SNCAIP p.Pro701=
c.2103G>T · VCV4971747
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00144%, 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 -13 | GERP -4.5 |
| Overall | ||
| CADD | 0.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00144%
European (non-Finnish) · 17/1,180,016 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00105%
17/1,614,096 alleles · very rare
exomes 17/1,461,844 · genomes 0/152,252 · 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
- SNCAIP
- Protein
- p.Pro701=
- Coding
- c.2103G>T
- MANE Select
- NM_005460
- Type
- single nucleotide variant
- Location
- chr5:122450950 (GRCh38)
- Gene constraint
- LOEUF 0.636 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98 · 1 PDB
- Residue 701
- the 'disordered' region
Similar variants
- SNCAIP p.Ala358Val Uncertain significance ★★ ⚠ same type
- SNCAIP p.Ala363Thr Uncertain significance ★★ ⚠ same type
- SNCAIP p.Glu237Lys Uncertain significance ★★ ⚠ same type
- SNCAIP p.Leu148= Uncertain significance ★★ same type
- SNCAIP p.Ser912Arg Uncertain significance ★★ ⚠ same type
- SNCAIP p.Val461Ile Uncertain significance ★★ ⚠ same type
- SNCAIP c.*103C>T Likely benign ★★ same type
- SNCAIP c.*46T>G Likely benign ★★ 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/sncaip-p-pro701 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown