SYN1 p.Val295=
c.885G>A · rs1160254110 · VCV1764917
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000335%, nfe)
Conditions
1
Inborn genetic diseases
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 1.1 | phastCons 1 |
| Overall | ||
| CADD | 6.659 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000335%
European (non-Finnish) · 3/895,349 alleles
Filtering AF
8.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5e-05%
Overall
0.000248%
3/1,210,160 alleles · very rare
exomes 2/1,098,237 · genomes 1/111,923 · 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
- SYN1
- Protein
- p.Val295=
- Coding
- c.885G>A
- MANE Select
- NM_006950
- dbSNP
- rs1160254110
- Type
- single nucleotide variant
- Location
- chrX:47576593 (GRCh38)
- Structure
- AlphaFold pLDDT 69.86
- Residue 295
- the 'c; actin-binding and synaptic-vesicle binding' region
Similar variants
- SYN1 p.Val295Met Uncertain significance ★★ ⚠ same residue
- SYN1 p.Ala441Asp Uncertain significance ★★ ⚠ same condition
- SYN1 p.Arg169Trp Uncertain significance ★★ ⚠ same condition
- SYN1 p.Arg424Trp Uncertain significance ★★ ⚠ same condition
- SYN1 p.Gly320Ala Uncertain significance ★★ ⚠ same condition
- SYN1 p.Gly440Arg Uncertain significance ★★ ⚠ same condition
- SYN1 p.Gly47Arg Uncertain significance ★★ ⚠ same condition
- SYN1 p.Gly571Ser 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/syn1-p-val295 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown