ClinVar Miner

Submissions for variant NM_015141.4(GPD1L):c.370A>G (p.Ile124Val) (rs72552293)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000029945 SCV000050768 likely benign SUDDEN INFANT DEATH SYNDROME 2013-06-24 criteria provided, single submitter research
Integrated Genetics/Laboratory Corporation of America RCV000170920 SCV000052600 likely benign not specified 2018-07-25 criteria provided, single submitter clinical testing Variant summary: GPD1L c.370A>G (p.Ile124Val) results in a conservative amino acid change located in the N-terminal of the Glycerol-3-phosphate dehydrogenase, NAD-dependent domain (IPR011128) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0029 in 277792 control chromosomes in the gnomAD database and publications, including 7 homozygotes. The observed variant frequency is approximately 289-fold of the estimated maximal expected allele frequency for a pathogenic variant in GPD1L causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is benign. The variant, c.370A>G, has been reported in the literature in individuals affected with SIDS, sudden death, and atrial fibrillation (VanNorstrand_2007, Skinner_2014, Husser_2017). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (VanNorstrand_2007). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
GeneDx RCV000170920 SCV000223478 likely benign not specified 2017-12-18 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001081825 SCV000262445 benign Brugada syndrome 2019-12-31 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000170920 SCV000539250 benign not specified 2016-03-29 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC: 1.2% (82/6614) Finnish chromosomes
Ambry Genetics RCV000620285 SCV000737734 likely benign Cardiovascular phenotype 2018-10-09 criteria provided, single submitter clinical testing In silico models in agreement (benign);General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000000824 SCV000883145 likely benign Brugada syndrome 2 2018-11-21 criteria provided, single submitter clinical testing
Center for Advanced Laboratory Medicine, UC San Diego Health,University of California San Diego RCV000852958 SCV000995707 likely benign Hypertrophic cardiomyopathy 2018-03-12 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000203752 SCV001153827 uncertain significance not provided 2018-12-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000000824 SCV001157163 benign Brugada syndrome 2 2019-01-14 criteria provided, single submitter clinical testing
OMIM RCV000000824 SCV000020974 pathogenic Brugada syndrome 2 2007-11-13 no assertion criteria provided literature only
Blueprint Genetics RCV000157243 SCV000206970 likely benign Primary familial hypertrophic cardiomyopathy; Long QT syndrome 2014-11-04 no assertion criteria provided clinical testing

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