SNAP29 p.Arg256=
c.768A>T · rs755306200 · VCV2861499
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -0.44 | GERP -2.8, phastCons 0.001 |
| Overall | ||
| CADD | 4.862 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,002 alleles
Overall
6.2e-05%
1/1,614,152 alleles · very rare
exomes 1/1,461,782 · genomes 0/152,370 · joint denominator
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
- SNAP29
- Protein
- p.Arg256=
- Coding
- c.768A>T
- MANE Select
- NM_004782
- dbSNP
- rs755306200
- Type
- single nucleotide variant
- Location
- chr22:20887827 (GRCh38)
- Gene constraint
- LOEUF 0.833 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.85 · 2 PDB
- Residue 256
- the t-snare coiled-coil homology domain
Similar variants
- SNAP29 p.Arg256Gln Uncertain significance ★ ⚠ same residue
- SNAP29 p.Arg256Ter Uncertain significance ★ same residue
- SNAP29 p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
- SNAP29 p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
- SNAP29 c.-76G>A Uncertain significance ★★ same type
- SNAP29 c.*3014C>T Uncertain significance ★★ same type
- SNAP29 c.*840G>C Uncertain significance ★★ same type
- SNAP29 p.Ala20Pro 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/snap29-p-arg256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown