TRAPPC4 p.Phe115=
c.345C>T · rs3802881 · VCV1275542
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 22.1%, sas) — too common for a highly-penetrant pathogenic allele
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 1.5 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 13.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22.1%
South Asian · 20,121/91,010 alleles
Filtering AF
21.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 21.7%
Overall
9.49%
152,928/1,612,310 alleles · common
exomes 140,023/1,460,114 · genomes 12,905/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 22.1% | 5 |
| Finnishnot grpmax-eligible | 13.8% | 7 |
| Amishnot grpmax-eligible | 9.78% | 10 |
| East Asian | 9.38% | 11 |
| Remaining individualsnot grpmax-eligible | 9.08% | 11 |
| European (non-Finnish) | 8.79% | 11 |
| Middle Eastern | 7.49% | 13 |
| African / African-American | 6.83% | 15 |
| Admixed American | 6.12% | 16 |
| Ashkenazi Jewishnot grpmax-eligible | 3.91% | 26 |
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
- TRAPPC4
- Protein
- p.Phe115=
- Coding
- c.345C>T
- MANE Select
- NM_016146
- dbSNP
- rs3802881
- Type
- single nucleotide variant
- Location
- chr11:119019312 (GRCh38)
- Gene constraint
- LOEUF 1.689 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.02 · 3 PDB
- Residue 115
- an α-helix
Similar variants
- TRAPPC4 c.454+3A>G Pathogenic/Likely pathogenic ★★ same type
- TRAPPC4 c.176-31C>G Benign ★★ same type
- TRAPPC4 c.176-40C>G Benign ★★ same type
- TRAPPC4 c.176-43C>T Benign ★★ same type
- TRAPPC4 c.350+129T>C Benign ★★ same type
- TRAPPC4 c.350+58C>T Benign ★★ same type
- TRAPPC4 c.351-58C>A Benign ★★ same type
- TRAPPC4 c.454+225G>T 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/trappc4-p-phe115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown