Is ACTG1 p.Ala347Ser (c.1039G>T) pathogenic?

ACTG1 p.Ala347Ser (c.1039G>T) is classified Uncertain significance in ACTG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-12-16). AlphaMissense: ambiguous (0.376); Absent from gnomAD v4.1.

How common is ACTG1 p.Ala347Ser (c.1039G>T) in the general population?

ACTG1 p.Ala347Ser (c.1039G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACTG1 p.Ala347Ser (c.1039G>T)?

AlphaMissense predicts ambiguous (score 0.376) — an in-silico prediction, not a clinical call.

ACTG1 p.Ala347Ser

c.1039G>T · rs1555666373 · VCV434078

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.376 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.376	ambiguous
REVEL	0.672	pathogenic-leaning
SaProt	LLR -11.02	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 0.69, phastCons 1
Regional constraint	o/e 0.33	constrained · MANE · 397 bp · p 8e-16 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

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: ACTG1
Protein: p.Ala347Ser
Coding: c.1039G>T
MANE Select: NM_001614
dbSNP: rs1555666373
Type: single nucleotide variant
Location: chr17:81510779 (GRCh38)
Gene constraint: LOEUF 0.617 · pLI 0.46 (gnomAD)
Structure: AlphaFold pLDDT 95.44 · 11 PDB
Residue 347: an α-helix

Full ACTG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACTG1 p.Ala347= Likely benign ★ same residue
ACTG1 p.Ala135Val Pathogenic/Likely pathogenic ★★ same type
ACTG1 p.Ala204Gly Likely pathogenic ★★ same type
ACTG1 p.Arg183Gln Pathogenic/Likely pathogenic ★★ same type
ACTG1 p.Arg183Trp Pathogenic/Likely pathogenic ★★ same type
ACTG1 p.Arg206Gln Pathogenic/Likely pathogenic ★★ same type
ACTG1 p.Arg210Cys Pathogenic ★★ same type
ACTG1 p.Arg254Trp Pathogenic/Likely pathogenic ★★ 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/actg1-p-ala347ser (accessed [today's date]).

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