OSBP

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

Basic information

Region (hg38): 11:59574398-59615774

Links

ENSG00000110048 ∙ NCBI:5007 ∙ OMIM:167040 ∙ HGNC:8503 ∙ Uniprot:P22059 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OSBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	0	24	6	3

Variants in OSBP

This is a list of pathogenic ClinVar variants found in the OSBP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-59576586-G-T		not specified	Uncertain significance (Jul 22, 2022)
11-59576701-T-C		not specified	Uncertain significance (Oct 14, 2023)
11-59576850-A-C		not specified	Uncertain significance (Feb 13, 2024)
11-59576874-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-59578155-G-C		not specified	Uncertain significance (Dec 27, 2023)
11-59580231-G-C		not specified	Uncertain significance (Jun 17, 2022)
11-59580251-C-A		not specified	Uncertain significance (Dec 27, 2023)
11-59580263-C-T		not specified	Uncertain significance (Dec 14, 2023)
11-59581494-G-A		not specified	Uncertain significance (Apr 26, 2024)
11-59594000-G-A			Benign (Sep 19, 2018)
11-59594048-G-A		Short stature	Pathogenic (Nov 18, 2001)
11-59594182-C-T		not specified	Uncertain significance (Mar 15, 2023)
11-59594258-GT-G		OSBP-related disorder	Benign (Dec 31, 2019)
11-59600871-C-T		not specified	Uncertain significance (Feb 13, 2024)
11-59601315-C-G		not specified	Uncertain significance (Dec 16, 2023)
11-59601340-T-C		not specified	Uncertain significance (Mar 07, 2024)
11-59601354-G-A		OSBP-related disorder	Likely benign (-)
11-59601367-T-C		not specified	Uncertain significance (Apr 27, 2023)
11-59601675-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-59601712-G-A		not specified	Uncertain significance (Apr 17, 2024)
11-59601725-C-T		OSBP-related disorder	Likely benign (Feb 22, 2019)
11-59601762-T-C		not specified	Uncertain significance (Jun 29, 2023)
11-59601777-T-C		not specified	Uncertain significance (Mar 15, 2024)
11-59608542-A-G		not specified	Uncertain significance (Jun 22, 2024)
11-59608657-T-C		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBP	protein_coding	protein_coding	ENST00000263847	14	41747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00145	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.58	214	421	0.508	0.0000234	5259
Missense in Polyphen		66	197	0.33502		2305
Synonymous	-0.125	157	155	1.01	0.00000832	1573
Loss of Function	5.42	6	45.5	0.132	0.00000290	473

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000955	0.0000924
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid transporter involved in lipid countertransport between the Golgi complex and membranes of the endoplasmic reticulum: specifically exchanges sterol with phosphatidylinositol 4-phosphate (PI4P), delivering sterol to the Golgi in exchange for PI4P, which is degraded by the SAC1/SACM1L phosphatase in the endoplasmic reticulum (PubMed:24209621). Binds cholesterol and a range of oxysterols including 25-hydroxycholesterol (PubMed:15746430, PubMed:17428193). Cholesterol binding promotes the formation of a complex with PP2A and a tyrosine phosphatase which dephosphorylates ERK1/2, whereas 25-hydroxycholesterol causes its disassembly (PubMed:15746430). Regulates cholesterol efflux by decreasing ABCA1 stability (PubMed:18450749). {ECO:0000269|PubMed:15746430, ECO:0000269|PubMed:17428193, ECO:0000269|PubMed:18450749, ECO:0000269|PubMed:24209621}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Metabolism of steroids;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.256
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.486
• hipred: Y
• hipred_score: 0.662
• ghis: 0.637

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbp

Gene ontology

• Biological process: bile acid biosynthetic process;sterol transport;intracellular cholesterol transport;positive regulation of growth of symbiont in host
• Cellular component: Golgi membrane;nucleus;nucleoplasm;nucleolus;cytoplasm;endoplasmic reticulum membrane;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;membrane;cell junction;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;perinuclear endoplasmic reticulum
• Molecular function: protein binding;oxysterol binding;lipid binding;sterol transporter activity;protein domain specific binding;sterol binding;phosphatidylinositol-4-phosphate binding