TRAPPC9 p.Ala347=
c.1041G>A · rs368293322 · VCV1770231
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.111 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -2.6 |
| Overall | ||
| CADD | 0.171 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,086 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00378%
61/1,614,028 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,386 |
| European (non-Finnish) | 0.00415% | 24,082 |
| African / African-American | 0.004% | 24,973 |
| Admixed American | 0.00167% | 59,992 |
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
- TRAPPC9
- Protein
- p.Ala347=
- Coding
- c.1041G>A
- MANE Select
- NM_001160372
- dbSNP
- rs368293322
- Type
- single nucleotide variant
- Location
- chr8:140397713 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- TRAPPC9 p.Ala347Val Uncertain significance ★★ same residue
- TRAPPC9 p.Arg472Ter Pathogenic/Likely pathogenic ★★ same condition
- TRAPPC9 p.Glu123Ter Pathogenic ★★ same condition
- TRAPPC9 p.Glu97Ter Pathogenic ★★ same condition
- TRAPPC9 c.-212G>C Uncertain significance ★★ same condition
- TRAPPC9 c.-4C>A Uncertain significance ★★ same condition
- TRAPPC9 c.-69C>T Uncertain significance ★★ same condition
- TRAPPC9 c.-74C>A 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/trappc9-p-ala347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown