SNAP25 p.Arg17=
c.51G>A · rs1439231615 · VCV2169250
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00339%, amr)
Conditions
1
congenital myasthenic syndrome 18
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 2.2 | GERP 0.62, phastCons 1 |
| Overall | ||
| CADD | 10.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00339%
Admixed American · 2/59,002 alleles
Filtering AF
0.000562%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00021%
Overall
0.000125%
2/1,602,056 alleles · very rare
exomes 2/1,449,698 · genomes 0/152,358 · 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
- SNAP25
- Protein
- p.Arg17=
- Coding
- c.51G>A
- MANE Select
- NM_130811
- dbSNP
- rs1439231615
- Type
- single nucleotide variant
- Location
- chr20:10275542 (GRCh38)
- Gene constraint
- LOEUF 0.29 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.14 · 14 PDB
- Residue 17
- the 'interaction with cenpf' region; an α-helix; the 'disordered' region
Similar variants
- SNAP25 p.Ala199Glu Pathogenic/Likely pathogenic ★★ same condition
- SNAP25 p.Arg198Pro Likely pathogenic ★★ same condition
- SNAP25 p.Gln197Ter Likely pathogenic ★★ same condition
- SNAP25 p.Gly43Arg Pathogenic/Likely pathogenic ★★ same condition
- SNAP25 p.Ile67Asn Pathogenic/Likely pathogenic ★★ same condition
- SNAP25 p.Lys40Glu Likely pathogenic ★★ ⚠ same condition
- SNAP25 p.Met71Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SNAP25 p.Ala2Thr Uncertain significance ★★ ⚠ same condition
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/snap25-p-arg17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown