SCAPER p.Arg259=
c.777G>A · VCV4926007
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0114%, sas)
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 -0.41 | GERP -3.7, phastCons 0.071 |
| Overall | ||
| CADD | 8.682 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0114%
South Asian · 10/87,636 alleles
Filtering AF
0.00615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00469%
Overall
0.000691%
11/1,592,014 alleles · ultra-rare
exomes 11/1,439,796 · genomes 0/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0114% | 8,764 |
| African / African-American | 0.00135% | 73,938 |
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.Arg259=
- Coding
- c.777G>A
- MANE Select
- NM_020843
- Type
- single nucleotide variant
- Location
- chr15:76775113 (GRCh38)
- Gene constraint
- LOEUF 0.666 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.35 · 2 PDB
- Residue 259
- the 'disordered' region
Similar variants
- SCAPER p.Arg259Gln Uncertain significance ★ ⚠ same residue
- SCAPER p.Arg259Trp Uncertain significance ★ ⚠ same residue
- SCAPER p.Arg112Ter Likely pathogenic ★★ same type
- SCAPER p.Lys869Ter Pathogenic/Likely pathogenic ★★ same type
- SCAPER p.Arg255Cys Uncertain significance ★★ ⚠ same type
- SCAPER p.Arg500His Uncertain significance ★★ ⚠ same type
- SCAPER p.Arg580Trp Uncertain significance ★★ ⚠ same type
- SCAPER p.Asn460Asp 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/scaper-p-arg259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown