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.

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.

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						0
missense			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	2	0

Variants in OSBPL3

This is a list of pathogenic ClinVar variants found in the OSBPL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-24800272-C-T		not specified	Uncertain significance (Aug 23, 2021)
7-24804361-G-A		not specified	Uncertain significance (May 17, 2023)
7-24804379-G-C		not specified	Uncertain significance (Dec 21, 2023)
7-24806897-T-C		not specified	Uncertain significance (May 28, 2023)
7-24809893-C-T		not specified	Uncertain significance (Aug 10, 2021)
7-24809938-C-G		not specified	Uncertain significance (Mar 31, 2024)
7-24815145-C-T		not specified	Uncertain significance (Dec 06, 2021)
7-24815171-G-A		not specified	Uncertain significance (Dec 28, 2023)
7-24815186-T-C		not specified	Uncertain significance (Jan 05, 2022)
7-24816611-C-A		not specified	Uncertain significance (Jan 24, 2023)
7-24816614-G-A		not specified	Uncertain significance (May 10, 2024)
7-24816680-A-G		not specified	Uncertain significance (May 03, 2023)
7-24820208-G-T		not specified	Uncertain significance (Sep 17, 2021)
7-24820238-C-T		not specified	Uncertain significance (Mar 16, 2022)
7-24830802-C-T		not specified	Uncertain significance (Mar 02, 2023)
7-24830818-T-C		not specified	Uncertain significance (Mar 29, 2024)
7-24830877-G-A		not specified	Uncertain significance (Nov 22, 2023)
7-24834670-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-24834670-G-C		not specified	Uncertain significance (Oct 29, 2021)
7-24834700-C-T		not specified	Uncertain significance (Jun 21, 2022)
7-24834709-G-A		not specified	Uncertain significance (Jun 13, 2024)
7-24834734-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-24842304-A-G		not specified	Uncertain significance (Apr 09, 2024)
7-24849085-C-A		not specified	Uncertain significance (Oct 27, 2022)
7-24849110-C-T		not specified	Uncertain significance (Dec 28, 2022)

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