rs142993240
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000371696.7(AGPAT2):c.475C>T(p.Arg159Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00516 in 1,570,472 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R159L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000371696.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGPAT2 | NM_006412.4 | c.475C>T | p.Arg159Cys | missense_variant | 3/6 | ENST00000371696.7 | NP_006403.2 | |
AGPAT2 | NM_001012727.2 | c.475C>T | p.Arg159Cys | missense_variant | 3/5 | NP_001012745.1 | ||
AGPAT2 | XM_047422636.1 | c.166C>T | p.Arg56Cys | missense_variant | 3/6 | XP_047278592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGPAT2 | ENST00000371696.7 | c.475C>T | p.Arg159Cys | missense_variant | 3/6 | 1 | NM_006412.4 | ENSP00000360761 | P1 | |
AGPAT2 | ENST00000371694.7 | c.475C>T | p.Arg159Cys | missense_variant | 3/5 | 1 | ENSP00000360759 | |||
AGPAT2 | ENST00000472820.1 | n.403C>T | non_coding_transcript_exon_variant | 1/4 | 1 | |||||
AGPAT2 | ENST00000470861.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00451 AC: 671AN: 148742Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00514 AC: 1277AN: 248240Hom.: 9 AF XY: 0.00561 AC XY: 756AN XY: 134796
GnomAD4 exome AF: 0.00523 AC: 7438AN: 1421596Hom.: 30 Cov.: 38 AF XY: 0.00541 AC XY: 3823AN XY: 706970
GnomAD4 genome AF: 0.00451 AC: 671AN: 148876Hom.: 6 Cov.: 32 AF XY: 0.00450 AC XY: 327AN XY: 72600
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | AGPAT2: BS2 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 30, 2021 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 07, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 19, 2022 | 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. - |
Congenital generalized lipodystrophy type 1 Benign:1Other:1
Uncertain risk allele, criteria provided, single submitter | research | Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic | - | 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. - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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. - |
AGPAT2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | 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). - |
Monogenic diabetes Benign:1
Benign, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Feb 22, 2019 | 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 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at