Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion

A nonsense variant in the C-terminal transactivation domain of the EBF3 gene in an individual with intellectual disability and behavioural disorder: case report and literature review

Heterozygous variants in the Early B cell factor 3 ( EBF3 ) have been reported in individuals presenting with hypotonia, ataxia and delayed development syndrome (HADDS) (MIM#617330). However, individuals with pathogenic variants in EBF3 show phenotypic heterogeneity and very few variants in the C-terminal domain have been described. We report on a heterozygous de-novo variant in the EBF3 gene in an individual with neurodevelopmental delay and behavioural problems. The proband presented with speech delay, learning disability and behavioural problems that suggest an oppositional defiant disorder. He also has hyperactivity, irritability, hetero-aggressiveness, visual hallucinations, insomnia and decreased pain sensitivity. Whole exome sequencing revealed a de-novo heterozygous nonsense variant - c.1408C>T (p.Arg470*) - in the EBF3 gene, classified as pathogenic. The patient herein described, with a truncating variant in the C-terminal domain of EBF3 , supports the clinical variability of this condition and contributes to genotype-phenotype correlation of this rare disorder.

Genetic heterogeneity in patients with enlarged vestibular aqueduct and Pendred syndrome

BACKGROUND

Pathogenic variants in the SLC26A4 gene, encoding for Cl-/HCO3- and I- anion transporter pendrin, are associated with non-syndromic hearing loss with enlarged vestibular aqueduct (NSEVA) and Pendred syndrome (PDS). In the Caucasian population, up to 75% of patients fail to identify a genetic cause through biallelic mutations in the SLC26A4 gene. The CEVA haplotype could therefore play an important role in the diagnostics of NSEVA. The aim of the study was to determine the genetic etiology of hearing loss with EVA or with fully developed PDS in 37 probands and the functional characterization of novel variants identified in the SLC26A4 gene.

METHODS

To determine the genetic etiology, Sanger sequencing, WES and KASP genotyping assay were used. Functional characterization of SLC26A4 variants c.140G>A (p.R47Q), c.415G>A (p.G139R), c.441G>A (p.M147I), c.481T>A (p.F161I), c.1589A>C (p.Y530S) and c.2260del (p.D754Ifs*5) involved determination of iodide influx, total and plasma membrane pendrin expression level and subcellular localization of pendrin by confocal imaging. The nanopore sequencing of nasopharyngeal swab samples was performed to confirm the pathogenic effect of potential splice site variant c.415G>A.

RESULTS

Biallelic variants in the SLC26A4 gene (M2 genotype) were identified in ten probands and a complete CEVA haplotype was confirmed in three probands harbouring SLC26A4 monoallelic variants (M1 genotype). Fifteen variants in the SLC26A4 gene were identified in total, three of which are novel. The functional characterization of the novel variants and variants which were not yet functionally characterized confirmed the pathogenic potential of five out of six tested variants (p.G139R, p.M147I, p.Y530S, p.D754Ifs*5, and p.F161I). Analysis of nasopharyngeal swab samples confirmed exon 4 skipping due to novel variant SLC26A4:c.415G>A. Probands with biallelic SLC26A4 variants had significantly larger thyroid volume per m2 of body surface area than subjects with monoallelic SLC26A4 variants and the CEVA haplotype.

CONCLUSIONS

The genetic aetiology was determined in 13 out of 37 probands (35%), seven manifested with PDS and six with NSEVA. The present study highlights the importance of functional testing to confirm the pathogenicity of SLC26A4 variants and the phenotype-genotype correlation in SLC26A4-related disorders.

Blood RNA-seq in rare disease diagnostics: a comparative study of cases with and without candidate variants

BACKGROUND

Approximately 60% of rare disease cases remain unsolved after exome and genome sequencing (ES/GS). Blood RNA sequencing (RNA-seq) complements DNA-level diagnosis by revealing the functional impact of variants on gene expression and splicing, but to what extent RNA-driven approaches offer diagnostic benefits across different scenarios-with and without pre-existing candidate variants-remains uncertain.

METHODS

128 unrelated probands with suspected Mendelian disorders who had previously undergone ES/GS were recruited. A validation cohort (n = 7, with variants expected to alter RNA) and a test cohort (n = 121, including 10 with variants of uncertain significance (VUS) and 111 with no previously identified candidate variants) were analyzed. Blood RNA-seq was performed, and aberrant splicing (AS) and aberrant expression (AE) were detected using the DROP pipeline. SpliceAI predictions were compared with RNA-seq results for splicing-related VUS variants, and pathogenicity was re-evaluated. AS/AE outliers were evaluated for diagnostic potential in cases without candidate variants. The feasibility of an RNA-driven approach was assessed by ranking causal variant-associated aberrant events.

RESULTS

The pipeline correctly identified all expected AS/AE events in the validation cohort. In the test cohort with candidate VUS, RNA-seq provided a 60% (6/10) diagnostic uplift. Notably, SpliceAI predictions matched RNA-seq observations perfectly only in 40% of these VUS. A 2.7% (3/111) diagnostic uplift was achieved in the test cohort with no prior candidates. Overall, target AS and AE events ranked among the top eight in 14 of the 16 diagnosed cases using a purely RNA-driven approach; however, two cases would have been missed without prior candidate identification from DNA sequencing.

CONCLUSION

Blood RNA-seq is highly effective in refining the interpretation of splicing VUS, frequently leading to reclassification and diagnosis. Meanwhile, RNA-driven identification of causal variants shows a more modest yield in cases without prior candidates. This study supports an RNA-complementary approach as the preferred strategy for clinical utility.

Neonatal Onset Seizures and Hypotonia Due to D-Bifunctional Protein Deficiency

Peroxisomal disorders (PDs) are a diverse group of inherited conditions arising from impaired function of a specific peroxisomal enzyme, metabolite transporter, or defect in the peroxisome biogenesis system. Peroxisomal D-bifunctional protein (DBP) deficiency is generally classified as a Zellweger-like syndrome. This disorder is caused by mutations in the HSD17B4 gene, and only a limited number of confirmed cases have been reported to date.The authors report case of a 6-mo-old female infant presenting with neonatal-onset intractable seizures, characteristic facial features, hypotonia, and progressive hepatomegaly. An acylcarnitine profile revealed elevated very long-chain fatty acids, prompting the initiation of a medium-chain triglyceride (MCT) formula. Remarkably, this treatment led to seizure control, improved muscle tone, and a reduction in liver size. Whole exome sequencing identified a homozygous missense mutation in the HSD17B4 gene (c.1444A>T).This case suggests that MCT-containing formulas may offer therapeutic potential in the treatment of D-bifunctional protein deficiency.

Systematic analysis of genetic and phenotypic characteristics reveals antisense oligonucleotide therapy potential for one-third of neurodevelopmental disorders

BACKGROUND

Neurodevelopmental disorders (NDDs) are a challenging group of disorders to treat, but promising therapeutic interventions in the form of antisense oligonucleotides (AONs) have emerged in recent years. However, the applicability of AON therapy for NDDs varies based on genetic and phenotypic traits. In this study we systematically evaluated key characteristics for AON therapy suitability in NDDs, to estimate overall therapy potential and identify, both well- and less-studied, targetable NDDs.

METHODS

An NDD dataset was created and evaluated to identify potentially targetable NDDs for seven AON strategies. This involved examining the presence of a combination of critical factors including disease-gene properties, such as regulatory elements, effects of pathogenic variants, and disease-associated phenotypic features.

RESULTS

Through the systematic evaluation of the presence of targetable characteristic for each NDD and AON strategy, we identified 711 NDDs (38% of the total) with characteristics favorable for at least one AON strategy and predicted that 18% of affected individuals could benefit from AON therapy.

CONCLUSIONS

The results from our analysis demonstrate that there might be a more extensive potential for the use of AON therapy in NDDs than was anticipated thus far, underscoring AON therapy as a promising treatment option for NDDs while simultaneously contributing to informed therapy selection.

RPE65 variant p.(E519K) causes a novel dominant adult-onset maculopathy in 83 affected individuals

Recessive RPE65-related retinopathy is an inherited retinal disease (IRD) that is a well-established target for gene therapy. Dominant RPE65-related retinopathy, however, due to Irish founder variant p.(D477G), is extremely rare. Here, we report the discovery, replication and characterization of a novel dominant retinopathy caused by RPE65 variant p.(E519K), identified in 83 individuals of European ancestry across IRD registries (Belgian discovery cohort, n=2,873; replication cohort, n=18,796). Long-read sequencing-based haplotyping revealed a shared region of 464 kb, supporting a founder effect. Genotype-phenotype data support dominant inheritance and phenotypic variability respectively, characterized by late-onset macular dystrophy with two main subtypes, a pathognomonic mottled subtype and a pattern dystrophy subtype. Functional studies showed that the p.(E519K) variant affects RPE65 enzymatic activity, correlating with lower protein expression. Protein modelling and cellular thermal shift assays further supported a destabilizing effect on protein structure. Overall, our work provides strong genetic, clinical, molecular and functional evidence for a novel dominant RPE65 retinopathy in multiple families in Europe and North America due to a Belgian founder variant. This discovery reduces the diagnostic gap in dominant IRD, particularly in individuals of European ancestry. Finally, it lays the foundation for developing therapeutic strategies targeting dominant RPE65 retinopathy.

Accelerating genetic diagnostics in retinitis pigmentosa: implementation of a semi-automated bespoke cohort analysis workflow for Hong Kong Genome Project

The study aims to enhance the efficiency of the genetic variant curation process at the Hong Kong Genome Institute by developing a Semi-Automated Bespoke Cohort Analysis Workflow (S-BCAW) for patients with, or suspected to have, retinitis pigmentosa (RP) in the Hong Kong Genome Project (HKGP), leveraging advances in next-generation sequencing (NGS). A comparative analysis involving 79 RP patients was conducted using both the conventional manual workflow and the novel S-BCAW, which integrates initial filtering and variant classification based on ACMG guidelines, followed by detailed manual review. The diagnostic yields from both methods were identical, but the bespoke workflow reduced analysis time by approximately 60% (1.5 h/sample). This efficiency increase resulted from automated application of ACMG rules and systematic aggregation of supportive data, including disease-specific information. The study reports 25 positive cases with a diagnostic yield of 32%, including three novel variants. The S-BCAW significantly improves efficiency, helping to end the diagnostic odyssey for patients in the HKGP. This approach facilitates rapid assessment of variant pathogenicity, enhancing the feasibility and timeliness of NGS technology for clinical applications, especially in urgent scenarios.

Beyond genomics: using RNA-seq from dried blood spots to unlock the clinical relevance of splicing variation in a diagnostic setting

We aimed to assess the impact of splicing variants reported in our laboratory to gain insight into their clinical relevance. A total of 108 consecutive individuals, for whom 113 splicing variants had been reported, were selected for RNA-sequencing (RNA-seq), considering the gene expression in blood. A protocol was developed to perform RNA extraction and sequencing using the same sample (dried blood spots, DBS) provided for the DNA analysis, including library preparation and bioinformatic pipeline analysis. Splicing in genes of interest was inspected using IGV, with at least three unaffected individuals as controls. From the 113 variants, we confirmed an abnormal splicing in 64 variants (57%). In 15 variants (13%), we did not observe a splicing alteration. In the remaining 34 variants, no decision could be made on the splicing effect due to insufficient sample quality (21%) or a low number of reads (9%). The most common event leading to aberrant splicing was exon skipping, identified in 31 variants (48%). Other events included cryptic donor/acceptor site usage (n = 25; 39%), intron retention (n = 4; 6%), and other complex events (n = 4; 6%). In three patients, pathologically reduced enzymatic activity (measured using the same DBS) served as additional confirmation of the abnormal splicing caused by variants in HEXA, GAA, and GLA. We implemented an RNA-seq pipeline using the same sample provided for genomic testing. This multiomic approach, as implemented in our routine diagnostic processes, clarifies the clinical relevance of most of the analyzed variants and delivers more comprehensive genetic testing.

A Compound Heterozygous Pathogenic Variant in ZP2 Gene Causes Female Infertility

The oocyte maturation defect 6 is an autosomal recessive hereditary disease caused by a homozygous variant in ZP2 gene. It is characterized by female primary infertility due to an abnormally thin zona pellucida (ZP) and defective sperm binding. Here we identified a compound heterozygous variant (c.1924C > T and c.1695-2A > G) in ZP2 gene in a Chinese Han family. Quantitative real-time PCR showed that the variant c.1924C > T significantly decreased the expression of truncated ZP2 message RNA by the nonsense-mediated decay pathway. Minigene assays showed the c.1695-2A > G variant led to an extra-61-nt preservation of intron 15 at the junction between exons 15 and 16 during transcription. Both variants (c.1924C > T and c.1695-2A > G) resulted in truncated ZP2 proteins (p.R642X and p.C566Hfs*2) that lost the transmembrane domain, which prevented the secretion of the mutant ZP2 proteins and produced a structurally abnormal ZP, thus resulting in female infertility. This study further elucidated the pathogenic mechanism of these two variants and provided new support for the genetic diagnosis of female infertility.

Comprehensive functional splicing analysis of non-canonical CNGB3 variants using in vitro minigene splice assays

Variants in the CNGB3 gene, encoding the B3-subunit of the cone photoreceptor cyclic nucleotide gated channel, are a major cause of autosomal recessive achromatopsia, a rare inherited retinal disease. The mutation spectrum of achromatopsia-associated CNGB3 variants comprises all types of mutations, including those that are straightforward to evaluate in molecular genetic diagnostics, such as frame-shifting, nonsense, and canonical splice site variants. Additionally, variants have been identified within splice regions outside the conserved ±1,2 splice site dinucleotides, making their potential impact on disease association challenging to interpret. This poses a major hurdle for clinical interpretation of causality between the patient's genotype and the proposed clinical diagnosis, but also for the inclusion of such patients into clinical trials for gene augmentation therapy, for which only patients with confirmed (likely) pathogenic CNGB3 variants are eligible. We here performed comprehensive genetic functional analysis of 21 candidate spliceogenic CNGB3 variants-15 reported and 6 novel variants-by means of in vitro minigene splice assays and cDNA analysis, and characterization of spliceogenic events by subcloning, Sanger-sequencing, and capillary fragment analysis. For 16 variants, an impact on splicing was confirmed, supporting the reclassification of 86% of variants of uncertain significance as likely pathogenic or pathogenic according to the ACMG/AMP guidelines. This reclassification enables the confirmation of patients' genotypes, both retrospectively and prospectively. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

A retrospective single center analysis of fetuses with region of homozygosity detected by single nucleotide polymorphism array

We assessed the incidence and clinical significance of the fetal region of homozygosity (ROH) detected using single nucleotide polymorphism (SNP) array by analyzing clinical information and pregnancy outcomes. We collected data on 6176 mid- and late pregnancies. All fetuses were subjected to SNP array analysis. Fetuses with ROH were analyzed by karyotyping, parental SNP array verification, whole-exome sequencing, and/or placental studies. Eighty-seven ROHs met our reporting thresholds. Thirty-four fetuses were detected from noninvasive prenatal testing-positive results, with the most common detection rate (2.03%). Twenty-four cases were diagnosed using ultrasound abnormalities; fetal growth restriction was the indication with the highest diagnostic rate. Fifteen cases of uniparental disomy in mid- and late pregnancy were identified (0.24%). Nine cases were of ROH accompanied by aneuploidy or pathogenic/likely pathogenic copy number variants with an adverse pregnancy outcome rate of 88.9%. Of the remaining 78 cases, 14 carriers had adverse outcomes (including two cases of imprinting syndrome), 63 had normal development after birth, and one was lost to follow-up. ROH is relatively common in mid- and late-term pregnancies; its incidence is higher than that reported previously. SNP array is effective in assessing ROH and should be combined with multiple techniques to evaluate ROH's clinical relevance.

Novel homozygous frameshift mutation of ITGB3 in the Glanzmann thrombasthenia patient with abnormal bone metabolism and congenital bone defects

BACKGROUND

Glanzmann thrombasthenia (GT) is a rare inherited bleeding disorder caused by dysfunction of the integrin αIIbβ3 in platelets. The subunit β3, encoded by ITGB3 also plays a significant role in bone metabolism. Whether GT patients with β3 deficiency also suffer from bone pathology remains unclear.

METHOD

The 21-year-old female patient presenting with bleeding diathesis and multiple congenital bone defects in her right hand, and her seven family members were included in the study. Whole exome sequencing as well as Sanger sequencing were conducted to identify GT-associated mutations within the family. The platelet function of the family was detected by the platelet aggregation test and thromboelastography (TEG). The expression levels of CD41 (αIIb) and CD61 (β3) on the platelet surface and total in platelet were detected by flow cytometry and Western blot. Bioinformatics analysis was used to evaluate the pathogenicity of mutation sites and their effects on protein structure and function. X-ray imaging, bone densitometry and bone metabolism index were performed to evaluate bone development and metabolism.

RESULT

A novel homozygous frameshift mutation c.2143_2158delinsCT (p.Lys715Leufs*36) of ITGB3 was found in the proband. Platelet aggregation by ADP, collagen, epinephrine, and arachidonic acid was absent, TEG showed hypocoagulability and decreased platelet function, and the expression levels of αIIb and β3 on the platelet surface and total in platelet were significantly reduced (< 5%) in the proband. The parents, second elder sister and grandmother of proband were heterozygous carriers without bleeding symptoms and had normal platelet aggregation function and αIIb/β3 protein expression. Structural modeling strongly suggested that the mutation creates a truncation in cytoplasmic domains of β3, resulting in the mutant β3/αIIbβ3 inactivated and low expression. The proband was born with partial absence of phalanges in digits 2-4 and the deformity of fingers 1 and 5 in her right hand, bone densitometry indicated significant osteopenia and increased risk of fracture in her right radius, and no other gene mutations related to bone pathology were identified.

CONCLUSION

A novel mutation of ITGB3 which results in GT was identified. This is the third reported case of GT combined with bone defect. Our work expands ITGB3 mutation spectrum and provide further insights into the potential association between GT and bone development and metabolism.

Novel Truncating Variants in PODXL Represent a New Entity to Be Explored Among Podocytopathies

BACKGROUND/OBJECTIVES

Podocalyxin is a sialoprotein mainly expressed in the kidney cortex and lung tissue, which has been described as a component of the podocyte glycocalyx. This protein promotes the reorganization of the podocyte cytoskeleton, as well as the morphogenesis and differentiation of nascent podocytes, actively participating in glomerular filtration. Previous research has suggested that PODXL haploinsufficiency leads to podocytopathy with development of focal segmental glomerulosclerosis, a disorder that has been demonstrated in Podxl-deficient animal models and proposed as a primary cause in human families affected by this condition. However, only a few families have been reported, which limits the understanding about the spectrum of phenotype and prognosis of the disease.

METHODS

We performed high-throughput sequencing in a cohort of young adults with CKD, describing the clinical scenario of those who harbored truncating variants in the PODXL gene and testing the families for detected variants.

RESULTS

The PODXL gene exhibited a slight deviation in loss intolerance probability and moderate deviation in the observed/expected ratio of variation, which is typically observed in dominant genes with age-dependent incomplete penetrance or variable expression. We reported four novel truncating variants in the PODXL gene, along with a collection of previously published monoallelic truncating variants.

CONCLUSIONS

These findings further support evidence about genetic defects in the PODXL gene associated with a new molecular entity of podocytopathy with adult onset. Additionally, the nucleotide sequence of PODXL contains particularities that require careful analysis to interpret the effect of the variants detected in this gene.

Reclassifying NOBOX variants in primary ovarian insufficiency cases with a corrected gene model and a novel quantitative framework

STUDY QUESTION

How updated expression and genomic data combined with a disease/disorder-specific classification system can be used to correct a gene model for a better evaluation of the pathogenicity of variants found in patients?

SUMMARY ANSWER

By combining available genomic and transcriptomic data from several species and a quantitative classification framework with primary ovarian insufficiency (POI)-adjusted parameters, we correct the human NOBOX (newborn ovary homeobox) gene model and provide a reclassification of variants previously reported in POI cases.

WHAT IS KNOWN ALREADY

The NOBOX gene, encoding a gonad-specific transcription factor with a crucial role in early folliculogenesis and considered a major gene involved in POI, is currently described as being expressed as four transcripts, the longest one considered canonical. All the variants identified in POI cases have been evaluated according to this canonical transcript, and the various functional tests have been performed using the corresponding predicted protein.

STUDY DESIGN, SIZE, DURATION

We refined and corrected the NOBOX gene model using available genomic and RNAseq data in human and 16 other mammalian species. Expression data were selected for tissue specificity, strand specificity, and coverage. The analysis of RNAseq data from different ovarian fetal stages allows for a time-course description of NOBOX isoforms. Literature was scanned to retrieve NOBOX variants reported in POI cases, and NOBOX variants present in ClinVar and GnomAD 4 databases were also retrieved.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Strand-specific RNAseq data from human fetal ovaries and human adult testes were analysed to infer the correct human NOBOX gene isoforms. The conservation of the gene structure was verified by combining the aligned genomic sequences from 17 mammalian species covering a wide phylogenetic range and the relevant RNAseq data. As changing a gene model implies a reclassification of variants, we set up a quantitative framework with updated variant frequencies from GnomAD4 and POI-adjusted parameters following the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines. Using this framework, we reclassified 44 NOBOX variants reported in POI patients and families, 117 NOBOX variants reported in ClinVar, and 2613 NOBOX variants present in GnomAD4.

MAIN RESULTS AND THE ROLE OF CHANCE

The corrected NOBOX gene model proposes the invalidation of two transcripts, including the canonical one. The two correct isoforms were present in fetal ovarian samples, and only one was detected in adult testes. Only 14 variants remained as possibly causative for POI. Furthermore, this re-evaluation strongly suggests that NOBOX biallelic variants are the most likely cause of POI.

LARGE SCALE DATA

Large tables are provided as supplementary data sets on the Zenodo repository.

LIMITATIONS, REASONS FOR CAUTION

The proposed gene model is robust but relies on available transcriptomic data covering a range of time points and tissues. Our scoring system was manually adjusted and other laboratories can implement it with different parameters.

WIDER IMPLICATIONS OF THE FINDINGS

For the NOBOX variants that cannot be considered pathogenic or causative anymore, the genome/exome sequencing data of the corresponding patients should be reanalysed. Furthermore, the functional studies performed using the obsolete coding sequence should be reconsidered. The corrected gene model should be taken into account when evaluating novel NOBOX variants identified in POI patients. Our results highlight the importance of the careful assessment of the most updated expression data for validating a gene model, enabling a correct evaluation of the pathogenicity of variants found in patients. The proposed quantitative framework developed here can be used for the classification of variants in other genes underlying POI. Furthermore, the global approach based on quantitatively adjusting the ACMG/AMP guidelines could be extended to other inherited pathologies.

STUDY FUNDING/COMPETING INTEREST(S)

This project was not funded. All the authors have no conflict of interest to disclose.

Clinical spectrum, genetics and management insights of PAX2-related disorder in nine children

BACKGROUND

Renal coloboma syndrome (RCS) is a rare autosomal dominant genetic disorder associated with the paired box gene 2 (PAX2). Over the past three decades, PAX2 variants have manifested with vast phenotype and genotype heterogeneity, with limited experience gained regarding its clinical progression and management strategies.

METHODS

We included nine Chinese children diagnosed with PAX2-related disorder at Beijing Children's Hospital. The medical records were retrospectively reviewed, and the demographic data, clinical manifestations, genetic testing results, imaging examination findings, laboratory tests, and renal biopsy results were recorded and analyzed.

RESULTS

Eight distinct PAX2 pathogenic variants, including four novel variants, were identified in nine children. All patients exhibited developmental abnormalities of the urinary system, while two presented with ocular abnormalities with retinal myelinated nerve fibers identified as a novel manifestation of PAX2-related disorder. Cranial imaging examinations were performed on three patients, revealing vascular anatomical abnormalities. Five patients received empirical treatment with angiotensin-converting enzyme inhibitors (ACEIs), resulting in varied therapeutic outcomes.

CONCLUSION

PAX2 variants exhibit significant clinical diversity, and our findings further expand the genotype-phenotype spectrum of PAX2-related disorder. The variable efficacy of ACEIs highlights the importance of personalized evaluation and treatment strategies and extended follow-up periods in the future.

Data-driven insights to inform splice-altering variant assessment

Disease-causing genetic variants often disrupt mRNA splicing, an intricate process that is incompletely understood. Thus, accurate inference of which genetic variants will affect splicing and what their functional consequences will be is challenging, particularly for variants outside of the essential splice sites. Here, we describe a set of data-driven heuristics that inform the interpretation of human splice-altering variants (SAVs) based on the analysis of annotated exons, experimentally validated SAVs, and the currently understood principles of splicing biology. We defined requisite splicing criteria by examining around 202,000 canonical protein-coding exons and 19,000 experimentally validated splicing branchpoints. This analysis defined the sequence, spacing, and motif strength required for splicing, with 95.9% of the exons examined meeting these criteria. By considering over 12,000 experimentally validated variants from the SpliceVarDB, we defined a set of heuristics that inform the evaluation of putative SAVs. To ensure the applicability of each heuristic, only those supported by at least 10 experimentally validated variants were considered. This allowed us to establish a measure of spliceogenicity: the proportion of variants at a location (or motif site) that affected splicing in a given context. This study makes considerable advances toward bridging the gap between computational predictions and the biological process of splicing, offering an evidence-based approach to identifying SAVs and evaluating their impact. Our splicing heuristics enhance the current framework for genetic variant evaluation with a robust, detailed, and comprehensible analysis by adding valuable context over traditional binary prediction tools.

Detailed Clinical, Ophthalmic, and Genetic Characterization of MYO7A-Associated Usher Syndrome

Purpose

To analyze the clinical spectrum and natural history of MYO7A-associated Usher syndrome type I (USH1).

Methods

Patients with molecularly confirmed MYO7A-associated USH1 in a single tertiary referral center. Data was extracted from physical and electronic case notes, including imaging and electrophysiology. Genetic results were reviewed, and the detected variants were assessed. Main outcome measures were clinical findings, qualitative and quantitative analysis of retinal imaging, and electrophysiology.

Results

Eighty patients were identified and evaluated longitudinally. The mean age (±SD) of onset of symptoms was 12.0 ± 5.8 years of age, and a mean follow-up time of 16.2 years. BCVA was 0.4 ± 0.5 LogMAR at baseline, and 0.7 ± 0.8 LogMAR at the last visit for both eyes. The change in BCVA over time was 0.02 LogMAR per year. A hyperautofluorescent (hyperAF) ring was present in 51% of the patients. The mean ellipsoid zone width (EZW) at baseline was 2568.2 ± 1528.9 µm OD and 2527.9 ± 1609.3 µm OS, which decreased to 2012.3 ± 1705.1 µm OD and 1806.3 ± 1647.1 µm OS at last visit. Electrophysiology revealed rod and cone dysfunction with relative or complete sparing of macular function. There were statistically significant changes in BCVA, EZW, and hyperAF ring between baseline and follow-up. Genetic analysis identified 83 variants in MYO7A, including 18 novel variants.

Conclusions

Longitudinal analysis shows that the majority of patients retain central visual function and structure until the fifth decade of life, which informs advice on prognosis and the window for therapeutic intervention.

Phosphoribosyl pyrophosphate synthetase 1 (PRPS1) associated retinal degeneration: an international study

INTRODUCTION

Phosphoribosyl pyrophosphate synthetase 1 (PRPS1) is an X-linked gene critical for nucleotide metabolism. Pathogenic PRPS1 variants cause three overlapping phenotypes: Arts syndrome (severe neurological disease), Charcot-Marie-Tooth type 5 [CMTX5] (peripheral neuropathy), and non-syndromic sensorineural hearing loss (SNHL). Each may be associated with retinal dystrophy. Multicenter phenotypic studies are limited.

METHODS

A multicenter retrospective clinical case series of 15 patients from 12 pedigrees with PRPS1-associated retinal degeneration is presented.

RESULTS

Of 15 patients, 11 (73.3%) were female. Mean age of ocular disease onset was 8.5 years (range, 0.5-35 years). Many were diagnosed with Leber congenital amaurosis prior to genetic testing (n = 5). Five patients had clinical diagnoses of CMTX5 and Arts syndrome, two had isolated ocular disease, and one was asymptomatic. Mean initial VA (LogMAR) was 0.74, 0.74, 0.83, and 0.85 for isolated ocular disease, CMTX5, Arts, and SNHL, respectively. Ten patients were hyperopic and eight had asymmetric VA. Macular atrophy (n = 13), optic atrophy (n = 13), bone spicules (n = 10), and parafoveal outer retinal atrophy (n = 12) were common findings. Electroretinogram showed delayed and attenuated photopic and scotopic responses (n = 10). Median follow-up of 2.9 years (range, 1.5-11.6 years) in six patients showed retinal disease progression in two patients.

DISCUSSION

PRPS1-associated retinal degeneration predominantly manifests as a bilateral asymmetric cone and rod dystrophy, commonly associated with hyperopia and optic atrophy.

Delayed diagnosis of ataxia with oculomotor apraxia type 2 in a Peruvian patient, a case report

INTRODUCTION

Ataxia with oculomotor apraxia type 2 (AOA2) is a rare autosomal recessive cerebellar ataxia characterized by progressive cerebellar ataxia, sensorimotor peripheral neuropathy, and occasional oculomotor apraxia.

CASE REPORT

A 50-year-old male with a history of orthopedic shoe use since childhood presented with slowly progressive ataxia and neuropathy. Laboratory tests showed elevated serum alpha-fetoprotein levels and increased total cholesterol. Clinical whole genome sequencing identified a c.4853C > G (p.Ser1618Ter) homozygous pathogenic variant in SETX.

CONCLUSION

The case highlights the challenges identifying rare disorders like AOA2 due to limited access to genetic testing and socioeconomic and healthcare barriers.

A novel frameshift variant in the GJA1 gene is associated with recessive oculodentodigital dysplasia

BACKGROUND

Oculodentodigital dysplasia (ODDD) is a rare syndrome that causes a constellation of facial, ophthalmic, dental, and limb abnormalities. Variants in the gap junction alpha-1 (GJA1) gene have been described in patients with ODDD. Hereby we present the ocular manifestations in a patient with recessive ODDD due to a novel homozygous frameshift variant in GJA1.

MATERIAL AND METHODS

Detailed ophthalmic manifestation and clinical features of disease were documented through external color photography and ultrasound biomicroscopy (UBM). Genetic testing was performed through a congenital heart disease panel.

RESULTS

A six-year-old girl was referred for ophthalmic evaluation in the setting of numerous syndromic features compatible with ODDD. Clinical features included nasal thinning, alar hypoplasia, hypotrichosis, microdontia and enamel hypoplasia. Ocular manifestations included microcornea, microphthalmia, posterior synechiae, cataract, and persistent hyperplastic primary vitreous. Genetic testing revealed a novel homozygous variant in the GJA1 gene, c.565del p.(Arg189Glufs *35). This variant disrupts the fourth helical transmembrane domain of the protein as well as its C-terminal cytoplasmic tail.

CONCLUSION

Here we describe the clinical and ocular manifestations of a Brazilian patient with ODDD, report a novel frameshift homozygous variant in GJA1, and contribute to the ongoing expansion of scientific knowledge regarding ODDD.

Functional profiling of KCNE1 variants informs population carrier frequency of Jervell and Lange-Nielsen syndrome type 2

Congenital long-QT syndrome (LQTS) is most often associated with pathogenic variants in KCNQ1 encoding the pore-forming voltage-gated potassium channel subunit of the slow delayed rectifier current ( I Ks ). Generation of I Ks requires assembly of KCNQ1 with an auxiliary subunit encoded by KCNE1 , which is also associated with LQTS but causality of autosomal dominant disease is disputed. By contrast, KCNE1 is an accepted cause of recessive type 2 Jervell and Lange-Nielson syndrome (JLN2). The functional consequences of most KCNE1 variants have not been determined and the population prevalence of JLN2 is unknown. Methods : We determined the functional properties of 95 KCNE1 variants co-expressed with KCNQ1 in heterologous cells using high-throughput voltage-clamp recording. Experiments were conducted with each KCNE1 variant expressed in the homozygous state and then a subset was studied in the heterozygous state. The carrier frequency of JLN2 was estimated by considering the population prevalence of dysfunctional variants. Results : There is substantial overlap between disease-associated and population KCNE1 variants. When examined in the homozygous state, 68 KCNE1 variants exhibited significant differences in at least one functional property compared to WT KCNE1, whereas 27 variants did not significantly affect function. Most dysfunctional variants exhibited loss-of-function properties. We observed no evidence of dominant-negative effects. Most variants were scored as variants of uncertain significance (VUS) and inclusion of functional data resulted in revised classifications for only 14 variants. The population carrier frequency of JLN2 was calculated as 1 in 1034. Peak current density and activation voltage-dependence but no other biophysical properties were correlated with findings from a mutational scan of KCNE1. Conclusions : Among 95 disease-associated or population KCNE1 variants, many exhibit abnormal functional properties but there was no evidence of dominant-negative behaviors. Using functional data, we inferred a population carrier frequency for recessive JLN2. This work helps clarify the pathogenicity of KCNE1 variants.

Whole-genome sequencing, as a powerful diagnostic tool in hearing loss, reveals novel variants in PTPRQ missed by whole-exome sequencing

BACKGROUND/OBJECTIVES

Hearing loss (HL) is one of the most common congenital disorders, affecting 1-2 in 1,000 newborns. Modern genetic diagnostics using large gene panels and/or whole exome analysis (WES) can identify disease-causing mutations in 25-50 % of patients, with higher solve rates in individuals with earlier onset.

RESULTS

Here, we used whole-genome sequencing (WGS) to reanalyze 14 index patients/families who remained without genetic diagnosis by WES. We were able to identify the genetic cause of HL in 6 families ( ∼ 43 %). Two families were diagnosed with DFNB84A caused by compound heterozygous recessive mutations in PTPRQ. Three of the four underlying variants, including a structural variant, a deep intronic variant, and a splice variant, escaped detection by WES. Minigene assays confirmed the pathogenicity of the intronic and the splice variants. In addition, we used protein 3D structure prediction and rigid ligand docking to study the pathogenicity of variants that escape nonsense-mediated decay.

CONCLUSION

In our study, we present four novel variants in PTPRQ, three of which were detected only by WGS. To our knowledge, we report here the first pathogenic deep intronic PTPRQ variant causing HL. Our results suggest that the mutational spectrum of PTPRQ is not well covered by standard WES and that PTPRQ-associated hearing loss may be more frequent than previously thought. WGS provides an additional layer of information in the diagnostics of HL.

Association Analysis of ENPP1 Tissue Expression, Polymorphism, and Growth Traits in Xiangsu Pigs

Background: Pigs are vital agricultural animals, with growth traits serving as key indicators of their quality. Methods: In this study, we examined the mRNA expression of ENPP1 as a candidate gene in heart, liver, spleen, lungs, and kidneys at 3 days and 6 months of age by real-time polymerase chain reaction method and single-nucleotide polymorphism (SNP) loci in 165 Xiangsu pigs by Sanger sequencing. Results: The expression of ENPP1 in different tissues of Xiangsu pigs at different stages was significantly different, and it had high conservation in different species.. Sequence alignment with reference data identified five SNP sites: g.64275T→C and g.64429G→A in intron 19, g.64850T→C and g.64911G→A in intron 20, and g.64527T→C in exon 20. Association analysis revealed that g.64275T→C, g.64429G→A, and g.64527T→C significantly influence the growth performance of Xiangsu pigs (p < 0.05). Conclusions: These findings suggest that ENPP1 polymorphisms are closely associated with growth traits in Xiangsu pigs and may provide valuable insights for molecular breeding of this breed.

Brugada Syndrome and GPD1L: Definite Genotype-Phenotype Association?

The GPD1L gene encodes a small cytoplasmic protein that is involved in the regulation of sodium currents. Alterations in this gene have been associated with Brugada syndrome. This rare arrhythmogenic syndrome is characterized by a typical electrocardiographic pattern, incomplete penetrance, variable expressivity, and risk of sudden cardiac death. To date, few families with a clinical diagnosis of Brugada syndrome caused by a rare alteration in the GPD1L gene have been reported worldwide. The increase in data focused on genetic variants allows us to improve the interpretation of their role in Brugada syndrome. In our study, we have compiled the GPD1L variants reported so far in patients with a definitive clinical diagnosis or suspected Brugada syndrome. We performed an exhaustive update and interpretation of each variant following the guidelines of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Our results showed that none of the variants described to date can be classified as truly harmful in Brugada syndrome. Despite this fact, more clinical and genetic data are needed to definitively rule out the GPD1L gene as a cause of Brugada syndrome. In summary, to date, there is insufficient evidence to conclude a definitive association between GPD1L and Brugada syndrome.

Best Vitelliform Macular Dystrophy Natural History Study Report 2: Fundus Autofluorescence and OCT

PURPOSE

To analyze the retinal imaging findings and natural history of Best vitelliform macular dystrophy (BVMD).

DESIGN

Single-center retrospective, consecutive, observational study.

PARTICIPANTS

Patients with a clinical diagnosis of BVMD, from pedigrees with a likely disease-causing monoallelic variant in BEST1.

METHODS

Data were extracted from electronic and physical case notes. Retinal imaging with OCT and fundus autofluorescence (FAF) was analyzed cross-sectionally and longitudinally.

MAIN OUTCOME MEASURES

Qualitative and quantitative OCT and FAF analysis.

RESULTS

Two hundred twenty-two patients (127 men) from 141 families were included. Mean central retinal thickness on OCT at baseline was 337.2 μm for the right eye and 341.1 μm for the left eye, with a mean annual thickness loss of 5.7 and 5.2 μm, respectively. The presence of the OCT features: previtelliform lesion, solid vitelliform lesion, vitelliform lesion with subretinal fluid, and focal choroidal excavation were associated with a better mean visual acuity (VA), whereas the presence of intraretinal fluid and atrophy/fibrosis were correlated with a worse mean VA. Fundus autofluorescence showed an area of hyperautofluorescence at the posterior pole in 138 eyes (34.7%), a circumscribed area of hyperautofluorescence superior or superotemporal of the optic nerve head in 53 eyes (13.3%), fibrotic changes in 48 eyes (12.1%), and atrophy in 41 eyes (10.3%).

CONCLUSIONS

Best vitelliform macular dystrophy shows a wide spectrum of phenotypes on OCT and FAF imaging. The slow and variable disease course may pose a challenge in identification of early end points for therapeutic trials aimed at altering kinetics of degeneration.

FINANCIAL DISCLOSURE(S)

Proprietary or commercial disclosures may be found in the Footnotes and Disclosures at the end of this article.

Identification and Characterization of Novel FSHR Copy Number Variations Causing Premature Ovarian Insufficiency

Follicle stimulating hormone (FSH) is a key pituitary gonadotropic hormone implicated in human fertility and is crucial for folliculogenesis and recruitment of new antral follicles. Variations in its receptor, FSHR, can lead to diverse reproductive phenotypes including ovarian hyperstimulation syndrome (OHSS) and premature ovarian insufficiency (POI). This study reports a novel case of FSHR-related ovarian insufficiency in a patient with primary amenorrhea, subnormal AMH levels, and delayed puberty. Genetic exploration revealed two compound heterozygous intragenic deletions of FSHR. Specifically, the patient inherited a maternally derived deletion spanning exons 5-10 and a paternally derived deletion involving exons 3-6. Through chromosomal microarray analysis (CMA), exome sequencing, long-range PCR, and Sanger sequencing, we characterized the breakpoints and confirmed the compound heterozygous deletions. The findings reveal a complete loss of function of both FSHR alleles, contributing to the patient's POI phenotype. This case emphasizes the complexity of genotype-phenotype correlations in FSHR-related disorders and the role of CNVs in POI phenotypes. Although these events are rare, our results advocate for the inclusion of CNV detection in the diagnostic workup of POI to ensure accurate diagnosis and better patient management.

Modified Rules for Classification of Variants Associated With Disorders of Somatic Mosaicism

Disorders of somatic mosaicism (DoSMs) are rare genetic disorders arising from postzygotic alteration leading to segmental/nonsegmental disease. Current professional guidelines for standardized variant interpretation focus on germline and cancer variants, making them suboptimal for DoSM variant interpretation. The Brain Malformations Variant Curation Expert Panel (BMVCEP) modified existing guidelines to account for brain-specific disorders of somatic mosaicism, but applicability to other DoSM presentations is limited. At Washington University in St. Louis School of Medicine, we have adopted the BMVCEP interpretation framework but suggested alterations that make it more suitable for generalized DoSM variant classification. These modifications include (1) expanding applicability beyond genes associated with brain malformations, (2) introduction of a criterion to interpret truncating variants at the C-terminus of gain of function genes, (3) establishment of a variant allele fraction (VAF) cutoff for applying de novo criteria, and (4) demonstration that in silico prediction tools are relevant to interpretation of gain of function missense variants. Furthermore, modifications to BMVCEP guidelines reduce the number of variants classified as uncertain. The variant classification considerations that we propose have the potential to improve the accuracy of somatic variant classification, better inform clinical care, and may benefit clinical laboratories also conducting DoSM testing.

Trio Exome Sequencing in VACTERL Association

INTRODUCTION

Currently, there is only limited data on monogenic causes of vertebral defects, anorectal malformations, cardiac defects, esophageal atresia or tracheoesophageal fistula, renal malformations, and limb defects (VACTERL) association. The aim of this study was to extend the spectrum of disease-causing variants in known genes, to determine the diagnostic yield of monogenic causes, and to identify candidate genes and rare variants by applying comprehensive genetic testing or rare variant burden.

METHODS

The total cohort comprised 101 affected individuals and their parents. Trio exome sequencing was only performed in 96 individuals and their parents because of DNA quality reasons and case-control gene and pathway burden tests were calculated and evaluated by quantile-quantile plots, principal component analysis plots and family-based association test (FBAT).

RESULTS

In 5 of 96 individuals, disease-causing variants in known genes or loci were identified to be associated with the following 4 disorders: Kabuki syndrome, Sotos syndrome, MELAS syndrome, and deletion syndrome encompassing TWIST1. In 91 individuals, no disease-causing variants were found. FBAT showed 14 significant variants, 2 significant genes (LOC645752 and ZNF417), and 8 significant pathways.

CONCLUSION

This study shows that most individuals with VACTERL association do not have known discrete genetic syndromes, implying that pathomechanisms or variants not identifiable by exome sequencing may exist requiring further investigation.

PDE6A-Associated Retinitis Pigmentosa, Clinical Characteristics, Genetics, and Natural History

PURPOSE

To analyze the genetics, clinical characteristics, and natural history of PDE6A-associated retinitis pigmentosa.

DESIGN

Retrospective, longitudinal, observational cohort study.

PARTICIPANTS

Patients with molecularly confirmed PDE6A-associated retinal dystrophy in a single tertiary referral center.

METHODS

Review of medical records and retinal imaging, including fundus autofluorescence (FAF) imaging and spectral-domain OCT. Genetic results were reviewed, and the detected variants were assessed.

MAIN OUTCOME MEASURES

Molecular genetic testing, clinical findings including best-corrected visual acuity (BCVA), qualitative and quantitative retinal imaging analysis.

RESULTS

Sixteen patients (32 eyes) were identified and evaluated longitudinally. Genetic analysis identified 14 variants in the PDE6A gene, including 8 novel variants. The mean age (± standard deviation, range) was 34.8 years (± 17.4, 12-76) at baseline, with a mean follow-up time of 4.8 years. Best-corrected visual acuity was 0.45 ± 0.45 logarithm of the minimum angle of resolution (logMAR) (range 0.0-1.6) at baseline and 0.65 ± 0.7 logMAR (range 0.0-2.3) at the last visit. Best-corrected visual acuity was similar among eyes in 88% of patients. A hyperautofluorescent ring was observed on FAF in 50% and 43.8% of the eyes at baseline and follow-up visit, respectively, with a mean area of 9.7 ± 4.5 mm2 at baseline and mean of 8.6 ± 4.8 mm2 at the follow-up visit. Mean horizontal ellipsoid zone width (EZW) at baseline was 1765 ± 1093 μm, which decreased to 1580 ± 1077 μm at follow-up. Eighteen eyes exhibited cystoid macular edema at baseline (56%), and 17 eyes (53%) at follow-up. There were statistically significant changes during the follow-up period in terms of BCVA, hyperautofluorescent ring area, and the EZW.

CONCLUSIONS

This study highlights the natural history of PDE6A-retinopathy. Most patients in this cohort had mild BCVA loss, and slowly progressive disease, based on FAF and OCT measurements.

FINANCIAL DISCLOSURE(S)

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Two GNPTAB Variations Caused Mucolipidosis II Alpha/Beta in a Chinese Family

Introduction: Mucolipidosis II alpha/beta (ML II) is an autosomal recessive disorder with craniofacial dysmorphism and bone deformities. The variants in GNPTAB are associated with ML II. Materials and Methods: A female pediatric patient presented with bone deformities, mental and motor developmental abnormalities and craniofacial dysmorphism. We performed clinical whole-exome sequencing (WES) and verified the variants via qPCR, gap-PCR and Sanger sequencing. Results: Clinical WES identified a point variant c.1090C > T (p.R364*) and a copy number variation (CNV) in GNPTAB. Compared with normal control, GNPTAB expression was reduced in blood of the proband. Using Gap-PCR and Sanger sequencing, we identified the break point of CNV (NC_000012.11:g.102136912_102142973del), and successfully performed prenatal diagnosis for the proband's mother. Conclusion: To our knowledge, this is the first report of this novel CNV associated with ML II. Our findings expand the genotypes related to ML II and contribute to the gene diagnosis of ML II.

Evaluating reproductive carrier screening using biotinidase deficiency as a model: Variants identified, variant rates, and management

PURPOSE

To review biotinidase gene (BTD) variants identified in a large, diverse, reproductive carrier screening (RCS) cohort and outline management of heterozygotes with pathogenic or likely pathogenic (P/LP) variants.

METHODS

This retrospective observational study included samples tested from January 2020 to September 2022 in a 274-gene panel. The study involved females aged 18 to 55 years. Screening was performed using next-generation sequencing covering exons and 10 base-pair flanking introns. The heterozygote frequency was calculated for P/LP variants for the entire population and individual racial/ethnic groups.

RESULTS

Of the 91,637 women tested, 5625 (6.1%) had a P/LP variant in BTD. NM_000060.4:c.1330G>C p.(Asp444His) (referred to as D444H or D424H) alone, or in combination with another variant, accounted for 5193 (92.3%) of the positive tests. P/LP heterozygote rates differed between racial and ethnic groups. We ascertained 7 novel P/LP variants not previously recorded in databases.

CONCLUSION

The BTD P/LP variants identified through RCS were substantially compatible with those found through positive newborn screening. Therefore, RCS provides a potential for earlier diagnosis. We observed significant differences in P/LP heterozygote rates for biotinidase deficiency among different racial and ethnic groups. Most reported variants can be interpreted without requiring determination of serum biotinidase activity.

TTN:c.12478del in proximal I-band of titin represents a common molecular cause of dilated cardiomyopathy in Slovenian patients

BACKGROUND

Titin truncating variants (TTNtv-s) are the most common genetic cause of dilated cardiomyopathy (DCM). Only rare TTNtv-s in the constitutively expressed exons of the A-band of the protein titin are associated with DCM according to the guidelines, however, studies in large cohorts of patients with DCM suggest that the region where TTNtv-s are associated with DCM is wider, extending at least into the I-band. The aim of this study was to describe the molecular pathology of TTNtv-s in Slovenian patients with cardiomyopathy and to clinically characterise the most recurrent TTNtv.

RESULTS

We collected all TTNtv-s identified in patients with cardiomyopathy using next-generation sequencing genetic testing between 2010 and July 2024, resulting in 42 unique variants identified in 54 patients. The TTN:c.12478del variant, affecting not the A-band but the proximal I-band, specifically the cardiac-specific N2Bus region, was found to be the most recurrent variant, present in seven (11.6%) probands with DCM. Genetic characterisation revealed a probable founder origin of the variant. Clinical characterisation of these probands revealed a phenotype consistent with DCM and severely reduced left ventricular ejection fraction in all probands. Three (43%) of the probands had atrial fibrillation and/or non-sustained ventricular tachycardia. Based on literature reports and evidence supporting the pathogenicity of the TTN:c.12478del variant affecting the proximal I-band, we classified all rare TTNtv-s in constitutively expressed exons of the I-band as (likely) pathogenic. Therefore, 33 (78.6%) TTNtv-s were classified as (likely) pathogenic (13 in the I-band, affecting 19 probands and 20 in the A-band affecting 25 probands), meaning that TTNtv-s were identified in 44 genotype-positive Slovenian probands with DCM, explaining 73.3% of the molecular pathology of DCM.

CONCLUSION

We report an almost threefold higher diagnostic yield of TTNtv-s in probands with DCM compared to previously reported findings in cohorts of patients with DCM from other populations. We also highlight the need for screening for rare TTNtv-s in the constitutively expressed exons of the I-band and for TTN:c.12478del in patients with DCM in this geographical region.

A novel likely pathogenic germline variant in CDKN1B in a patient with MEN4 and medullary thyroid cancer

Multiple endocrine neoplasia type 4 (MEN4) is caused by a germline CDKN1B deleterious variant. CDKN1B encodes p27Kip1, a cyclin-dependent kinase inhibitor that acts as tumor-suppressor. Clinical presentation of MEN4 is similar to multiple endocrine neoplasia type 1 (MEN1) but the diagnosis of MEN4 can only be established once a germline CDKN1B pathogenic variant has been confirmed. We describe a unique case presenting with two -rare endocrine conditions. A 59-year-old female patient was diagnosed with medullary thyroid cancer (MTC) without evidence of a germline pathogenic variant in the RET proto-oncogene. Five years later, she developed Cushing's disease. A heterozygous germline variant was identified in the CDKN1B gene, specifically c.536del (p.Prol179GlnfsTer46), corresponding to a single-nucleotide deletion at position 536. This variant induces a frameshift, leading to an alternative stop codon. Immunostaining of the pituitary and thyroid tumors revealed a weak nuclear expression of p27/Kip1 without significant differences of expression between tumor and non-tumoral tissues. The NGS panel (Oncomine Comprehensive Assay v3) performed in both MTC and pituitary tissues identified the germline CDKN1B variant, as well as a pathogenic missense somatic variant c.182 A > G, p.(Gln61Arg) in HRAS in the MTC, without any RET somatic pathogenic variant. Evaluation of loss of heterozygosity (LOH) in both MTC and pituitary tissues showed compatibility with copy-neutral LOH, although further evidence is required for definitive confirmation. In conclusion, we report a clinical case of MTC coexisting with MEN4 due to a novel CDKN1B germline heterozygote frameshift variant.

Identification of mutations associated with congenital cataracts in nineteen Chinese families

BACKGROUND

Congenital cataracts (CC) are one of the leading causes of impaired vision or blindness in children, with approximately 8.3-25% being inherited. The aim of this study is to investigate the mutation spectrum and frequency of 9 cataract-associated genes in 19 Chinese families with congenital cataracts.

PURPOSE

To identify the gene variants associated with congenital cataracts.

METHODS

This study included a total of 58 patients from 19 pedigrees with congenital cataracts. All probands were initially screened by whole-exome sequencing(WES), and then validated by co-segregation analysis using Sanger sequencing.

RESULTS

Likely pathogenic variants were detected in 8 families, with a positivity rate of 42.1%. Variants in various genes were identified, including GJA3, CRYGD, CRYBA4, BFSP2, IARS2, CRYAA, CRYBA1, ARL2 and CRYBB3. Importantly, this study identified compound heterozygous variants of IARS2 in one family.

CONCLUSIONS

Our research findings have revealed multiple gene variants associated with cataracts, providing clinical guidance for improved molecular diagnosis of congenital cataracts in the era of precision medicine.

Identification of a novel single nucleotide deletion in the NHS causing Nance-Horan syndrome

BACKGROUND

Nance-Horan syndrome (NHS) is a rare X-linked dominant disorder caused by pathogenic variants in the NHS gene on chromosome Xp22.2-Xp22.13. Clinical manifestations consist of congenital cataracts, along with dysmorphic facial features and dental anomalies and, in certain instances, intellectual disability. This study aimed to identify the genetic cause responsible for NHS in a Chinese family with four individuals primarily presenting with congenital cataracts.

METHODS

Genomic DNA was collected from six family members, including four affected individuals (three females and one male) from a two-generation family. The family history and clinical data were documented. Whole-exome sequencing was performed on the proband, and candidate pathogenic variants were filtered through a series of screening steps and validated by Sanger sequencing. Co-segregation analysis was conducted to confirm the pathogenicity of the identified variant.

RESULTS

Genetic analysis revealed a novel frameshift pathogenic variant in NHS gene (c.1735delA: p.R579Gfs*91) present in all four affected members. All affected members exhibited congenital cataracts, congenital ptosis, strabismus, high myopia as well as dental and facial anomalies, and more severe characteristic features observed in the male patient. These clinical manifestations were consistent with the phenotype of NHS.

CONCLUSION

This study identified a novel NHS pathogenic variant in a Chinese family, expanding the mutational spectrum of NHS. Contrary to previous reports of female carriers exhibiting mild symptoms, we demonstrated severe ocular phenotypes in three affected females. These findings will assist in providing genetic counseling for NHS patients.

The ClinGen Severe Combined Immunodeficiency Disease Variant Curation Expert Panel: Specifications for classification of variants in ADA , DCLRE1C , IL2RG , IL7R , JAK3 , RAG1 , and RAG2

Purpose

This collaborative study, led by the Clinical Genome Resource Severe Combined Immunodeficiency Disease Variant Curation Expert Panel (ClinGen SCID-VCEP), implemented and adapted the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for interpreting germline variants in genes with established relationships to SCID. The effort focused on the 7 most common SCID-related genes identified by SCID newborn screening in North America: ADA , DCLRE1C , IL2RG , IL7R , JAK3 , RAG1 , and RAG2 .

Methods

The SCID-VCEP conducted a rigorous review of variants that involved database analyses, literature review, and expert feedback to derive gene-specific modifications to the ACMG/AMP guidelines. These specifications were validated using a pilot set of 90 variants. Results: Of these 90 variants, 25 were classified as pathogenic, 21 as likely pathogenic, 14 as variants of uncertain significance (VUS), 18 as likely benign, and 12 as benign. Seventeen variants with conflicting classifications in ClinVar were successfully resolved. The criteria included modifications to 20 of the 28 original ACMG/AMP criteria specific to SCID-related genes.

Conclusion

The SCID-specific variant curation guidelines developed by the SCID-VCEP will enhance the precision of SCID genetic diagnosis and provide a robust framework for interpreting variants in SCID-related genes, contributing to appropriate treatment of SCID.

Genotypes and clinical phenotypes of pediatric patients with NOG variants: Middle ear surgical outcomes from a Tertiary Center in South Korea

OBJECTIVE

Although NOG variants are linked to congenital stapes fixation and conductive hearing loss (CHL), little is known about middle ear surgery outcomes and the characteristics of accompanying inner ear anomalies. We explored auditory phenotypes in patients with NOG variants, with a focus on the outcomes of middle ear surgery.

METHODS

This study included 11 patients from five unrelated Korean families harboring NOG variants. Genomic investigations were conducted using whole-exome sequencing and whole-genome sequencing. The clinical phenotypes, including pre- and postoperative audiological profiles, radiological abnormalities, and other comorbidities, were analyzed.

RESULTS

The average age at genetic testing was 8.2 years (range, 0-13 years). Two previously reported NOG variants (c.509C > T:p.Pro170Leu and c.252dup:p.Glu85ArgfsTer97) and three novel NOG variants, including the c.187G > T: p.Glu63Ter and two cryptic large deletion within the 17q22.2 region, were identified. All patients exhibited non-progressive CHL. Inner ear anomalies were documented in two patients, with variations such as cochlea and vestibular dysplasia. In this study, seven ears of four patients underwent stapedotomy, resulting in a significantly reduced air-bone gap of 10.18 ± 1.48 dB (P = 0.016), with sustained improvement. Conversely, patients carrying p.Pro170Leu variant, which is associated with poor outcomes for middle ear surgery, were excluded from surgical consideration.

CONCLUSION

We expanded the spectrum of genotypes and auditory phenotypes associated with NOG variants. Surgical intervention for CHL underlying NOG variants elicits favorable outcomes. However, clinicians should consider the potential for poor prognosis in certain NOG variants. Collectively, identifying NOG variants could guide the treatment strategies to improve CHL.

Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia

Variation in the non-coding genome represents an understudied mechanism of disease and it remains challenging to predict if single nucleotide variants, small insertions and deletions, or structural variants in non-coding genomic regions will be detrimental. Our approach using complementary RNA-seq and targeted long-read DNA sequencing can prioritize identification of non-coding variants that lead to disease via alteration of gene splicing or expression. We have identified a patient with primary ciliary dyskinesia with a pathogenic coding variant on one allele of the SPAG1 gene, while the second allele appears normal by whole exome sequencing despite an autosomal recessive inheritance pattern. RNA sequencing revealed reduced SPAG1 transcript levels and exclusive allele specific expression of the known pathogenic allele, suggesting the presence of a non-coding variant on the second allele that impacts transcription. Targeted long-read DNA sequencing identified a heterozygous 3 kilobase deletion of the 5' untranslated region of SPAG1, overlapping the promoter and first non-coding exon. This non-coding deletion was missed by whole exome sequencing and gene-specific deletion/duplication analysis, highlighting the importance of investigating the non-coding genome in patients with "missing" disease-causing variation. This paradigm demonstrates the utility of both RNA and long-read DNA sequencing in identifying pathogenic non-coding variants in patients with unexplained genetic disease.

Clinical characteristics and genetic profile of children with WDR72-associated distal renal tubular acidosis: a nationwide experience

BACKGROUND

Limited data, primarily from small case series, exist regarding the clinical profile, genetic variants, and outcomes of WDR72-associated distal renal tubular acidosis (WDR72-dRTA).

METHODS

Our study enrolled children diagnosed with WDR72-dRTA below 18 years of age from 9 Indian centers and analyzed their clinical characteristics, genetic profiles, and outcomes. Potential genotype-phenotype correlations were explored.

RESULTS

We report 22 patients (59% female) with WDR72-dRTA who were diagnosed at a median age of 5.3 (3, 8) years with polyuria (n = 17; 77.3%), poor growth (16; 72.7%), and rickets (9; 40.9%). Amelogenesis imperfecta was present in 21 (95.5%) cases. At presentation, all patients had normal anion gap metabolic acidosis; hypokalemia and nephrocalcinosis were seen in 17 (77.3%) patients each. Seven (31.8%) patients had concomitant proximal tubular dysfunction. Genetic analysis identified biallelic nonsense variants in 18 (81.8%) patients, including novel variants in 6 cases. A previously reported variant, c.88C > T, and a novel variant, c.655C > T, were the most frequent variants, accounting for 10 (45.5%) cases. Over a median follow-up of 1.3 (1, 8) years, the height velocity improved by 0.74 (0.2, 1.2) standard deviation scores, while 3 children (13.6%) progressed to chronic kidney disease (CKD) stage 2, with eGFR ranging from 67 to 76 mL/min/1.73 m2, respectively, after 11.3-16 years of follow-up. No specific genotype-phenotype correlation could be established.

CONCLUSIONS

WDR72-dRTA should be considered in children with typical features of amelogenesis imperfecta and dRTA. Biallelic nonsense variants are common in Asians. While most patients respond well to treatment with improved growth and preserved eGFR, on long-term follow-up, a decline in eGFR may occur.

A novel RP1 truncating mutation that causes autosomal dominant retinitis pigmentosa (ADRP)

Background

Retinitis pigmentosa (RP) is a genetically and clinically heterogeneous group of hereditary degenerative disorders affecting approximately one in every 4000 people worldwide. Abnormalities in the retina's photoreceptors can cause night blindness or even complete vision loss. Retinitis Pigmentosa 1 (RP1), also known as the oxygen-regulated protein-1, is a microtubule-associated protein (MAP) that organizes the outer segment of the photoreceptor. Besides, mutations in the RP1 gene are associated with dominant or recessive form of RP. This study aims to identify the potential pathogenic genes in Chinese RP patients and to elucidate the association relationship between the mutant gene and the phenotypes.

Methods

Multiple ophthalmic examinations, whole-exome sequencing, sanger sequencing, and in silico analysis were performed to evaluate the clinical features and pathogenic genes in a five-generation Chinese family diagnosed with RP.

Results

Our findings revealed a novel truncating mutation c.2015_2018del p. (Lys672Argfs∗9) in RP1 that may result in the translation of a protein with deleterious effects on photoreceptors. Therefore, resulting in autosomal dominant retinitis pigmentosa (ADRP).

Conclusions

This study broaden the range of genetic mutations associated with RP1 in ADRP and make a valuable contribution to the ongoing endeavors aimed at characterizing the molecular aspects of Chinese ADRP. Future studies would pay more attention in determining the characterization of the mutantations in RP1 gene and the relationship between genotype and phenotype in RP patients.

A guide to gene-disease relationships in nephrology

The use of next-generation sequencing technologies such as exome and genome sequencing in research and clinical care has transformed our understanding of the molecular architecture of genetic kidney diseases. Although the capability to identify and rigorously assess genetic variants and their relationship to disease has advanced considerably in the past decade, the curation of clinically relevant relationships between genes and specific phenotypes has received less attention, despite it underpinning accurate interpretation of genomic tests. Here, we discuss the need to accurately define gene-disease relationships in nephrology and provide a framework for appraising genetic and experimental evidence critically. We describe existing international programmes that provide expert curation of gene-disease relationships and discuss sources of discrepancy as well as efforts at harmonization. Further, we highlight the need for alignment of disease and phenotype terminology to ensure robust and reproducible curation of knowledge. These collective efforts to support evidence-based translation of genomic sequencing into practice across clinical, diagnostic and research settings are crucial for delivering the promise of precision medicine in nephrology, providing more patients with timely diagnoses, accurate prognostic information and access to targeted treatments.

Study of the impact of ClinGen Revisions on ACMG/AMP variant semi-automatic classification for Rare Diseases diagnosis

With the rapid development of massive sequencing technologies, the analysis of genetic variants for clinical diagnosis has exponentially escalated, particularly in the context of Rare Diseases (RDs). Diagnosing them involves identifying the genetic variants responsible for the underlying pathology development. In 2015, the American College of Medical Genetics (ACMG) established a set of recommendations to assess the evidence associated with each variant, aiming to achieve a standardized five tier classification. Over the past 5 years, ClinGen, the NIH-funded Clinical Genome Resource, has reviewed these criteria in order to make variant classification a more reproducible and rigorous process. This paper examines the impact of ClinGen-Rev modifications on variant classification, comparing them with the ACMG-2015 original recommendations. After analyzing sets of genetic variants, extracted from VCFs samples, using both criteria, we observed a change in 8.0 % of the clinical verdicts for these variants. ClinGen-Rev modifications correctly categorized 89.2 % of the curated variants, representing a significant improvement compared to the 65.6 % achieved by ACMG-2015. We also analyzed the modifications impact in a real like clinical setting, showing a significant overall reduction of VUS variants and thus potential reduction in analysis time. Finally, we discuss the underlying reasons for the most relevant changes in terms of specific labels and present their implications on the prioritization and selection process of variants, identifying some recommendations of key significant importance.

Focusing on Rare Variants Related to Maturity-Onset Diabetes of the Young in Children

Background: In this study, we analysed the clinical and genetic characteristics and follow-up data of patients with maturity-onset diabetes of the young (MODY). Methods: From January 2015 to December 2022, patients with persistent hyperglycaemia suspected of having monogenic diabetes or diabetes syndrome were recruited, and next-generation sequencing (NGS) was performed at the Shanghai Children's Medical Center. Patients' clinical and laboratory findings were recorded preceding follow-ups. Candidate variants were verified using Sanger sequencing. Variant pathogenicity was evaluated according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Genetic testing was performed in 175 children. MODY-related pathogenic or likely pathogenic gene variants were identified in 30 patients from different families. Of these, 11 were diagnosed with GCK-MODY (36.7%), six with INS-MODY (20%), five with HNF1A-MODY (16.7%), five with ABCC8-MODY (16.7%), two with HNF1B-MODY (6.7%) and one with HNF4A-MODY (3.3%). There was one shift variant and seven splice-site variants, and the rest were missense variants. We discovered six novel variants. Of the 30 patients, 63.3% had a family history of diabetes, 13.3% had diabetic ketoacidosis (DKA), and 16.7% had positive diabetes-associated autoantibodies. The diabetes phenotype of patients with the INS variant was similar to that of patients with type 1 diabetes. All patients, including those having positive autoantibodies, required long-term insulin therapy during follow-ups. Four patients with the ABCC8 variant were unable to switch to oral sulfonylurea therapy and continued insulin therapy. Conclusion: Genetic testing is helpful for the precise diagnosis and treatment of patients with MODY, including those with DKA history and positive diabetes autoantibody. GCK-MODY is the most common type of MODY, and patients with INS variant account for a relatively large proportion of MODY cases in our cohort.

Pathogenicity assessment of genetic variants identified in patients with severe hypertriglyceridemia: Novel cases of familial chylomicronemia syndrome from the Dyslipidemia Registry of the Spanish Atherosclerosis Society

PURPOSE

Genetic testing is required to confirm a diagnosis of familial chylomicronemia syndrome (FCS). We assessed the pathogenicity of variants identified in the FCS canonical genes to diagnose FCS cases.

METHODS

245 patients with severe hypertriglyceridemia underwent next-generation sequencing. Preliminary variant pathogenicity criteria and classification, based on the American College of Medical Genetics and Genomics guidelines, were obtained online and verified. Phenotype evaluation was based on lipoprotein lipase activity deficiency, a clinical score, and/or type I hyperlipoproteinemia determined in 25 patients.

RESULTS

Twenty-four biallelic variants were analyzed. Evidence-based criteria allowed the reclassification of 8 likely pathogenic (LP) variants in the LPL, APOA5, and LMF1 genes into pathogenic (P) and the change of 2 variants of uncertain significance (VUS) to LP. Conversely, 2 variations in LMF1 remained as VUS. Additionally, 1 variant in LPL and 2 in GPIHBP1 were likely benign. Twenty FCS cases had biallelic P/LP variants and 1 patient, with an FCS phenotype, harbored biallelic VUS. FCS was excluded from 4 patients with pathogenic/likely benign combinations.

CONCLUSION

The analysis of the clinical and biochemical features of patients with variants in the FCS canonical genes allowed a confident variant classification that helped in the diagnosis of novel FCS cases.

Oligogenic effect is associated with the clinical heterogeneity of autosomal dominant deafness-15

Autosomal dominant deafness-15 which is caused by mutation in the POU4F3 gene, has been reported with a wide degree of clinical heterogeneity, even between intrafamilial members. However, the reason is still elusive. In this study, A four-generation Chinese family with 11 patients manifesting late-onset progressive non-syndromic hearing loss was recruited. The phenotype of hearing loss in this family showed a large variability in terms of onset age and progression speed. A novel mutation (c.706 C > T, p.L236F) was identified by the whole exome sequencing, and its pathogenicity was confirmed by altering the subcellular localization of POU4F3. In addition, we found that two individuals with earlier age of onset and more rapid progression of hearing loss carry additional pathogenic variants in other deafness genes (III-7, STRC:c.4057 C > T; IV-1, GJB2:c.109G > A; CDC14A:c.935G > A). By using the real time quantitative PCR, western blot, luciferase assays and electrophoretic mobility-shift assay, POU4F3 was proved to directly regulate the expression of STRC, GJB2 and CDC14A respectively. ChIP-seq further revealed that POU4F3 can also bind to a series of deafness genes. In summary we expanded the mutation spectrum of POU4F3 by identifying a novel mutation and its pathogenicity. Meanwhile, three genes STRC, GJB2 and CDC14A were validated as POU4F3 new targets, implicating that the variants in the three genes may play a role of genetic modifier to generate a synergistic and enhancement effect on the progression of DFNA15.

First Reported Case of Hemoglobin H Disease Caused by the Rare α-Globin Gene Mutation (HBA2 c.244delT) in a Chinese Family

Microcytosis of red cells and mild anemia are common in thalassemia carriers but those phenotypes are not specific. It is really a challenge for clinical interpretation of those variants. Co-segregation with disease in affected family members or specific phenotypes such as the abnormal Hb H are very helpful to assess the pathogenicity of rare variants. HBA2 c.244delT was only reported in a 19-year-old woman with mild microcytosis and hypochromia. There was no other information about this variant reported before. We first described the case of this variant compounded with SEA deletion who presented with moderate anemia. Co-segregation analysis was confirmed by Sanger sequencing. Our study gave evidence for predicting the pathogenicity of this rare missense variant.

Investigating TNNC1 gene inheritance and clinical outcomes through a comprehensive familial study

Hypertrophic cardiomyopathy (HCM) and restrictive cardiomyopathy (RCM) have significant phenotypic overlap and a similar genetic background, both caused mainly by variants in sarcomeric genes. HCM is the most common cardiomyopathy, while RCM is a rare and often underdiagnosed heart condition, with a poor prognosis. This study focuses on a large family with four infants diagnosed with fatal RCM associated with biventricular hypertrophy. Affected infants were found to be homozygous for NM_003280.3(TNNC1):c.23C>T(p.Ala8Val) variant. Interestingly, this variant resulted in a low penetrance and mild form of hypertrophic cardiomyopathy (HCM) in relatives carrying a single copy of the variant. Overall, this study underscores the complex nature of genetic inheritance in cardiomyopathies and the wide range of clinical presentations they can exhibit. This emphasizes the vital role of genetic testing in providing essential insights crucial for diagnosis, prognosis, early intervention, and the development of potential treatment strategies.

Genetic evaluation of patients with multiple primary cancers

Regarding inherited cancer predisposition, single gene carriers of pathogenic variants (PVs) have been extensively reported on in the literature, whereas the oligogenic coinheritance of heterozygous PVs in cancer-related genes is a poorly studied event. Currently, due to the increased number of cancer survivors, the probability of patients presenting with multiple primary cancers (MPCs) is higher. The present study included patients with MPCs aged ≤45 years without known PVs in common cancer predisposition genes. This study used whole exome sequencing (WES) of germline and tumoral DNA, chromosomal microarray analysis (CMA) of germline DNA (patients 1-7, 9 and 10), and a karyotype test of patient 8 to detect variants associated with the disease. The 10 patients included in the study presented a mean of 3 cancers per patient. CMA showed two microduplications and one microdeletion, while WES of the germline DNA identified 1-3 single nucleotide variants of potential interest to the disease in each patient and two additional copy number variants. Most of the identified variants were classified as variants of uncertain significance. The mapping of the germline variants into their pathways showed a possible additive effect of these as the cause of the cancer. A total of 12 somatic samples from 5 patients were available for sequencing. All of the germline variants were also present in the somatic samples, while no second hits were identified in the same genes. The sequencing of patients with early cancers, family history and multiple tumors is already a standard of care. However, growing evidence has suggested that the assessment of patients should not stop at the identification of one PV in a cancer predisposition gene.

Interpretation and classification of FBN1 variants associated with Marfan syndrome: consensus recommendations from the Clinical Genome Resource's FBN1 variant curation expert panel

BACKGROUND

In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) developed standardized variant curation guidelines for Mendelian disorders. Although these guidelines have been widely adopted, they are not gene- or disease-specific. To mitigate classification discrepancies, the Clinical Genome Resource FBN1 variant curation expert panel (VCEP) was established in 2018 to develop adaptations to the ACMG/AMP criteria for FBN1 in association with Marfan syndrome.

METHODS

The specific recommendations were developed through literature review, surveys, online expert panel discussions, and pilot testing of a set of 60 different variants. Consensus among experts was considered reached if at least 75% of the members agreed with a given rule specification. The final set of rules received approval from the ClinGen Sequence Variant Interpretation Working Group.

RESULTS

The developed specifications introduce modifications to 14 of the 28 ACMG/AMP evidence criteria and deem 6 criteria non-applicable. Some of these specifications include refining the minor allele frequency thresholds, creating a FBN1-specific flowchart for PVS1, defining functional domains of the protein, developing a point-based system of counting probands and instances of de novo occurrences, recommending a points-based method of accounting for family segregation data, and clarifying the applicable functional assays that should be considered. To date, this VCEP has curated 120 variants which have been deposited to ClinVar with the 3-star review status.

CONCLUSIONS

Establishing specific adaptations for FBN1 has provided a framework to foster greater classification concordance among clinical laboratories, ultimately improving clinical care for patients with Marfan syndrome.