SCAPER p.Ala170=
c.510A>C · VCV3351836
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00213%, nfe)
Conditions
1
SCAPER-related disorder
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 -3.3 | GERP -4.2 |
| Overall | ||
| CADD | 2.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00213%
European (non-Finnish) · 25/1,176,120 alleles
Filtering AF
0.00146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00155%
25/1,609,216 alleles · very rare
exomes 24/1,457,170 · genomes 1/152,046 · 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
- SCAPER
- Protein
- p.Ala170=
- Coding
- c.510A>C
- MANE Select
- NM_020843
- Type
- single nucleotide variant
- Location
- chr15:76800349 (GRCh38)
- Gene constraint
- LOEUF 0.666 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.35 · 2 PDB
Disease context
SCAPER-related disorder
Similar variants
- SCAPER p.Arg112Ter Likely pathogenic ★★ same condition
- SCAPER c.1035+1G>C Likely pathogenic ★ same condition
- SCAPER c.1613+1G>T Likely pathogenic ★ same condition
- SCAPER p.Arg277Ter Likely pathogenic ★ same condition
- SCAPER p.Arg366Ter Pathogenic ★ same condition
- SCAPER p.Gln551Ter Likely pathogenic ★ same condition
- SCAPER p.Glu885Ter Likely pathogenic ★ same condition
- SCAPER p.Ser832Ter Likely pathogenic ★ 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/scaper-p-ala170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown