TRAPPC12 p.Val331=
c.993G>A · rs140519986 · VCV2052049
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.747%, 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 1.8 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 9.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.747%
African / African-American · 558/74,698 alleles
Filtering AF
0.696%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.675%
Overall
0.0385%
616/1,599,032 alleles · rare
exomes 284/1,446,708 · genomes 332/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.747% | 134 |
| Remaining individualsnot grpmax-eligible | 0.0502% | 1,993 |
| Admixed American | 0.0357% | 2,805 |
| South Asian | 0.00337% | 29,681 |
| European (non-Finnish) | 0.000256% | 390,599 |
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
- TRAPPC12
- Protein
- p.Val331=
- Coding
- c.993G>A
- MANE Select
- NM_016030
- dbSNP
- rs140519986
- Type
- single nucleotide variant
- Location
- chr2:3388616 (GRCh38)
- Gene constraint
- LOEUF 1.192 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52
Similar variants
- TRAPPC12 p.Ala627Val Pathogenic/Likely pathogenic ★★ same type
- TRAPPC12 c.1531-3C>T Uncertain significance ★★ same type
- TRAPPC12 c.1603+5G>C Uncertain significance ★★ same type
- TRAPPC12 p.Ala309Val Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Ala485Thr Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Ala637Val Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Arg166Ser Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Arg533Gly 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/trappc12-p-val331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown