OSBP2

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

Basic information

Region (hg38): 22:30693781-30907824

Previous symbols: [ "OSBPL1" ]

Links

ENSG00000184792 ∙ NCBI:23762 ∙ OMIM:606729 ∙ HGNC:8504 ∙ Uniprot:Q969R2 ∙ 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 OSBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBP2 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				2	6	8
missense			36	2	2	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	36	4	10

Variants in OSBP2

This is a list of pathogenic ClinVar variants found in the OSBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30694919-G-A		not specified	Uncertain significance (Jul 12, 2022)
22-30694984-G-C			Benign (Nov 20, 2018)
22-30695087-C-T		not specified	Uncertain significance (Apr 08, 2024)
22-30695144-A-G		not specified	Uncertain significance (Oct 05, 2023)
22-30695167-G-A			Likely benign (Jan 01, 2023)
22-30695169-C-T		not specified	Uncertain significance (Jan 17, 2024)
22-30695175-A-G		not specified	Uncertain significance (Feb 12, 2024)
22-30695278-A-G			Benign (Oct 19, 2017)
22-30695318-C-T			Benign (Dec 31, 2019)
22-30695409-C-G		not specified	Uncertain significance (Mar 19, 2024)
22-30695458-C-G		not specified	Uncertain significance (Apr 25, 2023)
22-30695477-C-T		not specified	Uncertain significance (Mar 04, 2024)
22-30741268-G-C		not specified	Likely benign (Aug 16, 2021)
22-30741339-A-G		not specified	Uncertain significance (Jun 01, 2023)
22-30870477-A-C		not specified	Uncertain significance (Apr 22, 2024)
22-30870528-C-T		not specified	Uncertain significance (Oct 02, 2023)
22-30870559-T-C			Benign (Mar 07, 2019)
22-30870565-C-T			Benign (Nov 15, 2018)
22-30870587-G-A		not specified	Uncertain significance (Dec 01, 2023)
22-30870601-C-G		not specified	Uncertain significance (Jan 24, 2024)
22-30870603-C-T		not specified	Uncertain significance (Apr 08, 2024)
22-30870642-G-A		not specified	Uncertain significance (Aug 12, 2021)
22-30870665-T-G		not specified	Uncertain significance (May 17, 2023)
22-30887453-G-A		not specified	Uncertain significance (Aug 15, 2023)
22-30887463-G-A		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBP2	protein_coding	protein_coding	ENST00000332585	14	214043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000434	1.00	124819	0	50	124869	0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	438	562	0.780	0.0000350	5899
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000187
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.000334	0.000333
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000272	0.000265
Middle Eastern	0.000334	0.000333
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.733
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.573

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbp2
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: spermatid development;sterol transport
• Cellular component: cytosol;plasma membrane;membrane;intracellular membrane-bounded organelle;perinuclear endoplasmic reticulum;apical dendrite
• Molecular function: protein binding;lipid binding;sterol transporter activity;cholesterol binding;sterol binding