TRAPPC9 p.Asp131=
c.393C>T · rs151268445 · VCV2190004
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.04%, afr)
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 -3.1 | GERP -3.2 |
| Overall | ||
| CADD | 2.986 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.04%
African / African-American · 30/75,032 alleles
Filtering AF
0.0288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0249%
Overall
0.00353%
57/1,614,136 alleles · ultra-rare
exomes 36/1,461,872 · genomes 21/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.04% | 2,501 |
| South Asian | 0.00988% | 10,120 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| Finnishnot grpmax-eligible | 0.00156% | 64,024 |
| European (non-Finnish) | 0.0011% | 90,772 |
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.Asp131=
- Coding
- c.393C>T
- MANE Select
- NM_001160372
- dbSNP
- rs151268445
- Type
- single nucleotide variant
- Location
- chr8:140450981 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- TRAPPC9 p.Asp131Asn 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-asp131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown