ACTG1 p.Val139=
c.417G>C · rs1367861495 · VCV1328787
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Conditions
2
Baraitser-winter syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.7, phastCons 1 |
| Overall | ||
| CADD | 9.746 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,936 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000124%
2/1,613,698 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ACTG1
- Protein
- p.Val139=
- Coding
- c.417G>C
- MANE Select
- NM_001614
- dbSNP
- rs1367861495
- Type
- single nucleotide variant
- Location
- chr17:81511573 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.46 (gnomAD)
- Structure
- AlphaFold pLDDT 95.44 · 11 PDB
- Residue 139
- an α-helix
Similar variants
- 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
- ACTG1 p.Arg254Trp Pathogenic/Likely pathogenic ★★ same condition
- ACTG1 p.Arg335His Pathogenic/Likely 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-val139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown