TRAK1 p.Ser511=
c.1533G>A · rs201849317 · VCV1582193
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0418%, amr)
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 -6.3 | GERP -4.3 |
| Overall | ||
| CADD | 2.883 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0418%
Admixed American · 24/57,384 alleles
Filtering AF
0.0288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0245%
Overall
0.00414%
65/1,569,182 alleles · ultra-rare
exomes 41/1,416,844 · genomes 24/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0418% | 2,391 |
| African / African-American | 0.00813% | 12,300 |
| South Asian | 0.00697% | 14,357 |
| Remaining individualsnot grpmax-eligible | 0.00665% | 15,037 |
| East Asian | 0.0023% | 43,516 |
| European (non-Finnish) | 0.00209% | 47,943 |
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.Ser511=
- Coding
- c.1533G>A
- MANE Select
- NM_001042646
- dbSNP
- rs201849317
- Type
- single nucleotide variant
- Location
- chr3:42202541 (GRCh38)
- Gene constraint
- LOEUF 0.461 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.19
Similar variants
- TRAK1 p.Ser511Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown