TRAPPC12 p.Asp173=
c.519C>T · rs184956144 · VCV767779
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.34%, 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 -9.4 | GERP -4.9 |
| Overall | ||
| CADD | 4.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.34%
African / African-American · 2,480/74,200 alleles
Filtering AF
3.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.19%
Overall
0.188%
3,013/1,598,910 alleles · low-frequency
exomes 1,528/1,446,758 · genomes 1,485/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.34% | 30 |
| Admixed American | 0.364% | 274 |
| Remaining individualsnot grpmax-eligible | 0.301% | 333 |
| Middle Eastern | 0.217% | 462 |
| European (non-Finnish) | 0.00962% | 10,393 |
| South Asian | 0.00779% | 12,845 |
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
- TRAPPC12
- Protein
- p.Asp173=
- Coding
- c.519C>T
- MANE Select
- NM_016030
- dbSNP
- rs184956144
- Type
- single nucleotide variant
- Location
- chr2:3388142 (GRCh38)
- Gene constraint
- LOEUF 1.192 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52
- Residue 173
- the 'disordered' region
Similar variants
- TRAPPC12 p.Ala627Val Pathogenic/Likely pathogenic ★★ same type
- TRAPPC12 c.1531-3C>T Uncertain significance ★★ same type
- TRAPPC12 c.1603+5G>C Uncertain significance ★★ same type
- TRAPPC12 p.Ala309Val Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Ala485Thr Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Ala637Val Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Arg166Ser Uncertain significance ★★ ⚠ same type
- TRAPPC12 p.Arg533Gly Uncertain significance ★★ 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/trappc12-p-asp173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown