ACTG1 p.Val339=
c.1017G>C · rs111305526 · VCV288524
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
rare (popmax 0.677%, 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 0.76 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 5.727 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.677%
African / African-American · 508/75,040 alleles
Filtering AF
0.628%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.609%
Overall
0.0364%
587/1,614,026 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.677% | 148 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,894 |
| Admixed American | 0.0383% | 2,610 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00186% | 53,637 |
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.Val339=
- Coding
- c.1017G>C
- MANE Select
- NM_001614
- dbSNP
- rs111305526
- Type
- single nucleotide variant
- Location
- chr17:81510801 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.46 (gnomAD)
- Structure
- AlphaFold pLDDT 95.44 · 11 PDB
- Residue 339
- 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-val339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown