TRAIP p.Asp315=
c.945T>C · rs376933772 · VCV3007516
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0522%, 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 1.5 | GERP -0.54, phastCons 1 |
| Overall | ||
| CADD | 9.503 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0522%
South Asian · 47/90,016 alleles
Filtering AF
0.0403%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0361%
Overall
0.00305%
49/1,607,628 alleles · ultra-rare
exomes 49/1,455,360 · genomes 0/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0522% | 1,915 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,108 |
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.Asp315=
- Coding
- c.945T>C
- MANE Select
- NM_005879
- dbSNP
- rs376933772
- Type
- single nucleotide variant
- Location
- chr3:49832008 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.24 · 1 PDB
- Residue 315
- 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-asp315 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown