TRAPPC12 p.Ser301=
c.903C>T · rs753525355 · VCV1995629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 -8 | GERP -5.4 |
| Overall | ||
| CADD | 8.973 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,004 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000248%
4/1,613,058 alleles · very rare
exomes 4/1,460,760 · genomes 0/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,001 |
| Finnishnot grpmax-eligible | 0.00158% | 63,370 |
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.Ser301=
- Coding
- c.903C>T
- MANE Select
- NM_016030
- dbSNP
- rs753525355
- Type
- single nucleotide variant
- Location
- chr2:3388526 (GRCh38)
- Gene constraint
- LOEUF 1.192 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52
- Residue 301
- a UniProt-annotated variant site (in)
Similar variants
- TRAPPC12 p.Ser301Gly Benign ★★ same residue
- TRAPPC12 p.Ser301Arg Uncertain significance ★ ⚠ same residue
- 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
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-ser301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown