OSBP2

protein-coding

oxysterol binding protein 2, the group of Oxysterol binding proteins|Pleckstrin homology domain containing|MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene contains a pleckstrin homology (PH) domain and an oxysterol-binding region. It binds oxysterols such as 7-ketocholesterol and may inhibit their cytotoxicity. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2013]

Previous symbols:

OSBPL1

MANE transcript

NM_030758.4

Inheritance

—

ClinVar variants

U:129B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr22:30,693,782-30,907,824

External References & Databases

Ensembl (ENSG00000184792)

Transcript & Mutation Effects

hg38 • Region Span ~214.0 kb

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GenCC 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 OSBP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030758.4. 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 clinvar	3 clinvar	4 clinvar	8
missense			128 clinvar	5 clinvar	2 clinvar	135
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	129	8	6	143

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030758.4	RefSeq	NP_110385.1	14	MANE Select
ENST00000332585.11	Ensembl	ENSP00000332576.6	14	MANE Select
NM_001282738.2	RefSeq	NP_001269667.1	15	Standard
NM_001282739.2	RefSeq	NP_001269668.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatid development
sterol transport

Molecular Function

protein binding
lipid binding
sterol transporter activity
cholesterol binding
sterol binding

Cellular Component

cytosol
plasma membrane
membrane
intracellular membrane-bounded organelle
perinuclear endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332585
Coding exons: 14
Length: 214043
Individuals with no LoFs: 124819
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 124869
p: 0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.86	438	562	0.780	0.0000350	5899
Missense (PolyPhen)		182	271.46	0.67044		2854
Synonymous	-0.216	255	251	1.02	0.0000164	1839
Loss of Function	4.06	14	42.6	0.329	0.00000215	478

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds 7-ketocholesterol.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.586
RVIS EVS: -0.57
RVIS percentile EVS: 19.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.573

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium