rs797044959
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_001615.4(ACTG2):c.770G>A(p.Arg257His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. R257C) has been classified as Pathogenic.
Frequency
Consequence
NM_001615.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACTG2 | NM_001615.4 | c.770G>A | p.Arg257His | missense_variant | 7/9 | ENST00000345517.8 | NP_001606.1 | |
ACTG2 | NM_001199893.2 | c.641G>A | p.Arg214His | missense_variant | 6/8 | NP_001186822.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACTG2 | ENST00000345517.8 | c.770G>A | p.Arg257His | missense_variant | 7/9 | 1 | NM_001615.4 | ENSP00000295137.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1449758Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 719538
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Visceral myopathy 1 Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | High rate of a poor outcome (mortality and/or multivisceral transplantation) or microcolon - |
Pathogenic, criteria provided, single submitter | clinical testing | Genomic Medicine Lab, University of California San Francisco | Mar 26, 2020 | - - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2012 | Co-segregation data for this variant is currently unavailable. This amino acid position is highly conserved in available vertebrate species.This alteration is predicted to be probably damaging with a score of 0.988 (sensitivity: 0.53; specificity: 0.95) - |
Megacystis-microcolon-intestinal hypoperistalsis syndrome 5 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 2021 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); 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: 26647307, 25998219, 24901346, 26813947, 27481187, 27007401, 31965297) - |
Chronic intestinal pseudoobstruction;C1855311:Megacystis Pathogenic:1
Pathogenic, no assertion criteria provided | research | UOSD Genetics and Genomics of Rare Diseases, Istituto Giannina Gaslini | May 02, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at