ACTG1 p.Pro164=
c.492C>T · rs1207365676 · VCV993778
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0935%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.5 | GERP -0.49, phastCons 1 |
| Overall | ||
| CADD | 13.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0935%
East Asian · 42/44,896 alleles
Filtering AF
0.0711%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0632%
Overall
0.00316%
51/1,613,762 alleles · ultra-rare
exomes 50/1,461,526 · genomes 1/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0935% | 1,069 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| African / African-American | 0.00133% | 74,942 |
| European (non-Finnish) | 0.000508% | 196,674 |
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.Pro164=
- Coding
- c.492C>T
- MANE Select
- NM_001614
- dbSNP
- rs1207365676
- Type
- single nucleotide variant
- Location
- chr17:81511498 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.46 (gnomAD)
- Structure
- AlphaFold pLDDT 95.44 · 11 PDB
- Residue 164
- a β-strand
Similar variants
- 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
- ACTG1 p.Arg335His 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-pro164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown