SNCAIP p.Ser406=
c.1218C>T · rs148152880 · VCV350494
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.618%, afr)
Conditions
1
Parkinson Disease, Dominant/Recessive
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 -4.5 | GERP -4 |
| Overall | ||
| CADD | 4.549 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.618%
African / African-American · 462/74,768 alleles
Filtering AF
0.571%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.553%
Overall
0.034%
545/1,604,850 alleles · rare
exomes 288/1,452,780 · genomes 257/152,070 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.618% | 162 |
| Middle Eastern | 0.0828% | 1,208 |
| Admixed American | 0.0518% | 1,931 |
| Remaining individualsnot grpmax-eligible | 0.0499% | 2,006 |
| South Asian | 0.0088% | 11,358 |
| East Asian | 0.00223% | 44,774 |
| European (non-Finnish) | 0.000597% | 167,424 |
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
- SNCAIP
- Protein
- p.Ser406=
- Coding
- c.1218C>T
- MANE Select
- NM_005460
- dbSNP
- rs148152880
- Type
- single nucleotide variant
- Location
- chr5:122432004 (GRCh38)
- Gene constraint
- LOEUF 0.636 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98 · 1 PDB
Disease context
Parkinson Disease, Dominant/Recessive
Similar variants
- SNCAIP p.Ala363Thr Uncertain significance ★★ ⚠ same condition
- SNCAIP p.Glu237Lys Uncertain significance ★★ ⚠ same condition
- SNCAIP p.Leu148= Uncertain significance ★★ same condition
- SNCAIP p.Ser912Arg Uncertain significance ★★ ⚠ same condition
- SNCAIP c.*103C>T Likely benign ★★ same condition
- SNCAIP c.*46T>G Likely benign ★★ same condition
- SNCAIP c.*70C>G Benign/Likely benign ★★ same condition
- SNCAIP p.Arg621Cys Likely benign ★★ 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/sncaip-p-ser406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown