The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001100.4(ACTA1):c.685A>G (p.Met229Val)

CA246018

197716 (ClinVar)

Gene: ACTA1 (HGNC:58)
Condition: alpha-actinopathy (MONDO:0100084)
Inheritance Mode: Autosomal dominant inheritance
UUID: e8dcc3d8-e1f4-4926-9e27-80bebb190bd5
Approved on: 2026-06-08
Published on: 2026-06-23

HGVS expressions

NM_001100.4(ACTA1):c.685A>G (p.Met229Val)
NM_001100.4:c.685A>G
NC_000001.11:g.229432117T>C
CM000663.2:g.229432117T>C
NC_000001.10:g.229567864T>C
CM000663.1:g.229567864T>C
NC_000001.9:g.227634487T>C
NG_006672.1:g.6980A>G
ENST00000366683.4:c.685A>G
ENST00000684723.1:c.550A>G
ENST00000366683.3:c.480-255A>G
ENST00000366684.7:c.685A>G
NM_001100.3:c.685A>G
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Pathogenic

Met criteria codes 7
PS4_Moderate PS2 PP4 PP3 PP2 PM5 PM2_Supporting
Not Met criteria codes 4
BA1 BS1 BP4 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Congenital Myopathies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ACTA1 Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The NM_001100.4(ACTA1):c.685A>G (p.Met229Val) variant in ACTA1 is a missense variant predicted to cause a substitution of methionine by valine at amino acid 229 (p.Met229Val). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). 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 dominant disease (PP2). The computational predictor REVEL gives a score of 0.854, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3). Six different missense variants, [c.685A>T (p.Met229Leu), c.686T>G (p.Met229Arg), c.686T>C (p.Met229Thr), c.687G>A (p.Met229Ile), c.687G>C (p.Met229Ile), c.687G>T (p.Met229Ile)], in the same codon have been reported in patients with congenital myopathies (PMIDs: 12921789, 19562689, VCEP internal contributor], of which at least one has met the criteria to be classified as pathogenic by the ClinGen Congenital Myopathies VCEP (PM5). This variant has been observed in the heterozygous state in 4 individuals including a de novo occurrence in twins with clinical and histological features compatible with ACTA1-related myopathy including presence of numerous nemaline bodies (PS2, PS4_Moderate, PP4; PMIDs: 19562689, 15236405, 12921789). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PS2, PS4_Moderate, PM5, PM2_Supporting, PP2, PP3, PP4 (ClinGen Congenital Myopathies VCEP specifications version 2.0.0).
Met criteria codes
PS4_Moderate
This variant has been observed in the heterozygous state in four individuals with features of nemaline myopathy (PS4_Moderate; PMIDs: 19562689, 15236405, 12921789).
PS2
This variant has been reported as de novo occurrence in at least one individual (PMIDs: 19562689, 15236405, 12921789).
PP4
One individual with this variant was reported with pathological findings of type I fiber predominance and numerous nemaline bodies which meets PP4.
PP3
The REVEL score is 0.854, which is above the threshold of 0.7 to apply PP3.
PP2
ACTA1 is a gene that is constrained for missense variation. The Z-score on gnomAD v4.1.0 is 6.63 meeting PP2.
PM5
Six different missense variants, [c.685A>T (p.Met229Leu), c.686T>G (p.Met229Arg), c.686T>C (p.Met229Thr), c.687G>A (p.Met229Ile), c.687G>C (p.Met229Ile), c.687G>T (p.Met229Ile)], in the same codon have been reported in patients with congenital myopathies (PMIDs: 12921789, 19562689, VCEP internal contributor], of which at least one has met the criteria to be classified as pathogenic by the ClinGen Congenital Myopathies VCEP.
PM2_Supporting
This variant is absent on gnomAD v4.1, meeting PM2_Supporting.
Not Met criteria codes
BA1
This variant is absent on gnomAD v4.1, meeting PM2_Supporting.
BS1
This variant is absent on gnomAD v4.1, meeting PM2_Supporting.
BP4
The REVEL score is 0.854, which is above the threshold of 0.7 to apply PP3.
BP1
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Curation History
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