TRAIP p.Val288=
c.864C>T · rs377353118 · VCV2182266
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, 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 2.7 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 10.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00409%
66/1,614,086 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| European (non-Finnish) | 0.00525% | 19,033 |
| South Asian | 0.0022% | 45,545 |
| African / African-American | 0.00133% | 74,940 |
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
- TRAIP
- Protein
- p.Val288=
- Coding
- c.864C>T
- MANE Select
- NM_005879
- dbSNP
- rs377353118
- Type
- single nucleotide variant
- Location
- chr3:49839792 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.24 · 1 PDB
- Residue 288
- the 'interaction with cyld' region
Similar variants
- TRAIP p.Arg436Cys Uncertain significance ★★ ⚠ same type
- TRAIP p.Arg436His Uncertain significance ★★ ⚠ same type
- TRAIP p.Asp244His Uncertain significance ★★ ⚠ same type
- TRAIP p.Asp431Gly Uncertain significance ★★ ⚠ same type
- TRAIP p.Gln36Arg Uncertain significance ★★ ⚠ same type
- TRAIP p.Glu209Lys Uncertain significance ★★ ⚠ same type
- TRAIP p.Gly421Ser Uncertain significance ★★ ⚠ same type
- TRAIP p.Ile104Met 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/traip-p-val288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown