OSBPL2 p.Pro181=
c.543C>G · rs139386621 · VCV1217597
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.304%, afr)
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 -8.9 | GERP -5.3 |
| Overall | ||
| CADD | 0.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.304%
African / African-American · 228/75,058 alleles
Filtering AF
0.271%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.259%
Overall
0.0155%
250/1,614,182 alleles · rare
exomes 123/1,461,846 · genomes 127/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.304% | 329 |
| Admixed American | 0.01% | 10,004 |
| South Asian | 0.00988% | 10,121 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| European (non-Finnish) | 0.000254% | 393,331 |
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
- OSBPL2
- Protein
- p.Pro181=
- Coding
- c.543C>G
- MANE Select
- NM_144498
- dbSNP
- rs139386621
- Type
- single nucleotide variant
- Location
- chr20:62279208 (GRCh38)
- Gene constraint
- LOEUF 0.467 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.92 · 1 PDB
- Residue 181
- a β-strand
Similar variants
- OSBPL2 p.Ala442Val Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Arg434Trp Uncertain significance ★★ same type
- OSBPL2 p.Asp475Asn Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Gln125Pro Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Gln58Pro Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Glu284Gly Uncertain significance ★★ same type
- OSBPL2 p.Gly149Ser Uncertain significance ★★ ⚠ same type
- OSBPL2 p.Gly245Arg 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/osbpl2-p-pro181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown