SCARB1

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

Basic information

Region (hg38): 12:124776856-124882668

Previous symbols: [ "CD36L1" ]

Links

ENSG00000073060 ∙ NCBI:949 ∙ OMIM:601040 ∙ HGNC:1664 ∙ Uniprot:Q8WTV0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 47.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000261693.11	ENSP00000261693.6	12	yes	-
ENST00000339570.9	ENSP00000343795.4	12	-	-
ENST00000415380.6	ENSP00000414979.2	12	-	-
ENST00000544327.1	ENSP00000444851.1	10	-	-

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 (154 variants)
• not_specified (41 variants)
• SCARB1-related_disorder (11 variants)
• HIGH_DENSITY_LIPOPROTEIN_CHOLESTEROL_LEVEL_QUANTITATIVE_TRAIT_LOCUS_6 (8 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. These statistics are base on transcript: NM_000005505.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	38	9	48
missense			87	5	1	93
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1					1
Total	1	0	90	43	10

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
		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

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

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