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.686T>C (p.Met229Thr)

CA345147061

2635623 (ClinVar)

Gene: ACTA1 (HGNC:58)
Condition: alpha-actinopathy (MONDO:0100084)
Inheritance Mode: Autosomal dominant inheritance
UUID: a4cb3486-db59-4166-810b-1b8f655301da
Approved on: 2026-06-08
Published on: 2026-06-22

HGVS expressions

NM_001100.4(ACTA1):c.686T>C (p.Met229Thr)
NM_001100.4:c.686T>C
NC_000001.11:g.229432116A>G
CM000663.2:g.229432116A>G
NC_000001.10:g.229567863A>G
CM000663.1:g.229567863A>G
NC_000001.9:g.227634486A>G
NG_006672.1:g.6981T>C
ENST00000366683.4:c.686T>C
ENST00000684723.1:c.551T>C
ENST00000366683.3:c.480-254T>C
ENST00000366684.7:c.686T>C
NM_001100.3:c.686T>C
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Pathogenic

Met criteria codes 5
PS4_Supporting PP3 PP2 PS2 PM2_Supporting
Not Met criteria codes 5
BA1 BP4 BP1 BS1 PM5

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 variant NM_001100.4:c.686T>C in ACTA1 is a missense variant predicted to cause substitution of methionine by threonine at amino acid 229 (p.Met229Thr). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The REVEL computational prediction analysis tool produced a score of 0.934, which is above the threshold predicting a damaging impact on ACTA1 function. 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). Six different missense variants, [c.685A>G (p.Met229Val), c.686T>G (p.Met229Arg), c.685A>T (p.Met229Leu), 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]. This variant has been reported as de novo occurrences in at least three probands with features of nemaline myopathy, of which one was de novo with confirmed parentage (PS2, PS4_Supporting; PMIDs: 12921789, 19562689, 35810298, 38982518, 40225930; Institut de Génétique et Biologie Moléculaire et Cellulaire, ClinVar Accession: SCV005038471.2). At least one patient with this variant displayed characteristic muscle biopsy with fiber size variability, intranuclear rods, cytoplasmic bodies, and other features, which is highly compatible with alpha-actinopathy (PP4_Moderate, PMIDs:35810298, 38982518). In summary, the variant meets criteria to be classified as pathogenic for autosomal dominant alpha-actinopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PS2, PP4_M, PS4_P, PM2_P, PP2, PP3 (ClinGen Congenital Myopathies VCEP specifications version 2.0.0).
Met criteria codes
PS4_Supporting
This variant has been reported in at least three probands with features of nemaline myopathy (PS4_Supporting; PMIDs: 12921789, 19562689, 35810298, 38982518, 40225930; Institut de Génétique et Biologie Moléculaire et Cellulaire, ClinVar Accession: SCV005038471.2).
PP3
The REVEL score is 0.934 which is above the threshold to apply PP3.
PP2
The Z-score in gnomAD v2.1.1 is 4.53 which is above the threshold for PP2.
PS2
Three probands have been reported as de novo occurrences with features of nemaline myopathy, of which one was de novo with confirmed parentage (PS2, PMIDs: 12921789, 19562689, 35810298, 38982518, 40225930; Institut de Génétique et Biologie Moléculaire et Cellulaire, ClinVar Accession: SCV005038471.2).
PM2_Supporting
The variant is absent from gnomAD v4.1.0
Not Met criteria codes
BA1
The variant is absent from gnomAD v4.1.0
BP4
The REVEL score is 0.934 which is above the threshold to apply PP3.
BP1
The Z-score in gnomAD v2.1.1 is 4.53 which is above the threshold for PP2.
BS1
The variant is absent from gnomAD v4.1.0
PM5
Six different variants in the same residue have been identified in patients with congenital myopathy, however PM5 was applied to the other variants.
Curation History
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