TRAPPC9 p.Pro128=
c.384G>A · rs140509196 · VCV437040
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0706%, afr)
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 -4.4 | GERP -3.2 |
| Overall | ||
| CADD | 3.274 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0706%
African / African-American · 53/75,042 alleles
Filtering AF
0.0554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.05%
Overall
0.0039%
63/1,614,152 alleles · ultra-rare
exomes 30/1,461,860 · genomes 33/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0706% | 1,416 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| East Asian | 0.00446% | 22,437 |
| Admixed American | 0.00333% | 30,008 |
| European (non-Finnish) | 0.000169% | 590,019 |
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.Pro128=
- Coding
- c.384G>A
- MANE Select
- NM_001160372
- dbSNP
- rs140509196
- Type
- single nucleotide variant
- Location
- chr8:140450990 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- TRAPPC9 p.Pro128Leu 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
- TRAPPC9 p.Arg51Ter 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-pro128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown