SCARB1 p.Pro322=
c.966G>A · VCV4798284
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00933%, afr)
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 -20 | GERP -3.6 |
| Overall | ||
| CADD | 0.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00933%
African / African-American · 7/75,032 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00308%
Overall
0.00254%
41/1,614,124 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00933% | 10,719 |
| South Asian | 0.00549% | 18,216 |
| Admixed American | 0.00333% | 30,003 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
| East Asian | 0.00223% | 44,874 |
| European (non-Finnish) | 0.00203% | 49,168 |
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
- SCARB1
- Protein
- p.Pro322=
- Coding
- c.966G>A
- MANE Select
- NM_005505
- Type
- single nucleotide variant
- Location
- chr12:124807804 (GRCh38)
- Gene constraint
- LOEUF 0.71 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.25
- Residue 322
- a disulfide bond
Similar variants
- SCARB1 p.Arg45Cys Uncertain significance ★★ ⚠ same type
- SCARB1 p.Lys482Asn Uncertain significance ★★ same type
- SCARB1 p.Met136Lys Uncertain significance ★★ ⚠ same type
- SCARB1 p.Pro48Ala Uncertain significance ★★ ⚠ same type
- SCARB1 c.1128+73C>A Benign ★★ same type
- SCARB1 c.1202+80G>A Likely benign ★★ same type
- SCARB1 c.1255-41C>G Benign ★★ same type
- SCARB1 c.1255-52T>G Benign ★★ 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/scarb1-p-pro322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown