TRAF7 p.Cys459=
c.1377C>T · rs377479113 · VCV3050387
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.25 | GERP -1.4, phastCons 0.22 |
| Overall | ||
| CADD | 11.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Middle Eastern · 7/6,084 alleles
Filtering AF
0.054%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0383%
Overall
0.00824%
133/1,613,670 alleles · rare
exomes 117/1,461,450 · genomes 16/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.115% | 869 |
| Admixed American | 0.0567% | 1,765 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,975 |
| South Asian | 0.00988% | 10,121 |
| African / African-American | 0.00934% | 10,706 |
| European (non-Finnish) | 0.00466% | 21,454 |
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
- TRAF7
- Protein
- p.Cys459=
- Coding
- c.1377C>T
- MANE Select
- NM_032271
- dbSNP
- rs377479113
- Type
- single nucleotide variant
- Location
- chr16:2175141 (GRCh38)
- Gene constraint
- LOEUF 0.675 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.16 · 1 PDB
Similar variants
- TRAF7 p.Arg524Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Arg655Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Leu402Val Pathogenic ★★ ⚠ same type
- TRAF7 p.Leu625Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Ser558Phe Pathogenic ★★ ⚠ same type
- TRAF7 p.Ser629Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Arg316Cys Uncertain significance ★★ ⚠ same type
- TRAF7 p.Arg371Trp 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/traf7-p-cys459 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown