chr1-229431559-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PP4_ModeratePP2PP3PS4_SupportingPM2_Supporting
This summary comes from the ClinGen Evidence Repository: The c.1074G>T (p.Trp358Cys) variant in ACTA1 is a missense variant predicted to cause substitution of tryptophan by cysteine at amino acid 358. This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.957, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3). ACTA1, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant has been reported in 2 probands, one with nemaline rods in muscle biopsy (as well as dilated cardiomyopathy) and the other an infant with hypotonia (PS4_Supporting, PP4_Moderate; PMID:23650303, Invitae SCV001393788.5). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PP4_Moderate, PS4_Supporting, PM2_Supporting, PP2, PP3. (Congenital Myopathies VCEP specifications version 2; 08/27/2024) LINK:https://erepo.genome.network/evrepo/ui/classification/CA269775/MONDO:0100084/147
Frequency
Consequence
NM_001100.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACTA1 | NM_001100.4 | c.1074G>T | p.Trp358Cys | missense_variant | 7/7 | ENST00000366684.7 | NP_001091.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACTA1 | ENST00000366684.7 | c.1074G>T | p.Trp358Cys | missense_variant | 7/7 | 1 | NM_001100.4 | ENSP00000355645 | P1 | |
ENST00000702606.1 | n.194C>A | non_coding_transcript_exon_variant | 1/1 | |||||||
ACTA1 | ENST00000366683.4 | c.996G>T | p.Trp332Cys | missense_variant | 7/7 | 5 | ENSP00000355644 | |||
ACTA1 | ENST00000684723.1 | c.939G>T | p.Trp313Cys | missense_variant | 6/6 | ENSP00000508084 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Actin accumulation myopathy Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2013 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 04, 2023 | In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ACTA1 protein function. ClinVar contains an entry for this variant (Variation ID: 127188). This missense change has been observed in individuals with clinical features of autosomal dominant ACTA1-related conditions (PMID: 23650303; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 358 of the ACTA1 protein (p.Trp358Cys). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at