SCAPER p.Val393=
c.1179A>G · VCV4925993
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00568%, 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 -0.2 | GERP -2.1 |
| Overall | ||
| CADD | 3.303 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00568%
European (non-Finnish) · 67/1,179,444 alleles
Filtering AF
0.00454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00417%
Overall
0.00422%
68/1,613,144 alleles · very rare
exomes 65/1,461,050 · genomes 3/152,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00568% | 17,604 |
| African / African-American | 0.00133% | 74,910 |
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.Val393=
- Coding
- c.1179A>G
- MANE Select
- NM_020843
- Type
- single nucleotide variant
- Location
- chr15:76771811 (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-val393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown