TRAK1 p.Pro783=
c.2349G>A · rs371605989 · VCV3015874
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.214%, mid)
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 -0.72 | GERP -3.7, phastCons 0.002 |
| Overall | ||
| CADD | 6.504 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.214%
Middle Eastern · 13/6,084 alleles
Filtering AF
0.126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.1%
Overall
0.00378%
61/1,613,982 alleles · rare
exomes 55/1,461,876 · genomes 6/152,106 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.214% | 468 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0439% | 2,277 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| Admixed American | 0.00833% | 11,998 |
| Finnishnot grpmax-eligible | 0.00625% | 16,004 |
| European (non-Finnish) | 0.00144% | 69,412 |
| African / African-American | 0.00133% | 74,920 |
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.Pro783=
- Coding
- c.2349G>A
- MANE Select
- NM_001042646
- dbSNP
- rs371605989
- Type
- single nucleotide variant
- Location
- chr3:42223224 (GRCh38)
- Gene constraint
- LOEUF 0.461 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.19
- Residue 783
- the 'disordered' region
Similar variants
- TRAK1 p.Pro783Arg Benign/Likely benign ★★ 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-pro783 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown