OSBP p.Ser351=
c.1053C>T · rs145963268 · VCV3040584
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.103%, 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 -0.16 | GERP -4.6, phastCons 0.003 |
| Overall | ||
| CADD | 8.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
Admixed American · 62/59,980 alleles
Filtering AF
0.0827%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0752%
Overall
0.00856%
138/1,612,900 alleles · rare
exomes 121/1,460,732 · genomes 17/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.103% | 967 |
| African / African-American | 0.0213% | 4,686 |
| Middle Eastern | 0.0165% | 6,054 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| South Asian | 0.00988% | 10,118 |
| European (non-Finnish) | 0.00314% | 31,865 |
| Finnishnot grpmax-eligible | 0.00313% | 31,983 |
| East Asian | 0.00223% | 44,868 |
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
- OSBP
- Protein
- p.Ser351=
- Coding
- c.1053C>T
- MANE Select
- NM_002556
- dbSNP
- rs145963268
- Type
- single nucleotide variant
- Location
- chr11:59601354 (GRCh38)
- Gene constraint
- LOEUF 0.394 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.40 · 2 PDB
- Residue 351
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- OSBP c.1557+10C>T Benign ★★ same type
- OSBP p.Glu189= Benign ★★ same type
- OSBP p.Ala271Ser Uncertain significance ★ ⚠ same type
- OSBP p.Ala90Ser Uncertain significance ★ ⚠ same type
- OSBP p.Arg171His Uncertain significance ★ ⚠ same type
- OSBP p.Arg266Gly Uncertain significance ★ ⚠ same type
- OSBP p.Arg376His Uncertain significance ★ ⚠ same type
- OSBP p.Arg462Gln 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/osbp-p-ser351 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown