TRAPPC2 p.Phe109=
c.327T>C · rs766525300 · VCV746280
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, amr)
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 5.2 | GERP 0.19, phastCons 1 |
| Overall | ||
| CADD | 12.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
Admixed American · 5/37,351 alleles
Filtering AF
0.00526%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00333%
Overall
0.00046%
5/1,086,229 alleles · ultra-rare
exomes 5/972,148 · genomes 0/114,081 · joint denominator
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
- TRAPPC2
- Protein
- p.Phe109=
- Coding
- c.327T>C
- MANE Select
- NM_001011658
- dbSNP
- rs766525300
- Type
- single nucleotide variant
- Location
- chrX:13714503 (GRCh38)
- Structure
- AlphaFold pLDDT 92.44
Similar variants
- TRAPPC2 p.Arg122Ter Pathogenic ★★ same type
- TRAPPC2 c.*1436C>T Uncertain significance ★★ same type
- TRAPPC2 c.*942G>T Uncertain significance ★★ same type
- TRAPPC2 c.*1052T>C Benign ★★ same type
- TRAPPC2 c.*1229C>T Likely benign ★★ same type
- TRAPPC2 c.*1739C>G Benign ★★ same type
- TRAPPC2 c.*29C>T Likely benign ★★ same type
- TRAPPC2 c.*830G>C Benign ★★ 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/trappc2-p-phe109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown