TRAPPC9 p.Pro679=
c.2037G>A · rs371880751 · VCV212423
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.009 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.9 |
| Overall | ||
| CADD | 0.528 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Admixed American · 20/60,026 alleles
Filtering AF
0.0221%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0184%
Overall
0.00279%
45/1,614,146 alleles · ultra-rare
exomes 38/1,461,884 · genomes 7/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0333% | 3,001 |
| Finnishnot grpmax-eligible | 0.00312% | 32,017 |
| African / African-American | 0.00267% | 37,516 |
| European (non-Finnish) | 0.00169% | 59,001 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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.Pro679=
- Coding
- c.2037G>A
- MANE Select
- NM_001160372
- dbSNP
- rs371880751
- Type
- single nucleotide variant
- Location
- chr8:140283966 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- TRAPPC9 p.Pro679Leu 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-pro679 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown