SCAPER p.Val303=
c.909A>G · VCV3357376
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
SCAPER-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.52 | donor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.5 | GERP -3.7 |
| Overall | ||
| CADD | 3.657 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,040 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,848 alleles · very rare
exomes 3/1,461,538 · genomes 0/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,040 |
| European (non-Finnish) | 0.00017% | 589,890 |
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.Val303=
- Coding
- c.909A>G
- MANE Select
- NM_020843
- Type
- single nucleotide variant
- Location
- chr15:76774981 (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-val303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown