Is ACTG1 p.Met153Ile (c.459G>A) pathogenic?

ACTG1 p.Met153Ile (c.459G>A) is classified Likely pathogenic in ACTG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-20). AlphaMissense: likely pathogenic (0.635); Absent from gnomAD v4.1; Associated with Baraitser-winter syndrome 2.

What condition is associated with ACTG1 p.Met153Ile (c.459G>A)?

ACTG1 p.Met153Ile (c.459G>A) is associated with Baraitser-winter syndrome 2 (ClinVar).

How common is ACTG1 p.Met153Ile (c.459G>A) in the general population?

ACTG1 p.Met153Ile (c.459G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACTG1 p.Met153Ile (c.459G>A)?

AlphaMissense predicts likely pathogenic (score 0.635) — an in-silico prediction, not a clinical call.

ACTG1 p.Met153Ile

c.459G>A · rs2143779081 · VCV1333817

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.635 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Baraitser-winter syndrome 2

Computational evidence

Protein change
AlphaMissense	0.635	likely pathogenic ✓ concordant with ClinVar
REVEL	0.486	indeterminate
SaProt	LLR -13.02	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP -0.78, phastCons 1
Regional constraint	o/e 0.09	constrained · MANE · 164 bp · p 4.4e-16 · regional, not allelic
Overall
CADD	25.7	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.Met153Ile
Coding: c.459G>A
MANE Select: NM_001614
dbSNP: rs2143779081
Type: single nucleotide variant
Location: chr17:81511531 (GRCh38)
Gene constraint: LOEUF 0.617 · pLI 0.46 (gnomAD)
Structure: AlphaFold pLDDT 95.44 · 11 PDB
Residue 153: a β-strand

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

Disease context

Baraitser-winter syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACTG1 p.Met153Val Likely pathogenic ★ ⚠ same residue
ACTG1 p.Met153Thr Uncertain significance ★ ⚠ same residue
ACTG1 p.Ala135Val Pathogenic/Likely pathogenic ★★ same condition
ACTG1 p.Ala204Gly Likely pathogenic ★★ same condition
ACTG1 p.Arg183Gln Pathogenic/Likely pathogenic ★★ same condition
ACTG1 p.Arg183Trp Pathogenic/Likely pathogenic ★★ same condition
ACTG1 p.Arg206Gln Pathogenic/Likely pathogenic ★★ same condition
ACTG1 p.Arg210Cys Pathogenic ★★ 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/actg1-p-met153ile (accessed [today's date]).

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