TRAPPC9 p.Pro886=
c.2658G>A · rs150252117 · VCV1336037
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.112%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.146 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.8 |
| Overall | ||
| CADD | 0.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.112%
Admixed American · 67/60,012 alleles
Filtering AF
0.0902%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0823%
Overall
0.024%
387/1,614,082 alleles · rare
exomes 320/1,461,848 · genomes 67/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.112% | 896 |
| European (non-Finnish) | 0.0232% | 4,307 |
| South Asian | 0.0209% | 4,794 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| African / African-American | 0.0173% | 5,769 |
| Middle Eastern | 0.0165% | 6,060 |
| East Asian | 0.00446% | 22,440 |
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.Pro886=
- Coding
- c.2658G>A
- MANE Select
- NM_001160372
- dbSNP
- rs150252117
- Type
- single nucleotide variant
- Location
- chr8:140023978 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- TRAPPC9 p.Pro886Leu Uncertain significance ★★ ⚠ same residue
- TRAPPC9 p.Pro886Arg Uncertain significance ★ ⚠ same residue
- TRAPPC9 c.2700-2A>T Pathogenic/Likely pathogenic ★★ same type
- TRAPPC9 c.2811-1G>A Likely pathogenic ★★ same type
- TRAPPC9 c.3279+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRAPPC9 c.-204C>T Pathogenic/Likely pathogenic ★★ same type
- TRAPPC9 p.Arg377Ter Pathogenic ★★ same type
- TRAPPC9 p.Arg472Ter Pathogenic/Likely pathogenic ★★ 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/trappc9-p-pro886 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown