Is ACTA1 p.Pro132Ser (c.394C>T) pathogenic?

ACTA1 p.Pro132Ser (c.394C>T) is classified Uncertain significance in ACTA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-07). AlphaMissense: likely pathogenic (0.9028); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ACTA1 p.Pro132Ser (c.394C>T)?

ACTA1 p.Pro132Ser (c.394C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ACTA1 p.Pro132Ser (c.394C>T) in the general population?

ACTA1 p.Pro132Ser (c.394C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACTA1 p.Pro132Ser (c.394C>T)?

AlphaMissense predicts likely pathogenic (score 0.9028) — an in-silico prediction, not a clinical call.

ACTA1 p.Pro132Ser

c.394C>T · VCV4001377

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9028 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9028	likely pathogenic
REVEL	0.943	strongly pathogenic-leaning
SaProt	LLR -13.44	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 0.33	constrained · MANE · 1,613 bp · p 1.6e-54 · regional, not allelic
Overall
CADD	29.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ACTA1
Protein: p.Pro132Ser
Coding: c.394C>T
MANE Select: NM_001100
Type: single nucleotide variant
Location: chr1:229432616 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.21 · 5 PDB
Residue 132: a β-strand

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACTA1 p.His103Tyr Uncertain significance ★★ ⚠ same condition
ACTA1 p.Ile73Ser Likely pathogenic ★ same condition
ACTA1 p.Ala133Ser Uncertain significance ★ ⚠ same condition
ACTA1 p.Ala28Gly Uncertain significance ★ ⚠ same condition
ACTA1 p.Ala312Ser Uncertain significance ★ ⚠ same condition
ACTA1 p.Asp27Tyr Uncertain significance ★ ⚠ same condition
ACTA1 p.Glu4Gly Uncertain significance ★ ⚠ same condition
ACTA1 p.Gly303Ala Uncertain significance ★ ⚠ same condition

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-pro132ser (accessed [today's date]).

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