OSBPL6

oxysterol binding protein like 6, the group of Oxysterol binding proteins

Basic information

Region (hg38): 2:178194481-178402893

Links

ENSG00000079156 ∙ NCBI:114880 ∙ OMIM:606734 ∙ HGNC:16388 ∙ Uniprot:Q9BZF3 ∙ 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 OSBPL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBPL6 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			64	2		66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	64	3	0

Variants in OSBPL6

This is a list of pathogenic ClinVar variants found in the OSBPL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-178306203-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-178306204-G-T		not specified	Uncertain significance (May 26, 2024)
2-178306283-G-C		not specified	Uncertain significance (Oct 03, 2024)
2-178324178-G-A		not specified	Uncertain significance (Dec 03, 2024)
2-178324208-C-T		not specified	Uncertain significance (May 31, 2023)
2-178324216-G-A		not specified	Uncertain significance (Nov 23, 2024)
2-178324247-C-A		not specified	Uncertain significance (Sep 10, 2024)
2-178328293-T-C		not specified	Uncertain significance (Nov 26, 2024)
2-178328299-A-C		not specified	Uncertain significance (Jul 22, 2024)
2-178328361-T-G		not specified	Uncertain significance (Jul 13, 2022)
2-178332704-A-C		not specified	Uncertain significance (Jul 07, 2024)
2-178332707-G-A		not specified	Uncertain significance (Feb 09, 2022)
2-178332924-G-A			Likely benign (Apr 01, 2022)
2-178332978-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-178332988-A-G		not specified	Uncertain significance (Aug 29, 2023)
2-178336350-G-A		not specified	Uncertain significance (Oct 03, 2023)
2-178336361-A-G		not specified	Uncertain significance (Aug 27, 2024)
2-178336400-C-A		not specified	Uncertain significance (Oct 25, 2024)
2-178336422-G-A		not specified	Uncertain significance (Mar 30, 2024)
2-178338997-C-A		not specified	Uncertain significance (May 05, 2023)
2-178338997-C-T		not specified	Uncertain significance (Oct 03, 2022)
2-178339705-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-178339706-G-C		not specified	Uncertain significance (Mar 29, 2022)
2-178339706-G-T		not specified	Uncertain significance (Apr 06, 2022)
2-178339708-G-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBPL6	protein_coding	protein_coding	ENST00000392505	24	204953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000111	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	413	528	0.782	0.0000282	6324
Missense in Polyphen		142	252.3	0.56282		3027
Synonymous	1.10	170	189	0.898	0.0000102	1778
Loss of Function	6.36	6	58.5	0.103	0.00000304	670

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.0000329	0.0000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Weakly binds 25-hydroxycholesterol. {ECO:0000269|PubMed:17428193}.
• 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: 0.0949

Intolerance Scores

• loftool: 0.655
• rvis_EVS: -1.3
• rvis_percentile_EVS: 4.92

Haploinsufficiency Scores

• pHI: 0.206
• hipred: Y
• hipred_score: 0.601
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbpl6

Gene ontology

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