TRAK1 p.Val41=
c.123C>T · rs61742102 · VCV1600230
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.88%, 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 -4.6 | GERP -5.4 |
| Overall | ||
| CADD | 5.828 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.88%
South Asian · 3,532/91,064 alleles
Filtering AF
3.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.73%
Overall
0.366%
5,907/1,614,130 alleles · low-frequency
exomes 5,488/1,461,854 · genomes 419/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.88% | 26 |
| Middle Eastern | 2.39% | 42 |
| Remaining individualsnot grpmax-eligible | 0.51% | 196 |
| Ashkenazi Jewishnot grpmax-eligible | 0.507% | 197 |
| African / African-American | 0.193% | 518 |
| Admixed American | 0.18% | 556 |
| European (non-Finnish) | 0.127% | 787 |
| East Asian | 0.0111% | 8,976 |
| Finnishnot grpmax-eligible | 0.00469% | 21,343 |
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.Val41=
- Coding
- c.123C>T
- MANE Select
- NM_001042646
- dbSNP
- rs61742102
- Type
- single nucleotide variant
- Location
- chr3:42125451 (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-val41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown