SNCA p.Glu61=
c.183G>A · rs1737231816 · VCV1711594
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.15 | GERP 1, phastCons 0.98 |
| Overall | ||
| CADD | 8.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,048 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,220 alleles · very rare
exomes 3/1,461,870 · genomes 0/152,350 · 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
- SNCA
- Protein
- p.Glu61=
- Coding
- c.183G>A
- MANE Select
- NM_000345
- dbSNP
- rs1737231816
- Type
- single nucleotide variant
- Location
- chr4:89822369 (GRCh38)
- Gene constraint
- LOEUF 0.691 · pLI 0.80 (gnomAD)
- Structure
- AlphaFold pLDDT 74.29 · 185 PDB
- Residue 61
- a β-strand; the '4 x 11 aa tandem repeats of [egs]-k-t-k-[eq]-[gq]-v-x(4)' region
Similar variants
- SNCA p.Glu61Val Uncertain significance ★ ⚠ same residue
- SNCA p.Ala53Glu Pathogenic ★★ ⚠ same type
- SNCA p.Ala53Thr Pathogenic ★★ ⚠ same type
- SNCA c.-219G>C Uncertain significance ★★ same type
- SNCA c.*2037T>C Uncertain significance ★★ same type
- SNCA p.His50Gln Uncertain significance ★★ ⚠ same type
- SNCA p.Pro117Thr Uncertain significance ★★ ⚠ same type
- SNCA p.Pro128Thr 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/snca-p-glu61 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown