TRAPPC9 p.Ala405=
c.1215G>A · rs148641824 · VCV737762
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.114%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.066 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -3.8 |
| Overall | ||
| CADD | 9.515 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.114%
East Asian · 51/44,890 alleles
Filtering AF
0.0887%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0799%
Overall
0.00477%
77/1,614,200 alleles · rare
exomes 56/1,461,818 · genomes 21/152,382 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.114% | 880 |
| Admixed American | 0.0217% | 4,618 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| South Asian | 0.0022% | 45,544 |
| European (non-Finnish) | 0.000508% | 196,670 |
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.Ala405=
- Coding
- c.1215G>A
- MANE Select
- NM_001160372
- dbSNP
- rs148641824
- Type
- single nucleotide variant
- Location
- chr8:140371100 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- 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
- TRAPPC9 p.Arg614Ter 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-ala405 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown