SCARB1

protein-coding

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

Gene summary

The protein encoded by this gene is a plasma membrane receptor for high density lipoprotein cholesterol (HDL). The encoded protein mediates cholesterol transfer to and from HDL. In addition, this protein is a receptor for hepatitis C virus glycoprotein E2 and facilitates cell entry by the virus, SARS-CoV2. [provided by RefSeq, Oct 2021]

Previous symbols:

CD36L1

MANE transcript

NM_005505.5

Inheritance

—

ClinVar variants

P:1U:90B:53

Top phenotype

SCARB1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr12:124,776,856-124,882,668

External References & Databases

Ensembl (ENSG00000073060)

Transcript & Mutation Effects

hg38 • Region Span ~105.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCARB1 variants in ClinVar

4 Conditions Cataloged

not providedTotal: 154

not specifiedTotal: 41

SCARB1-related disorderTotal: 11

HIGH DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 6Total: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005505.5. 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			1 clinvar	38 clinvar	9 clinvar	48
missense			87 clinvar	5 clinvar	1 clinvar	93
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	1	0	90	43	10	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 105 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005505.5	RefSeq	NP_005496.4	12	MANE Select
ENST00000261693.11	Ensembl	ENSP00000261693.6	12	MANE Select
NM_001082959.2	RefSeq	NP_001076428.1	12	Standard
NM_001367981.1	RefSeq	NP_001354910.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

endothelial cell proliferation
androgen biosynthetic process
cholesterol catabolic process
receptor-mediated endocytosis
positive regulation of endothelial cell migration

Molecular Function

lipopolysaccharide binding
amyloid-beta binding
virus receptor activity
phosphatidylserine binding
lipopolysaccharide receptor activity

Cellular Component

lysosomal membrane
plasma membrane
integral component of plasma membrane
caveola
cell surface

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261693
Coding exons: 12
Length: 105813
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125748
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.60	223	301	0.741	0.0000186	3358
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00046	0.00046	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0999

Intolerance Scores

LoFtool: 0.635
RVIS EVS: -0.16
RVIS percentile EVS: 42.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.641

Gene Damage Prediction

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