OSBPL1A

oxysterol binding protein like 1A, the group of Ankyrin repeat domain containing|Oxysterol binding proteins

Basic information

Region (hg38): 18:24162045-24397880

Previous symbols: [ "OSBPL1B" ]

Links

ENSG00000141447 ∙ NCBI:114876 ∙ OMIM:606730 ∙ HGNC:16398 ∙ Uniprot:Q9BXW6 ∙ 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 OSBPL1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSBPL1A 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			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	0	0

Variants in OSBPL1A

This is a list of pathogenic ClinVar variants found in the OSBPL1A region.

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

Position	Type	Phenotype	Significance	ClinVar
18-24163268-C-T		not specified	Uncertain significance (Oct 04, 2022)
18-24165104-C-T		not specified	Uncertain significance (Jun 23, 2023)
18-24165105-G-A		not specified	Uncertain significance (Aug 02, 2022)
18-24166614-C-T		not specified	Uncertain significance (Feb 27, 2024)
18-24167349-G-A		not specified	Uncertain significance (Aug 11, 2021)
18-24167427-A-T		not specified	Uncertain significance (Apr 19, 2024)
18-24170376-T-C		not specified	Uncertain significance (Sep 17, 2021)
18-24170380-C-T		not specified	Uncertain significance (Jun 27, 2022)
18-24170404-T-C		not specified	Uncertain significance (Nov 30, 2022)
18-24170442-A-G		not specified	Uncertain significance (Jan 04, 2024)
18-24171461-C-T		not specified	Uncertain significance (May 13, 2024)
18-24172478-T-C		not specified	Uncertain significance (Jun 12, 2023)
18-24178102-G-C		not specified	Uncertain significance (Jun 23, 2023)
18-24178193-T-C		not specified	Uncertain significance (Mar 16, 2022)
18-24179742-C-G		not specified	Uncertain significance (Aug 15, 2023)
18-24179835-A-G		not specified	Uncertain significance (Aug 22, 2023)
18-24181167-G-C		not specified	Uncertain significance (Mar 01, 2023)
18-24181183-T-C		not specified	Uncertain significance (Apr 17, 2023)
18-24225187-C-T		not specified	Uncertain significance (Mar 29, 2024)
18-24239249-C-T		not specified	Uncertain significance (Sep 22, 2022)
18-24280946-T-C		not specified	Uncertain significance (Mar 19, 2024)
18-24303651-C-A		not specified	Uncertain significance (Feb 26, 2024)
18-24303655-C-G		not specified	Uncertain significance (Dec 22, 2023)
18-24303675-T-C		not specified	Uncertain significance (Nov 13, 2023)
18-24312006-G-C		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSBPL1A	protein_coding	protein_coding	ENST00000319481	27	235837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-7	1.00	125076	1	671	125748	0.00268

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	405	503	0.805	0.0000256	6304
Missense in Polyphen		109	177.33	0.61467		2141
Synonymous	0.00543	182	182	0.999	0.00000988	1685
Loss of Function	4.62	23	62.4	0.369	0.00000326	731

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00607	0.00606
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000326	0.000326
Finnish	0.000279	0.000277
European (Non-Finnish)	0.00372	0.00365
Middle Eastern	0.000326	0.000326
South Asian	0.00185	0.00180
Other	0.00418	0.00392

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds phospholipids; exhibits strong binding to phosphatidic acid and weak binding to phosphatidylinositol 3- phosphate (By similarity). Stabilizes GTP-bound RAB7A on late endosomes/lysosomes and alters functional properties of late endocytic compartments via its interaction with RAB7A (PubMed:16176980). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193). {ECO:0000250, ECO:0000269|PubMed:16176980, 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: 0.110

Intolerance Scores

• loftool: 0.877
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.83

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.554
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.638

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Osbpl1a

Gene ontology

• Biological process: bile acid biosynthetic process;cholesterol metabolic process;sterol transport;vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II
• Cellular component: late endosome;cytosol;membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;phospholipid binding;lipid binding;sterol transporter activity;cholesterol binding;sterol binding