CAP1 p.Tyr31=
c.93T>C · rs35336518 · VCV773108
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.04%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.46 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.84 | GERP -4.3 |
| Overall | ||
| CADD | 6.342 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.04%
African / African-American · 2,278/74,872 alleles
Filtering AF
2.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.9%
Overall
0.393%
6,325/1,607,522 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.04% | 33 |
| Middle Eastern | 1.01% | 99 |
| South Asian | 0.634% | 158 |
| Admixed American | 0.485% | 206 |
| Remaining individualsnot grpmax-eligible | 0.469% | 213 |
| European (non-Finnish) | 0.237% | 421 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0643% | 1,556 |
| Finnishnot grpmax-eligible | 0.0281% | 3,557 |
| East Asian | 0.00223% | 44,862 |
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
- CAP1
- Protein
- p.Tyr31=
- Coding
- c.93T>C
- MANE Select
- NM_006367
- dbSNP
- rs35336518
- Type
- single nucleotide variant
- Location
- chr1:40059439 (GRCh38)
- Gene constraint
- LOEUF 0.361 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85 · 5 PDB
- Residue 31
- a modified residue (phosphotyrosine)
Similar variants
- CAP1 p.Ala73= Benign ★★ same type
- CAP1 p.Ala145Ser Uncertain significance ★ ⚠ same type
- CAP1 p.Ala161Ser Uncertain significance ★ same type
- CAP1 p.Ala259Ser Uncertain significance ★ ⚠ same type
- CAP1 p.Ala259Thr Uncertain significance ★ ⚠ same type
- CAP1 p.Ala270Gly Uncertain significance ★ ⚠ same type
- CAP1 p.Ala302Val Uncertain significance ★ ⚠ same type
- CAP1 p.Ala52Val Uncertain significance ★ ⚠ 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/cap1-p-tyr31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown