TRAK1 p.Ser229=
c.687C>T · rs141503991 · VCV1539306
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.203%, afr)
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 -3.7 |
| Overall | ||
| CADD | 1.374 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.203%
African / African-American · 152/74,986 alleles
Filtering AF
0.176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.166%
Overall
0.0122%
196/1,611,004 alleles · rare
exomes 112/1,458,692 · genomes 84/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.203% | 493 |
| Admixed American | 0.0267% | 3,751 |
| South Asian | 0.0165% | 6,067 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,935 |
| European (non-Finnish) | 0.00034% | 294,282 |
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.Ser229=
- Coding
- c.687C>T
- MANE Select
- NM_001042646
- dbSNP
- rs141503991
- Type
- single nucleotide variant
- Location
- chr3:42189121 (GRCh38)
- Gene constraint
- LOEUF 0.461 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.19
- Residue 229
- the hap1 n-terminal domain
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-ser229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown