OSBPL6

protein-coding

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

Gene summary

This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

MANE transcript

NM_032523.4

Inheritance

—

ClinVar variants

U:121B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr2:178,194,481-178,402,893

External References & Databases

Ensembl (ENSG00000079156)

Transcript & Mutation Effects

hg38 • Region Span ~208.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OSBPL6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 124

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032523.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			120 clinvar	1 clinvar		121
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	121	2	0	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 177 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032523.4	RefSeq	NP_115912.1	23	MANE Select
ENST00000190611.9	Ensembl	ENSP00000190611.4	23	MANE Select
NM_001201480.2	RefSeq	NP_001188409.1	24	Standard
NM_001201481.2	RefSeq	NP_001188410.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Synthesis of bile acids and bile salts
Bile acid and bile salt metabolism
Metabolism of steroids

Biological Process

bile acid biosynthetic process
sterol transport

Molecular Function

protein binding
lipid binding
sterol transporter activity
cholesterol binding
sterol binding

Cellular Component

endoplasmic reticulum membrane
cytosol
plasma membrane
membrane
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392505
Coding exons: 24
Length: 204953
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125748
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.78	413	528	0.782	0.0000282	6324
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0949

Intolerance Scores

LoFtool: 0.655
RVIS EVS: -1.3
RVIS percentile EVS: 4.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.884

Gene Damage Prediction

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