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

Genomes: not found (cov: 32)

Consequence

ACTA1
NM_001100.4 missense

Scores

13
2
3

Clinical Significance

Likely pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 7.86
Variant links:
Genes affected
ACTA1 (HGNC:129): (actin alpha 1, skeletal muscle) The product encoded by this gene belongs to the actin family of proteins, which are highly conserved proteins that play a role in cell motility, structure and integrity. Alpha, beta and gamma actin isoforms have been identified, with alpha actins being a major constituent of the contractile apparatus, while beta and gamma actins are involved in the regulation of cell motility. This actin is an alpha actin that is found in skeletal muscle. Mutations in this gene cause a variety of myopathies, including nemaline myopathy, congenital myopathy with excess of thin myofilaments, congenital myopathy with cores, and congenital myopathy with fiber-type disproportion, diseases that lead to muscle fiber defects with manifestations such as hypotonia. [provided by RefSeq, Sep 2019]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PS4
For more information check the summary or visit ClinGen Evidence Repository.
PM2
For more information check the summary or visit ClinGen Evidence Repository.
PP2
For more information check the summary or visit ClinGen Evidence Repository.
PP3
For more information check the summary or visit ClinGen Evidence Repository.
PP4
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACTA1NM_001100.4 linkuse as main transcriptc.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
ACTA1ENST00000366684.7 linkuse as main transcriptc.1074G>T p.Trp358Cys missense_variant 7/71 NM_001100.4 ENSP00000355645 P1
ENST00000702606.1 linkuse as main transcriptn.194C>A non_coding_transcript_exon_variant 1/1
ACTA1ENST00000366683.4 linkuse as main transcriptc.996G>T p.Trp332Cys missense_variant 7/75 ENSP00000355644
ACTA1ENST00000684723.1 linkuse as main transcriptc.939G>T p.Trp313Cys missense_variant 6/6 ENSP00000508084

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Actin accumulation myopathy Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 01, 2013- -
Likely pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 04, 2023In 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.97
BayesDel_addAF
Pathogenic
0.52
D
BayesDel_noAF
Pathogenic
0.51
CADD
Pathogenic
32
DANN
Benign
0.97
DEOGEN2
Pathogenic
0.96
D;D
Eigen
Pathogenic
0.79
Eigen_PC
Pathogenic
0.69
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Pathogenic
0.98
D;D
M_CAP
Pathogenic
0.81
D
MetaRNN
Pathogenic
0.95
D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.3
M;.
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Pathogenic
0.94
D
PROVEAN
Pathogenic
-6.7
D;.
REVEL
Pathogenic
0.96
Sift4G
Benign
0.072
T;T
Polyphen
1.0
D;.
Vest4
0.89
MutPred
0.77
Loss of catalytic residue at W358 (P = 0.0217);.;
MVP
0.99
ClinPred
1.0
D
GERP RS
3.9
Varity_R
0.98
gMVP
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587777354; hg19: chr1-229567306; API