ClinVar Miner

Submissions for variant NM_173076.3(ABCA12):c.4540C>T (p.Arg1514Cys)

dbSNP: rs1266760446
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
3billion RCV002052258 SCV002318862 uncertain significance Autosomal recessive congenital ichthyosis 4A 2022-03-22 criteria provided, single submitter clinical testing The variant is absent from the gnomAD v2.1.1 dataset. Different pathogenic/likely pathogenic amino acid change has been reported with supporting evidence at the same codon (ClinVar ID: VCV000002857, PMID:30600594,12915478). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.863>=0.6, 3CNET: 0.968>=0.75). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.
Labcorp Genetics (formerly Invitae), Labcorp RCV003773526 SCV004613637 pathogenic not provided 2024-01-22 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1514 of the ABCA12 protein (p.Arg1514Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with congenital ichthyosis (PMID: 36980989). ClinVar contains an entry for this variant (Variation ID: 1526238). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCA12 protein function with a positive predictive value of 80%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the p.Arg1514 amino acid residue in ABCA12. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 36980989). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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