STAB2

stabilin 2, the group of Scavenger receptors

Basic information

Region (hg38): 12:103587273-103766719

Links

ENSG00000136011 ∙ NCBI:55576 ∙ OMIM:608561 ∙ HGNC:18629 ∙ Uniprot:Q8WWQ8 ∙ 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 STAB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAB2 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				9	9	18
missense			158	15	9	182
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	7	11
non coding				1	2	3
Total	0	0	158	25	20

Variants in STAB2

This is a list of pathogenic ClinVar variants found in the STAB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-103587480-A-G		not specified	Uncertain significance (Dec 12, 2023)
12-103587510-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-103587525-A-G		not specified	Uncertain significance (Jun 11, 2024)
12-103590914-G-T		not specified	Uncertain significance (Apr 26, 2023)
12-103590955-C-T		not specified	Uncertain significance (Jun 01, 2022)
12-103590976-G-T		not specified	Uncertain significance (Dec 21, 2023)
12-103591006-G-T		not specified	Uncertain significance (Nov 16, 2022)
12-103594442-G-A		not specified	Uncertain significance (Nov 01, 2021)
12-103594474-C-T		not specified	Uncertain significance (Feb 06, 2023)
12-103594475-G-A		not specified	Likely benign (Sep 06, 2022)
12-103594489-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-103594490-G-A		not specified	Likely benign (Oct 04, 2022)
12-103594490-G-T		not specified	Uncertain significance (Apr 09, 2024)
12-103622081-G-A		not specified	Uncertain significance (Sep 29, 2023)
12-103631608-T-C			Benign (Sep 11, 2018)
12-103631642-G-A			Benign (Sep 11, 2018)
12-103631668-G-A			Benign (Dec 31, 2019)
12-103631675-G-A		not specified	Uncertain significance (Dec 15, 2023)
12-103637165-C-T		not specified	Uncertain significance (Apr 19, 2024)
12-103637216-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-103637218-G-A		not specified	Uncertain significance (Jun 17, 2024)
12-103637219-A-G		not specified	Uncertain significance (May 29, 2024)
12-103637245-A-C			Benign (Dec 04, 2017)
12-103638039-A-G		not specified	Likely benign (Mar 25, 2024)
12-103638061-G-T		not specified	Uncertain significance (Jul 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAB2	protein_coding	protein_coding	ENST00000388887	69	179455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.23e-62	0.00231	125286	0	462	125748	0.00184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.157	1460	1.44e+3	1.01	0.0000802	16711
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00312	0.00312
Ashkenazi Jewish	0.000415	0.000397
East Asian	0.00225	0.00223
Finnish	0.00148	0.00148
European (Non-Finnish)	0.00178	0.00173
Middle Eastern	0.00225	0.00223
South Asian	0.00336	0.00317
Other	0.00265	0.00245

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Vesicle-mediated transport;Hyaluronan uptake and degradation;Hyaluronan metabolism;Metabolism of carbohydrates;Glycosaminoglycan metabolism;Metabolism;Scavenging by Class H Receptors;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Intolerance Scores

• loftool: 0.0771
• rvis_EVS: -2.68
• rvis_percentile_EVS: 0.72

Haploinsufficiency Scores

• pHI: 0.0815
• hipred: Y
• hipred_score: 0.554
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stab2
• Phenotype: renal/urinary system phenotype; neoplasm; 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); normal 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); respiratory system phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: stab2
• Affected structure: vascular lymphangioblast
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: angiogenesis;endocytosis;receptor-mediated endocytosis;cell adhesion;hyaluronan catabolic process;defense response to bacterium;defense response to Gram-positive bacterium;oxidation-reduction process
• Cellular component: cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;endocytic vesicle membrane
• Molecular function: low-density lipoprotein particle receptor activity;scavenger receptor activity;calcium ion binding;protein binding;hyaluronic acid binding;protein disulfide oxidoreductase activity;low-density lipoprotein particle binding