OSBPL9

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

Basic information

Region (hg38): 1:51577179-51798427

Links

ENSG00000117859 ∙ NCBI:114883 ∙ OMIM:606737 ∙ HGNC:16386 ∙ Uniprot:Q96SU4 ∙ 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 OSBPL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBPL9 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						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	26	0	0

Variants in OSBPL9

This is a list of pathogenic ClinVar variants found in the OSBPL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-51617114-G-A		not specified	Uncertain significance (Oct 28, 2023)
1-51617129-G-A		not specified	Uncertain significance (Jun 13, 2023)
1-51652019-G-T		not specified	Uncertain significance (Feb 12, 2024)
1-51652037-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-51669464-G-A		not specified	Uncertain significance (Feb 03, 2022)
1-51714006-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-51745542-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-51746715-T-G		not specified	Uncertain significance (Jan 19, 2022)
1-51746753-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-51750173-T-C		not specified	Uncertain significance (May 23, 2024)
1-51760724-C-T		not specified	Uncertain significance (Aug 01, 2022)
1-51760737-A-T		not specified	Uncertain significance (Mar 16, 2022)
1-51761938-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-51765972-G-A		not specified	Uncertain significance (Oct 02, 2023)
1-51772132-A-G		not specified	Uncertain significance (Feb 23, 2023)
1-51772174-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-51772673-G-A		not specified	Uncertain significance (Jan 27, 2022)
1-51772719-C-G		not specified	Uncertain significance (Jan 26, 2023)
1-51776893-T-A		not specified	Uncertain significance (Mar 16, 2024)
1-51781181-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-51781306-A-T		not specified	Uncertain significance (Jan 17, 2024)
1-51783960-A-G		not specified	Uncertain significance (Nov 22, 2023)
1-51784315-A-G		not specified	Uncertain significance (Dec 12, 2023)
1-51784446-A-G		not specified	Uncertain significance (May 02, 2024)
1-51786565-A-G		not specified	Uncertain significance (Jun 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBPL9	protein_coding	protein_coding	ENST00000447887	24	212039

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0244	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	246	394	0.624	0.0000196	4939
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000150
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000371	0.000370
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000348	0.0000327
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• 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: 0.123

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.507
• hipred: Y
• hipred_score: 0.662
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbpl9

Gene ontology

• Biological process: bile acid biosynthetic process;sterol transport
• Cellular component: Golgi apparatus;cytosol;membrane;late endosome membrane;intracellular membrane-bounded organelle
• Molecular function: lipid binding;sterol transporter activity;sterol binding