TRAK1 p.Pro933=
c.2799T>C · rs12487911 · VCV1281419
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 44.5%, afr) — too common for a highly-penetrant pathogenic allele
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 -11 | GERP -3.5 |
| Overall | ||
| CADD | 0.256 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
44.5%
African / African-American · 33,313/74,926 alleles
Filtering AF
44.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 43.9%
Overall
9.8%
158,103/1,613,806 alleles · common
exomes 130,288/1,461,750 · genomes 27,815/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 44.5% | 2 |
| Admixed American | 12.6% | 8 |
| Middle Eastern | 10% | 10 |
| Remaining individualsnot grpmax-eligible | 10% | 10 |
| East Asian | 9.41% | 11 |
| South Asian | 8.85% | 11 |
| Finnishnot grpmax-eligible | 8.52% | 12 |
| European (non-Finnish) | 7.75% | 13 |
| Amishnot grpmax-eligible | 6.81% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 3.93% | 25 |
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
- TRAK1
- Protein
- p.Pro933=
- Coding
- c.2799T>C
- MANE Select
- NM_001042646
- dbSNP
- rs12487911
- Type
- single nucleotide variant
- Location
- chr3:42223674 (GRCh38)
- Gene constraint
- LOEUF 0.461 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.19
Similar variants
- TRAK1 c.1963+258C>T Uncertain significance ★★ same type
- TRAK1 p.Ala334Thr Uncertain significance ★★ ⚠ same type
- TRAK1 p.Ala498Val Uncertain significance ★★ ⚠ same type
- TRAK1 p.Ala655Val Uncertain significance ★★ ⚠ same type
- TRAK1 p.Ala861Thr Uncertain significance ★★ ⚠ same type
- TRAK1 p.Arg117Gln Uncertain significance ★★ ⚠ same type
- TRAK1 p.Arg165Gln Uncertain significance ★★ ⚠ same type
- TRAK1 p.Arg279Cys 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/trak1-p-pro933 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown