SNAP29 p.Lys93=
c.279G>A · rs764625480 · VCV2993216
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, 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 3.7 | phastCons 1 |
| Overall | ||
| CADD | 9.284 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,876 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000372%
6/1,614,174 alleles · very rare
exomes 6/1,461,884 · genomes 0/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,219 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
| African / African-American | 0.00133% | 75,032 |
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.Lys93=
- Coding
- c.279G>A
- MANE Select
- NM_004782
- dbSNP
- rs764625480
- Type
- single nucleotide variant
- Location
- chr22:20870378 (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 93
- an α-helix
Similar variants
- 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
- SNAP29 p.Ala65Pro Uncertain significance ★★ ⚠ same type
- SNAP29 p.Arg215Cys 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-lys93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown