TRAPPC12 p.Pro312=
c.936C>T · rs371685284 · VCV1598900
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.19%, sas)
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 -1.9 | GERP -4.2 |
| Overall | ||
| CADD | 12.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.19%
South Asian · 1,078/90,964 alleles
Filtering AF
1.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1%
Overall
0.0737%
1,188/1,612,888 alleles · low-frequency
exomes 1,103/1,460,554 · genomes 85/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.19% | 84 |
| Remaining individualsnot grpmax-eligible | 0.0833% | 1,201 |
| Admixed American | 0.0217% | 4,613 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.0147% | 6,823 |
| European (non-Finnish) | 0.00271% | 36,866 |
| East Asian | 0.00223% | 44,852 |
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.Pro312=
- Coding
- c.936C>T
- MANE Select
- NM_016030
- dbSNP
- rs371685284
- Type
- single nucleotide variant
- Location
- chr2:3388559 (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-pro312 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown