TRAFD1 p.Glu232=
c.696G>A · rs61740854 · VCV788439
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.31%, afr)
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 0.73 | GERP -1.1, phastCons 0.12 |
| Overall | ||
| CADD | 6.271 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.31%
African / African-American · 980/74,980 alleles
Filtering AF
1.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.21%
Overall
0.0677%
1,093/1,613,950 alleles · low-frequency
exomes 536/1,461,842 · genomes 557/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.31% | 77 |
| Admixed American | 0.09% | 1,111 |
| Remaining individualsnot grpmax-eligible | 0.0816% | 1,226 |
| European (non-Finnish) | 0.000678% | 147,499 |
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
- TRAFD1
- Protein
- p.Glu232=
- Coding
- c.696G>A
- MANE Select
- NM_006700
- dbSNP
- rs61740854
- Type
- single nucleotide variant
- Location
- chr12:112142141 (GRCh38)
- Gene constraint
- LOEUF 0.749 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.45 · 1 PDB
- Residue 232
- the 'disordered' region
Similar variants
- TRAFD1 p.Ala56Thr Uncertain significance ★★ ⚠ same type
- TRAFD1 p.Ala147Thr Uncertain significance ★ ⚠ same type
- TRAFD1 p.Ala258Thr Uncertain significance ★ ⚠ same type
- TRAFD1 p.Ala317Thr Uncertain significance ★ ⚠ same type
- TRAFD1 p.Ala505Val Uncertain significance ★ ⚠ same type
- TRAFD1 p.Ala554Ser Uncertain significance ★ ⚠ same type
- TRAFD1 p.Arg112Trp Uncertain significance ★ ⚠ same type
- TRAFD1 p.Arg264Ser 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/trafd1-p-glu232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown