SCAPER p.Ser832=
c.2496A>G · rs117552750 · VCV3041971
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.83%, nfe)
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 -2.5 | GERP -3.1 |
| Overall | ||
| CADD | 4.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.83%
European (non-Finnish) · 56,935/1,179,366 alleles
Filtering AF
4.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.78%
Overall
4.09%
65,960/1,613,362 alleles · low-frequency
exomes 61,261/1,461,074 · genomes 4,699/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 4.83% | 21 |
| Middle Eastern | 4.47% | 22 |
| Remaining individualsnot grpmax-eligible | 3.95% | 25 |
| Ashkenazi Jewishnot grpmax-eligible | 3.57% | 28 |
| Admixed American | 3.17% | 32 |
| Finnishnot grpmax-eligible | 2.21% | 45 |
| South Asian | 1.51% | 66 |
| African / African-American | 0.705% | 142 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| East Asian | 0.0156% | 6,408 |
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.Ser832=
- Coding
- c.2496A>G
- MANE Select
- NM_020843
- dbSNP
- rs117552750
- Type
- single nucleotide variant
- Location
- chr15:76701770 (GRCh38)
- Gene constraint
- LOEUF 0.666 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.35 · 2 PDB
- Residue 832
- a modified residue (phosphoserine)
Similar variants
- SCAPER p.Ser832Ter Likely 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-ser832 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown