ACTG1 p.Leu299=
c.895C>T · rs781869067 · VCV512334
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 1.7 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 5.401 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,080 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00149%
24/1,613,934 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,770 |
| Admixed American | 0.00167% | 60,010 |
| European (non-Finnish) | 0.00161% | 62,108 |
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.Leu299=
- Coding
- c.895C>T
- MANE Select
- NM_001614
- dbSNP
- rs781869067
- Type
- single nucleotide variant
- Location
- chr17:81511016 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.46 (gnomAD)
- Structure
- AlphaFold pLDDT 95.44 · 11 PDB
- Residue 299
- a β-strand
Similar variants
- ACTG1 p.Leu299Pro Uncertain significance ★ 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-leu299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown