TRAPPC6B p.Arg31=
c.93A>G · rs760834484 · VCV2672559
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 0.49 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 7.823 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Filtering AF
0.00257%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00226%
Overall
0.00256%
41/1,603,350 alleles · ultra-rare
exomes 34/1,451,200 · genomes 7/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,058 |
| European (non-Finnish) | 0.00341% | 29,357 |
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
- TRAPPC6B
- Protein
- p.Arg31=
- Coding
- c.93A>G
- MANE Select
- NM_001079537
- dbSNP
- rs760834484
- Type
- single nucleotide variant
- Location
- chr14:39159539 (GRCh38)
- Gene constraint
- LOEUF 1.842 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.93 · 3 PDB
- Residue 31
- an α-helix
Similar variants
- TRAPPC6B p.Arg31Ter Pathogenic/Likely pathogenic ★★ same residue
- TRAPPC6B c.82-2A>G Pathogenic ★★ same type
- TRAPPC6B p.Asp54Val Uncertain significance ★★ ⚠ same type
- TRAPPC6B p.Lys98Arg Uncertain significance ★★ ⚠ same type
- TRAPPC6B p.Ser137Cys Uncertain significance ★★ ⚠ same type
- TRAPPC6B c.268-35A>G Benign ★★ same type
- TRAPPC6B c.445+14G>A Benign ★★ same type
- TRAPPC6B p.Leu158= Benign ★★ 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/trappc6b-p-arg31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown