SCARB1

scavenger receptor class B member 1, the group of Scavenger receptors

Basic information

Region (hg38): 12:124776855-124882668

Previous symbols: [ "CD36L1" ]

Links

ENSG00000073060 ∙ NCBI:949 ∙ OMIM:601040 ∙ HGNC:1664 ∙ Uniprot:Q8WTV0 ∙ 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 SCARB1 gene.

• not provided (101 variants)
• Inborn genetic diseases (13 variants)
• High density lipoprotein cholesterol level quantitative trait locus 6 (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCARB1 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				15	9	24
missense			34	4	2	40
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			3	2	2	7
non coding				20	24	44
Total	1	0	35	39	35

Variants in SCARB1

This is a list of pathogenic ClinVar variants found in the SCARB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-124778493-C-T			Benign (Apr 01, 2019)
12-124778515-C-T		SCARB1-related disorder	Benign (Jul 08, 2019)
12-124778572-G-A		SCARB1-related disorder	Likely benign (Mar 06, 2019)
12-124778698-G-A			Benign (May 27, 2019)
12-124778729-G-A			Likely benign (Apr 21, 2019)
12-124782605-C-T			Likely benign (Aug 16, 2019)
12-124782688-G-C			Uncertain significance (Mar 31, 2022)
12-124782709-A-G		not specified	Uncertain significance (Apr 25, 2022)
12-124782749-C-T			Likely benign (Apr 11, 2022)
12-124782783-C-A		not specified	Uncertain significance (Jun 28, 2023)
12-124782806-T-G			Uncertain significance (Oct 13, 2023)
12-124782827-G-A			Likely benign (Oct 12, 2021)
12-124782828-C-T			Likely benign (Aug 10, 2023)
12-124786183-A-G			Likely benign (Apr 21, 2019)
12-124786227-A-G			Benign (Oct 01, 2018)
12-124786399-G-A			Likely benign (Mar 31, 2021)
12-124786420-G-A			Likely benign (Jan 20, 2024)
12-124786425-G-A			Uncertain significance (May 18, 2021)
12-124786428-C-G			Uncertain significance (Sep 10, 2021)
12-124786501-G-A			Likely benign (Sep 29, 2023)
12-124786507-A-G			Likely benign (Sep 27, 2022)
12-124786513-C-T		SCARB1-related disorder	Likely benign (Apr 25, 2019)
12-124786544-G-C			Benign (Oct 01, 2018)
12-124786555-A-C			Benign (Oct 17, 2018)
12-124786572-C-T			Benign (Apr 21, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCARB1	protein_coding	protein_coding	ENST00000261693	12	105813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0662	0.934	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	223	301	0.741	0.0000186	3358
Missense in Polyphen		61	90.409	0.67471		1035
Synonymous	-0.208	130	127	1.02	0.00000898	965
Loss of Function	3.38	7	25.3	0.276	0.00000118	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000457	0.000457
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for different ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells (PubMed:12016218, PubMed:12519372, PubMed:21226579). Receptor for HDL, mediating selective uptake of cholesteryl ether and HDL-dependent cholesterol efflux (PubMed:26965621). Also facilitates the flux of free and esterified cholesterol between the cell surface and apoB-containing lipoproteins and modified lipoproteins, although less efficiently than HDL. May be involved in the phagocytosis of apoptotic cells, via its phosphatidylserine binding activity (PubMed:12016218). {ECO:0000269|PubMed:12016218, ECO:0000269|PubMed:12519372, ECO:0000269|PubMed:16020694, ECO:0000269|PubMed:21226579, ECO:0000269|PubMed:26965621}.
• Pathway: Cortisol synthesis and secretion - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Bile secretion - Homo sapiens (human);Vitamin digestion and absorption - Homo sapiens (human);Phagosome - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Statin Pathway, Pharmacodynamics;Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Statin Pathway;Vitamin A and Carotenoid Metabolism;Vesicle-mediated transport;HDL clearance;Plasma lipoprotein clearance;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance;Scavenging by Class B Receptors;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• loftool: 0.635
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.16

Haploinsufficiency Scores

• pHI: 0.137
• hipred: Y
• hipred_score: 0.704

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.641

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scarb1
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; liver/biliary system phenotype; embryo phenotype

Gene ontology

• Biological process: endothelial cell proliferation;androgen biosynthetic process;cholesterol catabolic process;receptor-mediated endocytosis;positive regulation of endothelial cell migration;positive regulation of triglyceride biosynthetic process;positive regulation of cholesterol storage;regulation of phosphatidylcholine catabolic process;phospholipid transport;lipopolysaccharide transport;lipopolysaccharide-mediated signaling pathway;detection of lipopolysaccharide;cholesterol efflux;high-density lipoprotein particle remodeling;low-density lipoprotein particle clearance;high-density lipoprotein particle clearance;vitamin transmembrane transport;wound healing;cholesterol homeostasis;blood vessel endothelial cell migration;recognition of apoptotic cell;reverse cholesterol transport;adhesion of symbiont to host;viral entry into host cell;regulation of phagocytosis;intestinal absorption;positive regulation of nitric-oxide synthase activity;triglyceride homeostasis;cholesterol import
• Cellular component: lysosomal membrane;plasma membrane;integral component of plasma membrane;caveola;cell surface;endocytic vesicle membrane;microvillus membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: lipopolysaccharide binding;amyloid-beta binding;virus receptor activity;phosphatidylserine binding;lipopolysaccharide receptor activity;scavenger receptor activity;transporter activity;protein binding;1-phosphatidylinositol binding;high-density lipoprotein particle binding;low-density lipoprotein particle binding;apolipoprotein binding;apolipoprotein A-I binding;protein homodimerization activity;high-density lipoprotein particle receptor activity