OSBPL9

protein-coding

oxysterol binding protein like 9, the group of Oxysterol binding proteins|Pleckstrin homology domain containing

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, although some members contain only the sterol-binding domain. This family member functions as a cholesterol transfer protein that regulates Golgi structure and function. Multiple transcript variants, most of which encode distinct isoforms, have been identified. Related pseudogenes have been identified on chromosomes 3, 11 and 12. [provided by RefSeq, Jul 2010]

MANE transcript

NM_024586.6

Inheritance

AD, AR

ClinVar variants

U:82

Top phenotype

Infantile epilepsy syndrome

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr1:51,577,179-51,798,427

External References & Databases

Ensembl (ENSG00000117859)

Transcript & Mutation Effects

hg38 • Region Span ~221.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

multiple congenital anomalies/dysmorphic syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019042

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OSBPL9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 66

Infantile epilepsy syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024586.6. 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			3 clinvar			3
missense			69 clinvar			69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	82	0	0	82

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 93 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024586.6	RefSeq	NP_078862.4	24	MANE Select
ENST00000428468.6	Ensembl	ENSP00000407168.1	24	MANE Select
NM_001330580.2	RefSeq	NP_001317509.1	17	Standard
NM_001350208.2	RefSeq	NP_001337137.1	16	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

lipid binding
sterol transporter activity
sterol binding

Cellular Component

Golgi apparatus
cytosol
membrane
late endosome membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000447887
Coding exons: 24
Length: 212039
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.66	246	394	0.624	0.0000196	4939
Missense (PolyPhen)		85	198.5	0.42821		2463
Synonymous	0.689	126	136	0.925	0.00000706	1329
Loss of Function	5.25	8	46.7	0.171	0.00000228	582

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000035	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.411
RVIS EVS: -0.2
RVIS percentile EVS: 38.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.903

Gene Damage Prediction

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