TRAF3IP1 p.Pro302=
c.906T>C · rs17854985 · VCV1167551
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 27.3%, afr) — too common for a highly-penetrant pathogenic allele
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 -15 | GERP -2.4 |
| Overall | ||
| CADD | 0.047 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
27.3%
African / African-American · 18,400/67,412 alleles
Filtering AF
27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 26.8%
Overall
5.88%
79,898/1,357,820 alleles · common
exomes 62,170/1,205,716 · genomes 17,728/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 27.3% | 4 |
| East Asian | 11% | 9 |
| Finnishnot grpmax-eligible | 10.4% | 10 |
| South Asian | 9.87% | 10 |
| Middle Eastern | 9.85% | 10 |
| Admixed American | 7.83% | 13 |
| Remaining individualsnot grpmax-eligible | 6.66% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 4.31% | 23 |
| European (non-Finnish) | 3.85% | 26 |
| Amishnot grpmax-eligible | 2.85% | 35 |
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
- TRAF3IP1
- Protein
- p.Pro302=
- Coding
- c.906T>C
- MANE Select
- NM_015650
- dbSNP
- rs17854985
- Type
- single nucleotide variant
- Location
- chr2:238329333 (GRCh38)
- Gene constraint
- LOEUF 0.723 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.95 · 2 PDB
- Residue 302
- the 'abolishes microtubules-binding when missing' region; the 'disordered' region; the 'disc1-interaction domain' region
Similar variants
- TRAF3IP1 p.Pro302Leu Uncertain significance ★ ⚠ same residue
- TRAF3IP1 p.Pro302Ser Uncertain significance ★ ⚠ same residue
- IFT54 c.1159+1G>C Likely pathogenic ★★ same type
- IFT54 c.988-1G>A Likely pathogenic ★★ same type
- IFT54 c.988-1G>C Likely pathogenic ★★ same type
- IFT54 p.Arg565Ter Pathogenic/Likely pathogenic ★★ same type
- IFT54 p.Trp572Ter Pathogenic/Likely pathogenic ★★ same type
- IFT54 c.1452-5T>G 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/traf3ip1-p-pro302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown