OSBPL3

oxysterol binding protein like 3, the group of Oxysterol binding proteins|Pleckstrin homology domain containing

Basic information

Region (hg38): 7:24796540-24981634

Previous symbols: [ "OSBP3" ]

Links

ENSG00000070882

∙ NCBI:26031 ∙ OMIM:606732 ∙ HGNC:16370 ∙ Uniprot:Q9H4L5 ∙ 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 OSBPL3 gene.

not_specified (106 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBPL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015550.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			103 clinvar	3 clinvar		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	103	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBPL3	protein_coding	protein_coding	ENST00000313367	22	185096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000159	1.00	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	419	493	0.851	0.0000269	5849
Missense in Polyphen		107	155.18	0.68952		1793
Synonymous	-1.20	217	196	1.11	0.0000118	1626
Loss of Function	4.29	20	54.0	0.370	0.00000278	634

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000149
Middle Eastern	0.000382	0.000381
South Asian	0.000265	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Phosphoinositide-binding protein which associates with both cell and endoplasmic reticulum (ER) membranes (PubMed:16143324). Can bind to the ER membrane protein VAPA and recruit VAPA to plasma membrane sites, thus linking these intracellular compartments (PubMed:25447204). The ORP3-VAPA complex stimulates RRAS signaling which in turn attenuates integrin beta-1 (ITGB1) activation at the cell surface (PubMed:18270267, PubMed:25447204). With VAPA, may regulate ER morphology (PubMed:16143324). Has a role in regulation of the actin cytoskeleton, cell polarity and cell adhesion (PubMed:18270267). Binds to phosphoinositides with preference for PI(3,4)P2 and PI(3,4,5)P3 (PubMed:16143324). Also binds 25- hydroxycholesterol and cholesterol (PubMed:17428193). {ECO:0000269|PubMed:16143324, ECO:0000269|PubMed:17428193, ECO:0000269|PubMed:18270267, ECO:0000269|PubMed:25447204}.;
Pathway: Metabolism of lipids;Metabolism;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Metabolism of steroids (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.750
rvis_EVS: -0.66
rvis_percentile_EVS: 16.07

Haploinsufficiency Scores

pHI: 0.110
hipred: N
hipred_score: 0.492
ghis: 0.526

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.762

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Osbpl3
Phenotype: skeleton phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: bile acid biosynthetic process;sterol transport
Cellular component: endoplasmic reticulum membrane;cytosol;plasma membrane;membrane;nuclear membrane;filopodium tip;intracellular membrane-bounded organelle;perinuclear endoplasmic reticulum
Molecular function: protein binding;lipid binding;sterol transporter activity;cholesterol binding;sterol binding