TRAPPC9 p.Ile124=
c.372C>T · rs377446017 · VCV2418277
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -1.9 | GERP -3.2 |
| Overall | ||
| CADD | 3.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,888 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.00173%
28/1,613,956 alleles · very rare
exomes 23/1,461,824 · genomes 5/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,963 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| European (non-Finnish) | 0.00178% | 56,191 |
| African / African-American | 0.00134% | 74,902 |
| South Asian | 0.0011% | 91,072 |
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.Ile124=
- Coding
- c.372C>T
- MANE Select
- NM_001160372
- dbSNP
- rs377446017
- Type
- single nucleotide variant
- Location
- chr8:140451002 (GRCh38)
- Gene constraint
- LOEUF 0.786 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.98
Similar variants
- TRAPPC9 p.Ile124Val Likely benign ★★ same residue
- TRAPPC9 p.Ile124Met 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-ile124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown