OSBPL5

oxysterol binding protein like 5, the group of Pleckstrin homology domain containing|Oxysterol binding proteins

Basic information

Region (hg38): 11:3087106-3166739

Links

ENSG00000021762 ∙ NCBI:114879 ∙ OMIM:606733 ∙ HGNC:16392 ∙ Uniprot:Q9H0X9 ∙ 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 OSBPL5 gene.

• Inborn genetic diseases (59 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBPL5 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				1	2	3
missense			55	4	3	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					4	4
non coding					2	2
Total	0	0	55	5	7

Variants in OSBPL5

This is a list of pathogenic ClinVar variants found in the OSBPL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-3088219-G-A		not specified	Likely benign (Nov 08, 2022)
11-3088263-C-A		not specified	Uncertain significance (Jun 22, 2021)
11-3088317-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-3089859-G-C		not specified	Uncertain significance (Dec 15, 2023)
11-3089877-A-G		not specified	Uncertain significance (Oct 05, 2021)
11-3089889-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-3089906-C-T		not specified	Uncertain significance (Jul 06, 2021)
11-3089910-G-A		not specified	Uncertain significance (Aug 04, 2023)
11-3089912-G-A		not specified	Uncertain significance (Sep 29, 2022)
11-3089927-C-A		not specified	Uncertain significance (Jan 10, 2023)
11-3089927-C-T		not specified	Uncertain significance (Sep 09, 2021)
11-3089946-C-A		not specified	Uncertain significance (Aug 12, 2021)
11-3090573-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-3090632-G-A		not specified	Uncertain significance (Mar 22, 2023)
11-3090648-C-T		not specified	Uncertain significance (Aug 26, 2022)
11-3090677-C-T		not specified	Uncertain significance (Jun 12, 2023)
11-3092466-G-A			Benign (Dec 31, 2019)
11-3092479-C-T		not specified	Likely benign (Mar 06, 2023)
11-3092500-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-3092545-C-T		not specified	Uncertain significance (Jul 30, 2023)
11-3092873-T-C		not specified	Uncertain significance (Dec 19, 2022)
11-3092876-C-A		not specified	Uncertain significance (Feb 01, 2023)
11-3092876-C-T		OSBPL5-related disorder	Likely benign (Dec 01, 2022)
11-3092894-G-A		not specified	Uncertain significance (Jan 26, 2023)
11-3092898-T-A		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBPL5	protein_coding	protein_coding	ENST00000263650	21	79624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000465	1.00	125673	0	22	125695	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.665	500	544	0.920	0.0000364	5603
Missense in Polyphen		165	212.32	0.77712		2164
Synonymous	0.730	234	249	0.941	0.0000182	1747
Loss of Function	4.02	18	48.1	0.374	0.00000248	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000256
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000528
Middle Eastern	0.0000544	0.0000544
South Asian	0.000234	0.000229
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid transporter involved in lipid countertransport between the endoplasmic reticulum and the plasma membrane: specifically exchanges phosphatidylserine with phosphatidylinositol 4-phosphate (PI4P), delivering phosphatidylserine to the plasma membrane in exchange for PI4P, which is degraded by the SAC1/SACM1L phosphatase in the endoplasmic reticulum. Binds phosphatidylserine and PI4P in a mutually exclusive manner (PubMed:23934110, PubMed:26206935). May cooperate with NPC1 to mediate the exit of cholesterol from endosomes/lysosomes (PubMed:21220512). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193). {ECO:0000269|PubMed:17428193, ECO:0000269|PubMed:21220512, ECO:0000269|PubMed:23934110, ECO:0000269|PubMed:26206935}.
• Pathway: Cholesterol metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0928

Intolerance Scores

• loftool: 0.695
• rvis_EVS: -0.52
• rvis_percentile_EVS: 20.96

Haploinsufficiency Scores

• pHI: 0.0921
• hipred: N
• hipred_score: 0.414
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.856

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbpl5

Gene ontology

• Biological process: Golgi to plasma membrane transport;cholesterol metabolic process;phospholipid transport;cholesterol transport;phosphatidylserine acyl-chain remodeling
• Cellular component: endoplasmic reticulum membrane;cytosol;membrane;integral component of membrane;intracellular membrane-bounded organelle;endoplasmic reticulum-plasma membrane contact site
• Molecular function: phosphatidylserine binding;phospholipid transporter activity;oxysterol binding;lipid binding;sterol transporter activity;cholesterol binding;sterol binding;phosphatidylinositol-4-phosphate binding