TRAPPC12 p.Ser52=
c.156G>A · rs145615349 · VCV2892735
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.116%, mid)
Conditions
1
Inborn genetic diseases
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 -8.3 | GERP -3.9 |
| Overall | ||
| CADD | 0.171 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
Middle Eastern · 7/6,060 alleles
Filtering AF
0.0542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0384%
Overall
0.00502%
81/1,613,094 alleles · rare
exomes 71/1,460,742 · genomes 10/152,352 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.116% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,920 |
| European (non-Finnish) | 0.00543% | 18,430 |
| Admixed American | 0.00167% | 59,964 |
| Finnishnot grpmax-eligible | 0.00156% | 63,944 |
| South Asian | 0.0011% | 90,876 |
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.Ser52=
- Coding
- c.156G>A
- MANE Select
- NM_016030
- dbSNP
- rs145615349
- Type
- single nucleotide variant
- Location
- chr2:3387779 (GRCh38)
- Gene constraint
- LOEUF 1.192 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52
- Residue 52
- the 'disordered' region
Similar variants
- TRAPPC12 p.Ser52Leu Uncertain significance ★ ⚠ same residue
- TRAPPC12 p.Ala309Val Uncertain significance ★★ ⚠ same condition
- TRAPPC12 p.Ala485Thr Uncertain significance ★★ ⚠ same condition
- TRAPPC12 p.Ala637Val Uncertain significance ★★ ⚠ same condition
- TRAPPC12 p.Arg533Gly Uncertain significance ★★ same condition
- TRAPPC12 p.Arg543Cys Uncertain significance ★★ ⚠ same condition
- TRAPPC12 p.Asp212Glu Uncertain significance ★★ ⚠ same condition
- TRAPPC12 p.Asp212Tyr Uncertain significance ★★ 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-ser52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown