TRAF3IP1 p.Val6=
c.18G>A · rs2106351680 · VCV1634440
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0015%, nfe)
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 6.3 | GERP 0.54, phastCons 1 |
| Overall | ||
| CADD | 16.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0015%
European (non-Finnish) · 16/1,066,740 alleles
Filtering AF
0.000888%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000718%
Overall
0.00114%
16/1,409,650 alleles · very rare
exomes 16/1,258,412 · genomes 0/151,238 · 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
- TRAF3IP1
- Protein
- p.Val6=
- Coding
- c.18G>A
- MANE Select
- NM_015650
- dbSNP
- rs2106351680
- Type
- single nucleotide variant
- Location
- chr2:238320680 (GRCh38)
- Gene constraint
- LOEUF 0.723 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.95 · 2 PDB
- Residue 6
- the 'abolishes microtubules-binding when missing' region; an α-helix
Similar variants
- 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
- IFT54 c.1910+3G>T Uncertain significance ★★ same type
- IFT54 p.Ala513Val 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-val6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown