TRAF3IP1 p.Arg19=
c.55A>C · VCV4693072
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00263%, 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 0.46 | GERP 0.47, phastCons 0.9 |
| Overall | ||
| CADD | 13.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00263%
South Asian · 2/76,112 alleles
Filtering AF
0.000436%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000163%
Overall
0.000622%
9/1,447,912 alleles · very rare
exomes 9/1,296,608 · genomes 0/151,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00263% | 38,056 |
| Admixed American | 0.00237% | 42,178 |
| Remaining individualsnot grpmax-eligible | 0.00186% | 53,790 |
| European (non-Finnish) | 0.000459% | 217,837 |
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.Arg19=
- Coding
- c.55A>C
- MANE Select
- NM_015650
- Type
- single nucleotide variant
- Location
- chr2:238320717 (GRCh38)
- Gene constraint
- LOEUF 0.723 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.95 · 2 PDB
- Residue 19
- the 'abolishes microtubules-binding when missing' region; a β-strand
Similar variants
- TRAF3IP1 p.Arg19Met Uncertain significance ★ ⚠ same residue
- TRAF3IP1 p.Arg19Ser 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-arg19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown