TRAPPC12 p.Ser142=
c.426C>T · rs762689919 · VCV3033106
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00893%, nfe)
Conditions
1
TRAPPC12-related disorder
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 -1.3 | GERP -4.8 |
| Overall | ||
| CADD | 7.991 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00893%
European (non-Finnish) · 101/1,130,490 alleles
Filtering AF
0.00747%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00697%
Overall
0.00713%
107/1,500,976 alleles · very rare
exomes 97/1,348,970 · genomes 10/152,006 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00893% | 11,193 |
| Admixed American | 0.00641% | 15,593 |
| Remaining individualsnot grpmax-eligible | 0.00172% | 58,134 |
| African / African-American | 0.00145% | 68,924 |
| South Asian | 0.00124% | 80,500 |
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.Ser142=
- Coding
- c.426C>T
- MANE Select
- NM_016030
- dbSNP
- rs762689919
- Type
- single nucleotide variant
- Location
- chr2:3388049 (GRCh38)
- Gene constraint
- LOEUF 1.192 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52
- Residue 142
- the 'disordered' region
Disease context
TRAPPC12-related disorder
Similar variants
- TRAPPC12 p.Gln284Ter Likely pathogenic ★ same condition
- TRAPPC12 c.*3G>C Likely benign same condition
- TRAPPC12 c.*5C>T Likely benign same condition
- TRAPPC12 p.Ala330= Likely benign same condition
- TRAPPC12 p.Ala599= Likely benign same condition
- TRAPPC12 p.Leu399= Likely benign same condition
- TRAPPC12 p.Pro23= Likely benign same condition
- TRAPPC12 p.Pro469= Likely benign same condition
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-ser142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown