TRAK1 p.Ser780=
c.2340T>A · rs370271663 · VCV3023017
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, 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 -0.7 | GERP -1.4, phastCons 0.008 |
| Overall | ||
| CADD | 6.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,928 alleles
Filtering AF
0.00623%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00467%
Overall
0.000558%
9/1,614,018 alleles · ultra-rare
exomes 3/1,461,882 · genomes 6/152,136 · joint denominator
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.Ser780=
- Coding
- c.2340T>A
- MANE Select
- NM_001042646
- dbSNP
- rs370271663
- Type
- single nucleotide variant
- Location
- chr3:42223215 (GRCh38)
- Gene constraint
- LOEUF 0.461 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.19
- Residue 780
- the 'disordered' region
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-ser780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown