SCAPER p.Pro1199=
c.3597C>T · rs150628682 · VCV778556
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.225%, afr)
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 0.25 | GERP -0.91, phastCons 0.002 |
| Overall | ||
| CADD | 4.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.225%
African / African-American · 169/75,038 alleles
Filtering AF
0.197%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.187%
Overall
0.0133%
214/1,613,706 alleles · rare
exomes 111/1,461,446 · genomes 103/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.225% | 444 |
| Middle Eastern | 0.148% | 674 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,124 |
| Admixed American | 0.0234% | 4,281 |
| European (non-Finnish) | 0.00017% | 589,915 |
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.Pro1199=
- Coding
- c.3597C>T
- MANE Select
- NM_020843
- dbSNP
- rs150628682
- Type
- single nucleotide variant
- Location
- chr15:76381486 (GRCh38)
- Gene constraint
- LOEUF 0.666 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.35 · 2 PDB
Similar variants
- 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
- SCAPER p.Asp224Asn Uncertain significance ★★ ⚠ same type
- SCAPER p.Gln1353His 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-pro1199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown