OSBPL10

oxysterol binding protein like 10, the group of Oxysterol binding proteins|Pleckstrin homology domain containing

Basic information

Region (hg38): 3:31657911-32077580

Links

ENSG00000144645 ∙ NCBI:114884 ∙ OMIM:606738 ∙ HGNC:16395 ∙ Uniprot:Q9BXB5 ∙ 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 OSBPL10 gene.

• Inborn genetic diseases (28 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBPL10 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		1
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in OSBPL10

This is a list of pathogenic ClinVar variants found in the OSBPL10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-31664095-T-C		not specified	Uncertain significance (Jan 10, 2022)
3-31664114-G-A		not specified	Uncertain significance (Oct 04, 2023)
3-31664120-T-A		not specified	Likely benign (Jan 04, 2024)
3-31664165-G-A		not specified	Uncertain significance (Aug 15, 2023)
3-31664201-G-A		not specified	Uncertain significance (Dec 22, 2023)
3-31668649-C-G		not specified	Uncertain significance (Aug 17, 2022)
3-31668650-C-G		not specified	Uncertain significance (Aug 17, 2022)
3-31668706-T-C		not specified	Uncertain significance (Aug 14, 2023)
3-31668708-G-A		not specified	Uncertain significance (Dec 04, 2023)
3-31668763-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-31670842-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-31670879-C-T		not specified	Uncertain significance (Jul 06, 2021)
3-31670900-A-T		not specified	Uncertain significance (Sep 20, 2023)
3-31670954-C-T		not specified	Uncertain significance (Jan 17, 2024)
3-31683721-C-T		not specified	Likely benign (Nov 02, 2023)
3-31683808-C-T		not specified	Uncertain significance (Mar 02, 2023)
3-31683811-C-T		not specified	Uncertain significance (Oct 18, 2021)
3-31683823-C-T		not specified	Uncertain significance (Apr 27, 2022)
3-31683843-C-T		not specified	Likely benign (May 25, 2022)
3-31683886-C-T		not specified	Uncertain significance (Nov 27, 2023)
3-31683943-C-T		not specified	Uncertain significance (Jul 12, 2022)
3-31684001-C-G		not specified	Uncertain significance (Dec 27, 2022)
3-31684003-C-T		not specified	Uncertain significance (Dec 12, 2023)
3-31684021-C-T		not specified	Uncertain significance (Mar 14, 2023)
3-31702414-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBPL10	protein_coding	protein_coding	ENST00000396556	12	419691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.33e-7	0.999	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.870	369	419	0.880	0.0000240	4955
Missense in Polyphen		125	175.36	0.71283		2078
Synonymous	-0.108	172	170	1.01	0.0000106	1530
Loss of Function	3.01	17	36.6	0.464	0.00000212	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00189	0.00189
East Asian	0.000218	0.000217
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000218	0.000217
South Asian	0.000196	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable lipid transporter involved in lipid countertransport between the endoplasmic reticulum and the plasma membrane. Its ability to bind phosphatidylserine, suggests that it specifically exchanges phosphatidylserine with phosphatidylinositol 4-phosphate (PI4P), delivering phosphatidylserine to the plasma membrane in exchange for PI4P (PubMed:23934110) (Probable). Plays a role in negative regulation of lipid biosynthesis (PubMed:19554302). Negatively regulates APOB secretion from hepatocytes (PubMed:19554302, PubMed:22906437). Binds cholesterol and acidic phospholipids (PubMed:22906437). Also binds 25-hydroxycholesterol (PubMed:17428193). Binds phosphatidylserine (PubMed:23934110). {ECO:0000269|PubMed:17428193, ECO:0000269|PubMed:19554302, ECO:0000269|PubMed:22906437, ECO:0000269|PubMed:23934110, ECO:0000305}.
• Pathway: Metabolism of lipids;Metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.786
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.1

Haploinsufficiency Scores

• pHI: 0.472
• hipred: N
• hipred_score: 0.377
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbpl10

Gene ontology

• Biological process: phospholipid transport;sterol transport;phosphatidylserine acyl-chain remodeling
• Cellular component: Golgi apparatus;cytosol;cytoskeleton;membrane;intracellular membrane-bounded organelle
• Molecular function: phosphatidylserine binding;phospholipid transporter activity;lipid binding;sterol transporter activity;cholesterol binding;sterol binding