SCARB1
scavenger receptor class B member 1, the group of Scavenger receptors
Basic information
Region (hg38): 12:124776856-124882668
Previous symbols: [ "CD36L1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (126 variants)
- not_specified (34 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 29 | 38 | ||||
| missense | 67 | 73 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 1 | 0 | 69 | 34 | 10 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- ghis
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