VAMP2 p.Cys103=
c.309C>T · rs755036825 · VCV3026123
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00907%, 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 8.6 | GERP 0.97, phastCons 1 |
| Overall | ||
| CADD | 15.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00907%
European (non-Finnish) · 107/1,180,018 alleles
Filtering AF
0.00766%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00708%
Overall
0.00719%
116/1,614,012 alleles · very rare
exomes 106/1,461,846 · genomes 10/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00907% | 11,028 |
| African / African-American | 0.00667% | 14,983 |
| East Asian | 0.00446% | 22,445 |
| South Asian | 0.0022% | 45,541 |
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
- VAMP2
- Protein
- p.Cys103=
- Coding
- c.309C>T
- MANE Select
- NM_014232
- dbSNP
- rs755036825
- Type
- single nucleotide variant
- Location
- chr17:8161498 (GRCh38)
- Gene constraint
- LOEUF 0.176 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.34 · 7 PDB
- Residue 103
- an α-helix; the 'required for interaction with sept8' region
Similar variants
- VAMP2 p.Ala74Val Uncertain significance ★★ ⚠ same type
- VAMP2 c.3-101G>T Likely benign ★★ same type
- VAMP2 c.334+12G>C Benign ★★ same type
- VAMP2 p.Ile98= Likely benign ★★ same type
- VAMP2 p.Leu54= Likely benign ★★ same type
- VAMP2 c.2+2T>C Likely pathogenic ★ same type
- VAMP2 p.Arg56Leu Likely pathogenic ★ same type
- VAMP2 p.Arg56Ter Pathogenic ★ 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/vamp2-p-cys103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown