Novel splice site mutation in CNNM4 gene in a family with Jalili syndrome

Functional and pathogenic insights into CNNM4 variants in Jalili syndrome

Jalili syndrome, an autosomal recessive disorder causing cone-rod dystrophy and amelogenesis imperfecta, is a rare genetic disorder impacting visual and dental development. Missense variants (c.1474G > T and c.1475G > A) previously identified in patients with Jalili syndrome have been linked to functional impairment of CNNM4, however, the biological consequences of these pathogenic variants remain largely unexplored. In this study, we investigated the functional implications of these CNNM4 missense variants, which correspond to p.(Gly492Cys) and p.(Gly492Asp) substitutions within the CBS domain of the CNNM4 protein. Our findings demonstrated that these variants exhibit significantly reduced protein stability and increased mRNA decay rates compared with wild type. Despite exhibiting normal Mg2+ localization, the mutant proteins demonstrated significantly reduced Mg²⁺ extrusion activity. This suggests that the pathogenic mechanism underlying Jalili syndrome associated with these variants likely involves decreased mRNA and/or protein stability, rather than mislocalization. Our study provides valuable insights into the interplay between genetic variations, molecular stability, and functional consequences in the context of CNNM4-related disorders, highlighting the importance of CNNM4-mediated Mg²⁺ transport in Jalili syndrome. Further investigation into the mechanisms regulating CNNM4 expression and protein stability may reveal potential therapeutic avenues.

Novel homozygous nonsynonymous variant of CNNM4 gene in a Chinese family with Jalili syndrome

Background

Jalili syndrome (JS) is a rare autosomal‐recessive inherited disorder characterized by cone‐rod dystrophy and amelogenesis imperfecta. It is often misdiagnosed in clinical practice due to its heterogeneity and rarity.

Methods

Two JS patients from a consanguineous family were included in this study. Detailed ophthalmic examinations were performed. Oral photography was taken. The DNA sample of the proband was sequenced using the customized capture panel, which includes 338 retinal disease genes. Sanger sequencing was performed for validation and segregation.

Results

The patients had poor vision, photophobia, and nystagmus from childhood. Fundus examination revealed diffused chorioretinal atrophy with a prominent macular coloboma. OCT showed a deep staphyloma, severely reduced retinal thickness, retinoschisis, loss of photoreceptor layer, and retinal pigment epithelium in the macular region. Amelogenesis imperfecta, dental decay, staining, irregular shapes, and loss of teeth were present. Next‐generation sequencing combined with Sanger validation identified a novel homozygous nonsynonymous variant c.598T>C (p.S200P) in CNNM4 gene (NM_020184.3).

Conclusions

We described the clinical features of a Chinese family with JS and identified a novel disease‐causing mutation. Our findings broadened the phenotypes and mutation spectrums of JS in Chinese population, as well as are helpful in the diagnosis of this rare disease.

Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4

The four member family of "Cyclin and Cystathionine β-synthase (CBS) domain divalent metal cation transport mediators", CNNMs, are the least-studied mammalian magnesium transport mediators. CNNM4 is abundant in the brain and the intestinal tract, and its abnormal activity causes Jalili Syndrome. Recent findings show that suppression of CNNM4 in mice promotes malignant progression of intestinal polyps and is linked to infertility. The association of CNNM4 with phosphatases of the regenerating liver, PRLs, abrogates its Mg2+-efflux capacity, thus resulting in an increased intracellular Mg2+ concentration that favors tumor growth. Here we present the crystal structures of the two independent intracellular domains of human CNNM4, i.e., the Bateman module and the cyclic nucleotide binding-like domain (cNMP). We also derive a model structure for the full intracellular region in the absence and presence of MgATP and the oncogenic interacting partner, PRL-1. We find that only the Bateman module interacts with ATP and Mg2+, at non-overlapping sites facilitating their positive cooperativity. Furthermore, both domains dimerize autonomously, where the cNMP domain dimer forms a rigid cleft to restrict the Mg2+ induced sliding of the inserting CBS1 motives of the Bateman module, from a twisted to a flat disk shaped dimer.

A novel pathogenic missense variant in CNNM4 underlying Jalili syndrome: Insights from molecular dynamics simulations

Background

Jalili syndrome (JS) is a rare cone‐rod dystrophy (CRD) associated with amelogenesis imperfecta (AI). The first clinical presentation of JS patients was published in 1988 by Jalili and Smith. Pathogenic mutations in the Cyclin and CBS Domain Divalent Metal Cation Transport Mediator 4 (CNNM4) magnesium transporter protein have been reported as the leading cause of this anomaly.

Methods

In the present study, a clinical and genetic investigation was performed in a consanguineous family of Pakistani origin, showing characteristic features of JS. Sanger sequencing was successfully used to identify the causative variant in CNNM4. Molecular dynamics (MD) simulations were performed to study the effect of amino acid change over CNNM4 protein.

Results

Sequence analysis of CNNM4 revealed a novel missense variant (c.1220G>T, p.Arg407Leu) in exon‐1 encoding cystathionine‐β‐synthase (CBS) domain. To comprehend the mutational consequences in the structure, the mutant p.Arg407Leu was modeled together with a previously reported variant (c.1484C>T, p.Thr495Ile) in the same domain. Additionally, docking analysis deciphered the binding mode of the adenosine triphosphate (ATP) cofactor. Furthermore, 60ns MD simulations were carried out on wild type (p.Arg407/p.Thr495) and mutants (p.Arg407Leu/p.Thr495Ile) to understand the structural and energetic changes in protein structure and its dynamic behavior. An evident conformational shift of ATP in the binding site was observed in simulated mutants disrupting the native ATP‐binding mode.

Conclusion

The novel identified variant in CNNM4 is the first report from the Pakistani population. Overall, the study is valuable and may give a novel insight into metal transport in visual function and biomineralization.

Current Structural Knowledge on the CNNM Family of Magnesium Transport Mediators

The cyclin and cystathionine β-synthase (CBS) domain magnesium transport mediators, CNNMs, are key players in maintaining the homeostasis of magnesium in different organs. The human family includes four members, whose impaired activity causes diseases such as Jalili Syndrome or Familial Hypomagnesemia, but is also linked to neuropathologic disorders, altered blood pressure, and infertility. Recent findings demonstrated that CNNMs are associated with the highly oncogenic phosphatases of the regenerating liver to promote tumor growth and metastasis, which has attracted renewed focus on their potential exploitation as targets for cancer treatment. However, the exact function of CNNMs remains unclear and is subject to debate, proposed as either direct transporters, sensors, or homeostatic factors. This review gathers the current structural knowledge on the CNNM family, highlighting similarities and differences with the closely related structural partners such as the bacterial Mg2+/Co2+ efflux protein CorC and the Mg2+ channel MgtE.

Features, genetics and their correlation in Jalili syndrome: a systematic review

Jalili syndrome is a rare genetic disorder first identified by Jalili in Gaza. Amelogenesis imperfecta and cone-rode dystrophy are simultaneously seen in Jalili syndrome patients as the main and primary manifestations. Molecular analysis has revealed that theCNNM4gene is responsible for this rare syndrome. Jalili syndrome has been observed in many countries around the world, especially in the Middle East and North Africa. In the current scoping systematic review we searched electronic databases to find studies related to Jalili syndrome. In this review we summarise the reported clinical symptoms,CNNM4gene and protein structure,CNNM4mutations, attempts to reach a genotype-phenotype correlation, the functional role ofCNNM4mutations, and epidemiological aspects of Jalili syndrome. In addition, we have analysed the reported mutations in mutation effect prediction databases in order to gain a better understanding of the mutation’s outcomes.

Jalili Syndrome: Cross-sectional and Longitudinal Features of Seven Patients With Cone-Rod Dystrophy and Amelogenesis Imperfecta

PURPOSE

To characterize a series of 7 patients with cone-rod dystrophy (CORD) and amelogenesis imperfecta (AI) owing to confirmed mutations in CNNM4, first described as "Jalili Syndrome."

DESIGN

Retrospective observational case series.

METHODS

Seven patients from 6 families with Jalili Syndrome were identified at 3 tertiary referral centers. We systematically reviewed their available medical records, spectral-domain optical coherence tomography (SD-OCT), fundus autofluorescence imaging (FAF), color fundus photography, and electrophysiological assessments.

RESULTS

The mean age at presentation was 6.7 years (range 3-16 years), with 6 male and 1 female patient. CNNM4 mutations were identified in all patients. The mean Snellen best-corrected visual acuity (BCVA) at presentation was 20/246 (range 20/98 to 20/399) in the right eye and 20/252 (range 20/98 to 20/480) in the left. Nystagmus was observed in all 7 patients, and photophobia was present in 6. Funduscopic findings at presentation were variable, ranging from only mild disc pallor to retinal vascular attenuation and macular atrophy. Multimodal imaging demonstrated disease progression in all 7 patients over time. Electroretinography uniformly revealed progressive cone-rod dysfunction.

CONCLUSIONS

Jalili Syndrome is a rare CORD associated with AI. We have further characterized its ocular phenotype, including describing SD-OCT, FAF, and electrophysiological features; and report several novel disease-causing sequence variants. Moreover, this study presents novel longitudinal data demonstrating structural and functional progression over time, allowing better informed advice on prognosis.

Report of two unrelated families with Jalili syndrome and a novel nonsense heterozygous mutation in CNNM4 gene

Jalili syndrome (JS) is an autosomal recessive disease characterized by a combination of cone-rode retinal dytrophy (CRD) and amelogenesis imperfect (AI). Mutations in cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene cause JS. Here we described 2 families (3 members) affected by JS. In the first family, JS was caused by the homozygous p.Leu324Pro (c.971T > C) missense mutation and the affected patient developed both CRD and AI. In the second family, a specific combination of a compound heterozygous mutation was found - the p.Leu324Pro (c.971T > C) missense transition and the novel p.Tyr581* (c.1743C > G) nonsense mutation. The proband showed CRD and AI, but her father just developed eye alterations. Together, these findings suggest that the p.Leu324Pro mutation in homozygosis induces a complete phenotype with both CRD and AI, but in heterozygosis and in composition with the novel p.Tyr581* nonsense mutation in CNNM4 promotes variable clinical expressivity, particularly with lack of dental phenotypes. These different phenotypes could be explained by deletions affecting the proband's homologous allele, epistasia or interactions with environmental factors leading to residual activity of protein.

Identification of a mutation in CNNM4 by whole exome sequencing in an Amish family and functional link between CNNM4 and IQCB1

We investigated an Amish family in which three siblings presented with an early-onset childhood retinal dystrophy inherited in an autosomal recessive fashion. Genome-wide linkage analysis identified significant linkage to marker D2S2216 on 2q11 with a two-point LOD score of 1.95 and a multi-point LOD score of 3.76. Whole exome sequencing was then performed for the three affected individuals and identified a homozygous nonsense mutation (c.C1813T, p.R605X) in the cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene located within the 2p14-2q14 Jalili syndrome locus. The initial assessment and collection of the family were performed before the clinical delineation of Jalili syndrome. Another assessment was made after the discovery of the responsible gene and the dental abnormalities characteristic of Jalili syndrome were retrospectively identified. The p.R605X mutation represents the first probable founder mutation of Jalili syndrome identified in the Amish community. The molecular mechanism underlying Jalili syndrome is unknown. Here we show that CNNM4 interacts with IQCB1, which causes Leber congenital amaurosis (LCA) when mutated. A truncated CNNM4 protein starting at R605 significantly increased the rate of apoptosis, and significantly increased the interaction between CNNM4 and IQCB1. Mutation p.R605X may cause Jalili syndrome by a nonsense-mediated decay mechanism, affecting the function of IQCB1 and apoptosis, or both. Our data, for the first time, functionally link Jalili syndrome gene CNNM4 to LCA gene IQCB1, providing important insights into the molecular pathogenic mechanism of retinal dystrophy in Jalili syndrome.