SCARB2 p.Val83=
c.249G>A · rs1475517096 · VCV2706601
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00144%, nfe)
Conditions
1
progressive myoclonus epilepsy
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 -2.2 | GERP -4 |
| Overall | ||
| CADD | 1.659 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00144%
European (non-Finnish) · 17/1,179,966 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00105%
17/1,613,948 alleles · very rare
exomes 16/1,461,748 · genomes 1/152,200 · joint denominator
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
- SCARB2
- Protein
- p.Val83=
- Coding
- c.249G>A
- MANE Select
- NM_005506
- dbSNP
- rs1475517096
- Type
- single nucleotide variant
- Location
- chr4:76195733 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 93.01 · 10 PDB
- Residue 83
- a β-strand
Similar variants
- SCARB2 c.704+1G>A Pathogenic ★★ same condition
- SCARB2 p.Arg121Ter Pathogenic/Likely pathogenic ★★ same condition
- SCARB2 p.Arg424Ter Pathogenic ★★ same condition
- SCARB2 p.Gln288Ter Pathogenic ★★ same condition
- SCARB2 p.Gln30Ter Pathogenic/Likely pathogenic ★★ same condition
- SCARB2 c.1188-3T>C Uncertain significance ★★ same condition
- SCARB2 c.612+5G>A Uncertain significance ★★ same condition
- SCARB2 c.704+5G>A Uncertain significance ★★ same condition
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/scarb2-p-val83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown