ClinVar Miner

Submissions for variant NM_006412.4(AGPAT2):c.475C>T (p.Arg159Cys)

gnomAD frequency: 0.00430  dbSNP: rs142993240
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000193694 SCV000246334 benign not specified 2018-11-07 criteria provided, single submitter clinical testing
Personalized Diabetes Medicine Program, University of Maryland School of Medicine RCV000445508 SCV000537070 benign Monogenic diabetes 2019-02-22 criteria provided, single submitter research ACMG criteria: BS1 (1% in gnomAD AJ population, 0.5% overall MAF in gnomAD; disease prevalence 1:10 million gives MAF of 0.03%), BS2 (8 homozygotes in gnomAD) [REVEL 0.582, BP4 (3 predictors), PP3 (6 predictors)= conflicting evidence, not using]; heterozygotes mutation found in brother and sister with lipodytrophy phenotype Simsir et al. 2015 ""Heterozygous AGPAT2 Mutation, Diabetes, and Lipodystrophy in Extremities"" (no PMID)= benign
Invitae RCV000883942 SCV001027285 benign not provided 2024-01-18 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001167076 SCV001329520 benign Congenital generalized lipodystrophy type 1 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000193694 SCV002103808 benign not specified 2022-02-19 criteria provided, single submitter clinical testing Variant summary: AGPAT2 c.475C>T (p.Arg159Cys) results in a non-conservative amino acid change located in the Phospholipid/glycerol acyltransferase domain (IPR002123) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0051 in 248240 control chromosomes in the gnomAD database, including 9 homozygotes. The observed variant frequency is approximately 5.9 fold of the estimated maximal expected allele frequency for a pathogenic variant in AGPAT2 causing Congenital Generalized Lipodystrophy phenotype (0.00087), strongly suggesting that the variant is benign. 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. Based on the evidence outlined above, the variant was classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000883942 SCV002541046 uncertain significance not provided 2021-12-30 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000883942 SCV004163912 likely benign not provided 2023-11-01 criteria provided, single submitter clinical testing AGPAT2: BS2
Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic RCV001167076 SCV004698173 uncertain risk allele Congenital generalized lipodystrophy type 1 criteria provided, single submitter research Potent mutations in AGPAT2 gene are associated with Congenital generalized lipodystrophy, type 1, which can present with insulin resistance, fatty liver and diabetes. rs142993240 variant is prevalent with Congenital Generalized Lipoatrophy. However, the role of this rs142993240 particular variant is yet to be ascertained.
PreventionGenetics, part of Exact Sciences RCV003917731 SCV004736081 benign AGPAT2-related disorder 2019-05-01 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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