SCARB1 p.Pro352=
c.1056G>A · rs372663606 · VCV2058875
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.09%, amr)
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 -15 | GERP -3 |
| Overall | ||
| CADD | 2.248 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.09%
Admixed American · 54/60,008 alleles
Filtering AF
0.0708%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0639%
Overall
0.0191%
308/1,613,932 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.09% | 1,111 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,716 |
| European (non-Finnish) | 0.0188% | 5,315 |
| African / African-American | 0.012% | 8,324 |
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.Pro352=
- Coding
- c.1056G>A
- MANE Select
- NM_005505
- dbSNP
- rs372663606
- Type
- single nucleotide variant
- Location
- chr12:124800196 (GRCh38)
- Gene constraint
- LOEUF 0.71 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.25
- Residue 352
- 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-pro352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown