TRAPPC12 p.Phe209=
c.627C>T · rs140551015 · VCV1671899
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -2.8 |
| Overall | ||
| CADD | 1.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
European (non-Finnish) · 17,145/1,177,796 alleles
Filtering AF
1.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.43%
Overall
1.15%
18,533/1,608,716 alleles · low-frequency
exomes 17,372/1,456,526 · genomes 1,161/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.46% | 69 |
| Amishnot grpmax-eligible | 1.43% | 70 |
| Remaining individualsnot grpmax-eligible | 0.886% | 113 |
| Middle Eastern | 0.629% | 159 |
| Admixed American | 0.449% | 223 |
| Ashkenazi Jewishnot grpmax-eligible | 0.282% | 355 |
| Finnishnot grpmax-eligible | 0.254% | 393 |
| African / African-American | 0.204% | 491 |
| South Asian | 0.135% | 743 |
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.Phe209=
- Coding
- c.627C>T
- MANE Select
- NM_016030
- dbSNP
- rs140551015
- Type
- single nucleotide variant
- Location
- chr2:3388250 (GRCh38)
- Gene constraint
- LOEUF 1.192 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.52
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-phe209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown