rs797045222
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_006412.4(AGPAT2):c.406G>A(p.Gly136Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,613,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G136E) has been classified as Uncertain significance.
Frequency
Consequence
NM_006412.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPAT2 | NM_006412.4 | c.406G>A | p.Gly136Arg | missense_variant | 3/6 | ENST00000371696.7 | |
AGPAT2 | NM_001012727.2 | c.406G>A | p.Gly136Arg | missense_variant | 3/5 | ||
AGPAT2 | XM_047422636.1 | c.97G>A | p.Gly33Arg | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPAT2 | ENST00000371696.7 | c.406G>A | p.Gly136Arg | missense_variant | 3/6 | 1 | NM_006412.4 | P1 | |
AGPAT2 | ENST00000371694.7 | c.406G>A | p.Gly136Arg | missense_variant | 3/5 | 1 | |||
AGPAT2 | ENST00000472820.1 | n.334G>A | non_coding_transcript_exon_variant | 1/4 | 1 | ||||
AGPAT2 | ENST00000470861.1 | n.700G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1460966Hom.: 0 Cov.: 37 AF XY: 0.00000550 AC XY: 4AN XY: 726782
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
Congenital generalized lipodystrophy type 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 06, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at