin Colclough
- Department of Molecular Genetics, Royal Devon and Exeter National Health Service Foundation Trust, Exeter, EX2 5DW, UK
| | - Matthew B Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Marc Abramowicz
- IRIBHM, Genetics Department, Erasmus Hospital, Université Libre de Bruxelles, Brussels, 1070, Belgium
| | - Leif Groop
- Lund University Diabetes Centre, Department of Clinical Sciences Malmö, Lund University, Skåne University Hospital, Malmö, SE, 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00100, Finland
| | - Päivi J Miettinen
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, 00029, Finland
- Molecular Neurology and Biomedicum Stem Cell Centre, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Maggie H Shepherd
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Tiinamaija Tuomi
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, 00029, Finland
- Folkhalsan Research Center, University of Helsinki, Helsinki, 00014, Finland
- Research Program of Diabetes and Obesity, Research Programs Unit, University of Helsinki, Helsinki, 00014, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00100, Finland
| | - Miriam Cnop
- ULB Center for Diabetes Research, Faculty of Medicine, Université Libre de Bruxelles, Brussels, 1070, Belgium.
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, 1070, Belgium.
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK.
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23
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Laver TW, Weedon MN, Caswell R, Hussain K, Ellard S, Flanagan SE. Analysis of large-scale sequencing cohorts does not support the role of variants in UCP2 as a cause of hyperinsulinaemic hypoglycaemia. Hum Mutat 2017; 38:1442-1444. [PMID: 28681398 DOI: 10.1002/humu.23289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | | | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
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24
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Flanagan SE, Vairo F, Johnson MB, Caswell R, Laver TW, Lango Allen H, Hussain K, Ellard S. A CACNA1D mutation in a patient with persistent hyperinsulinaemic hypoglycaemia, heart defects, and severe hypotonia. Pediatr Diabetes 2017; 18:320-323. [PMID: 28318089 PMCID: PMC5434855 DOI: 10.1111/pedi.12512] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/16/2017] [Accepted: 01/31/2017] [Indexed: 01/31/2023] Open
Abstract
Congenital hyperinsulinaemic hypoglycaemia (HH) can occur in isolation or it may present as part of a wider syndrome. For approximately 40%-50% of individuals with this condition, sequence analysis of the known HH genes identifies a causative mutation. Identifying the underlying genetic aetiology in the remaining cases is important as a genetic diagnosis will inform on recurrence risk, may guide medical management and will provide valuable insights into β-cell physiology. We sequenced the exome of a child with persistent diazoxide-responsive HH, mild aortic insufficiency, severe hypotonia, and developmental delay as well as the unaffected parents. This analysis identified a de novo mutation, p.G403D, in the proband's CACNA1D gene. CACNA1D encodes the main L-type voltage-gated calcium channel in the pancreatic β-cell, a key component of the insulin secretion pathway. The p.G403D mutation had been reported previously as an activating mutation in an individual with primary hyper-aldosteronism, neuromuscular abnormalities, and transient hypoglycaemia. Sequence analysis of the CACNA1D gene in 60 further cases with HH did not identify a pathogenic mutation. Identification of an activating CACNA1D mutation in a second patient with congenital HH confirms the aetiological role of CACNA1D mutations in this disorder. A genetic diagnosis is important as treatment with a calcium channel blocker may be an option for the medical management of this patient.
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Affiliation(s)
- SE Flanagan
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - F Vairo
- Medical Genetics ServiceHospital de Clínicas de Porto AlegrePorto AlegreRSBrazil
| | - MB Johnson
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - R Caswell
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - TW Laver
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - H Lango Allen
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
| | - K Hussain
- Developmental Endocrinology Research Group, Clinical and Molecular Genetics UnitUCL Institute of Child Health and Great Ormond Street HospitalLondonUK
| | - S Ellard
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterUK
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Laver TW, Colclough K, Shepherd M, Patel K, Houghton JAL, Dusatkova P, Pruhova S, Morris AD, Palmer CN, McCarthy MI, Ellard S, Hattersley AT, Weedon MN. The Common p.R114W HNF4A Mutation Causes a Distinct Clinical Subtype of Monogenic Diabetes. Diabetes 2016; 65:3212-7. [PMID: 27486234 PMCID: PMC5035684 DOI: 10.2337/db16-0628] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/26/2016] [Indexed: 12/21/2022]
Abstract
HNF4A mutations cause increased birth weight, transient neonatal hypoglycemia, and maturity onset diabetes of the young (MODY). The most frequently reported HNF4A mutation is p.R114W (previously p.R127W), but functional studies have shown inconsistent results; there is a lack of cosegregation in some pedigrees and an unexpectedly high frequency in public variant databases. We confirm that p.R114W is a pathogenic mutation with an odds ratio of 30.4 (95% CI 9.79-125, P = 2 × 10(-21)) for diabetes in our MODY cohort compared with control subjects. p.R114W heterozygotes did not have the increased birth weight of patients with other HNF4A mutations (3,476 g vs. 4,147 g, P = 0.0004), and fewer patients responded to sulfonylurea treatment (48% vs. 73%, P = 0.038). p.R114W has reduced penetrance; only 54% of heterozygotes developed diabetes by age 30 years compared with 71% for other HNF4A mutations. We redefine p.R114W as a pathogenic mutation that causes a distinct clinical subtype of HNF4A MODY with reduced penetrance, reduced sensitivity to sulfonylurea treatment, and no effect on birth weight. This has implications for diabetes treatment, management of pregnancy, and predictive testing of at-risk relatives. The increasing availability of large-scale sequence data is likely to reveal similar examples of rare, low-penetrance MODY mutations.
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Affiliation(s)
- Thomas W Laver
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K
| | - Kevin Colclough
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K. Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, U.K
| | - Maggie Shepherd
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K
| | - Kashyap Patel
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K
| | - Jayne A L Houghton
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K. Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, U.K
| | - Petra Dusatkova
- Department of Paediatrics, Second Faculty of Medicine, Charles University
and University Hospital Motol, Prague, Czech Republic
| | - Stepanka Pruhova
- Department of Paediatrics, Second Faculty of Medicine, Charles University
and University Hospital Motol, Prague, Czech Republic
| | - Andrew D Morris
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, U.K
| | - Colin N Palmer
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, U.K
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K. Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K. National Institute for Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Sian Ellard
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K. Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, U.K
| | - Andrew T Hattersley
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K
| | - Michael N Weedon
- Institute of Biomedical & Clinical Science, University of Exeter, Exeter, U.K.
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