ClinVar Miner

Submissions for variant NM_015141.4(GPD1L):c.817C>T (p.Arg273Cys)

gnomAD frequency: 0.00004  dbSNP: rs72552294
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000170922 SCV000223480 uncertain significance not provided 2024-08-27 criteria provided, single submitter clinical testing Identified in a patient with an unspecified arrhythmia and a case of sudden infant death syndrome (SIDS) (PMID: 30847666, 17967976); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17967976, 30847666, 31043699)
Ambry Genetics RCV000620875 SCV000737657 likely benign Cardiovascular phenotype 2022-03-11 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp RCV000703528 SCV000832431 uncertain significance Brugada syndrome 2023-09-15 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 273 of the GPD1L protein (p.Arg273Cys). This variant is present in population databases (rs72552294, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of GPD1L-related conditions (PMID: 17967976, 30847666). ClinVar contains an entry for this variant (Variation ID: 789). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GPD1L protein function. Experimental studies have shown that this missense change affects GPD1L function (PMID: 17967976). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV000000825 SCV002788601 uncertain significance Brugada syndrome 2 2021-10-16 criteria provided, single submitter clinical testing
OMIM RCV000000825 SCV000020975 pathogenic Brugada syndrome 2 2007-11-13 no assertion criteria provided literature only
Clinical Genetics, Academic Medical Center RCV000170922 SCV001921659 uncertain significance not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000170922 SCV001951496 uncertain significance not provided no assertion criteria provided clinical testing

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