OSBPL10
protein-codingoxysterol binding protein like 10, the group of Oxysterol binding proteins|Pleckstrin homology domain containing
Gene summary
This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Like most members, the encoded protein contains an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~419.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to OSBPL10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017784.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 95 | 8 | 103 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 97 | 9 | 0 | 106 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060254.2 | 12 | MANE Select | |
| Ensembl | ENSP00000379804.2 | 12 | MANE Select | |
| RefSeq | NP_001167531.1 | 11 | Standard | |
| Ensembl | ENSP00000399200.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Acyl chain remodelling of PS
- Glycerophospholipid biosynthesis
- Phospholipid metabolism
Biological Process
- phospholipid transport
- sterol transport
- phosphatidylserine acyl-chain remodeling
Molecular Function
- phosphatidylserine binding
- phospholipid transporter activity
- lipid binding
- sterol transporter activity
- cholesterol binding
Cellular Component
- Golgi apparatus
- cytosol
- cytoskeleton
- membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000396556
- Coding exons
- 12
- Length
- 419691
- Individuals with no LoFs
- 125683
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 65
- Defined
- 125748
- p
- 0.000258
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.870 | 369 | 419 | 0.880 | 0.0000240 | 4955 |
| Missense (PolyPhen) | 125 | 175.36 | 0.71283 | 2078 | ||
| Synonymous | -0.108 | 172 | 170 | 1.01 | 0.0000106 | 1530 |
| Loss of Function | 3.01 | 17 | 36.6 | 0.464 | 0.00000212 | 403 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0.0019 | 0.0019 | notable |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable lipid transporter involved in lipid countertransport between the endoplasmic reticulum and the plasma membrane. Its ability to bind phosphatidylserine, suggests that it specifically exchanges phosphatidylserine with phosphatidylinositol 4-phosphate (PI4P), delivering phosphatidylserine to the plasma membrane in exchange for PI4P (PubMed:23934110) (Probable). Plays a role in negative regulation of lipid biosynthesis (PubMed:19554302). Negatively regulates APOB secretion from hepatocytes (PubMed:19554302, PubMed:22906437). Binds cholesterol and acidic phospholipids (PubMed:22906437). Also binds 25-hydroxycholesterol (PubMed:17428193). Binds phosphatidylserine (PubMed:23934110). {ECO:0000269|PubMed:17428193, ECO:0000269|PubMed:19554302, ECO:0000269|PubMed:22906437, ECO:0000269|PubMed:23934110, ECO:0000305}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- LoFtool
- 0.786
- RVIS EVS
- -0.77
- RVIS percentile EVS
- 13.1
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.664
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |