Is ACTA1 p.Thr79fs (c.236_237delinsA) pathogenic?

ACTA1 p.Thr79fs (c.236237delinsA) is classified Likely pathogenic in ACTA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-30). Absent from gnomAD.

How common is ACTA1 p.Thr79fs (c.236_237delinsA) in the general population?

ACTA1 p.Thr79fs (c.236_237delinsA) is absent from gnomAD (gnomAD).

ACTA1 p.Thr79fs

c.236_237delinsA · rs2102736351 · VCV1323850

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.6	GERP 2.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ACTA1
Protein: p.Thr79fs
Coding: c.236_237delinsA
MANE Select: NM_001100
dbSNP: rs2102736351
Type: Indel
Location: chr1:229432773 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.21 · 5 PDB
Residue 79: a UniProt-annotated variant site (in cmyo2a)

Full ACTA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACTA1 p.Thr79Ile Pathogenic/Likely pathogenic ★★ same residue
ACTA1 c.809-14delinsCC Benign ★★ same type
ACTA1 p.Thr108_Ala110delinsIleGluVal Likely pathogenic ★ same type
ACTA1 p.Val47Glu Likely pathogenic ★ same type
ACTA1 c.130-11_130-10delinsTC Uncertain significance ★ same type
ACTA1 p.Ala233Asn Uncertain significance ★ same type
ACTA1 p.Ala274Ser Uncertain significance ★ same type
ACTA1 p.Ala28Cys Uncertain significance ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/acta1-p-thr79fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown