SCAPER p.Ile991=
c.2973C>A · rs769052649 · VCV2645583
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00222%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 13.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00222%
South Asian · 2/90,232 alleles
Filtering AF
0.000368%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000559%
9/1,609,648 alleles · very rare
exomes 7/1,457,660 · genomes 2/151,988 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00222% | 45,116 |
| European (non-Finnish) | 0.000594% | 168,297 |
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.Ile991=
- Coding
- c.2973C>A
- MANE Select
- NM_020843
- dbSNP
- rs769052649
- Type
- single nucleotide variant
- Location
- chr15:76471317 (GRCh38)
- Gene constraint
- LOEUF 0.666 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.35 · 2 PDB
- Residue 991
- an α-helix
Similar variants
- SCAPER p.Ile991Metfs Pathogenic ★ 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
- SCAPER p.Asp224Asn 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-ile991 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown