STAB2
protein-codingstabilin 2, the group of Scavenger receptors
Gene summary
This gene encodes a large, transmembrane receptor protein which may function in angiogenesis, lymphocyte homing, cell adhesion, or receptor scavenging. The protein contains 7 fasciclin, 15 epidermal growth factor (EGF)-like, and 2 laminin-type EGF-like domains as well as a C-type lectin-like hyaluronan-binding Link module. The protein is primarily expressed on sinusoidal endothelial cells of liver, spleen, and lymph node. The receptor has been shown to bind and endocytose ligands such as hyaluronan, low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein has been shown to cycle between the plasma membrane and lysosomes. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~179.4 kbGenCC 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 STAB2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017564.10. 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 | 4 | 9 | 10 | 23 | ||
| missense | 375 | 34 | 8 | 417 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 383 | 43 | 18 | 444 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060034.9 | 69 | MANE Select | |
| Ensembl | ENSP00000373539.2 | 69 | MANE Select | |
| Ensembl | ENSP00000449282.1 | 3 | Standard | |
| Ensembl | ENSP00000446629.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| stab2 | Danio rerio | Structure: vascular lymphangioblast Quality: hypoplastic abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Hyaluronan uptake and degradation
- Hyaluronan metabolism
- Metabolism of carbohydrates
- Glycosaminoglycan metabolism
Biological Process
- angiogenesis
- endocytosis
- receptor-mediated endocytosis
- cell adhesion
- hyaluronan catabolic process
Molecular Function
- low-density lipoprotein particle receptor activity
- scavenger receptor activity
- calcium ion binding
- protein binding
- hyaluronic acid binding
Cellular Component
- cytosol
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- endocytic vesicle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000388887
- Coding exons
- 69
- Length
- 179455
- Individuals with no LoFs
- 125286
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 462
- Defined
- 125748
- p
- 0.00184
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.157 | 1460 | 1.44e+3 | 1.01 | 0.0000802 | 16711 |
| Missense (PolyPhen) | 476 | 514.34 | 0.92545 | 5921 | ||
| Synonymous | -0.286 | 578 | 569 | 1.02 | 0.0000350 | 4828 |
| Loss of Function | 2.80 | 116 | 154 | 0.756 | 0.00000839 | 1775 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0016 | notable |
| Latino/Admixed American | 0.0015 | 0.0014 | notable |
| Ashkenazi Jewish | 0.00041 | 0.00040 | rare |
| East Asian | 0.0022 | 0.0022 | notable |
| Finnish | 0.0015 | 0.0015 | notable |
| European (Non-Finnish) | 0.0018 | 0.0017 | notable |
| South Asian | 0.0034 | 0.0032 | notable |
| Other | 0.0027 | 0.0024 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Hyaluronan receptor that binds to and mediates endocytosis of hyaluronic acid (HA). Acts also, in different species, as a primary systemic scavenger receptor for heparin (Hep), chondroitin sulfate (CS), dermatan sulfate (DS), nonglycosaminoglycan (GAG), acetylated low-density lipoprotein (AcLDL), pro-collagen propeptides and advanced glycation end products (AGE). May serve to maintain tissue integrity by supporting extracellular matrix turnover or it may contribute to maintaining fluidity of bodily liquids by resorption of hyaluronan. Counter receptor which plays an important role in lymphocyte recruitment in the hepatic vasculature. Binds to both Gram-positive and Gram-negative bacteria and may play a role in defense against bacterial infection. The proteolytically processed 190 kDa form also functions as an endocytosis receptor for heparin internalisation as well as HA and CS. {ECO:0000269|PubMed:12077138, ECO:0000269|PubMed:12473645, ECO:0000269|PubMed:15208308, ECO:0000269|PubMed:15572036, ECO:0000269|PubMed:17145755, ECO:0000269|PubMed:17675564, ECO:0000269|PubMed:17962816, ECO:0000269|PubMed:18230608, ECO:0000269|PubMed:18434317, ECO:0000269|PubMed:18573870, ECO:0000269|PubMed:19359419}.;
Intolerance Scores
- LoFtool
- 0.0771
- RVIS EVS
- -2.68
- RVIS percentile EVS
- 0.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.654
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |