BST2
bone marrow stromal cell antigen 2, the group of CD molecules
Basic information
Region (hg38): 19:17402939-17405630
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BST2 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 | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in BST2
This is a list of pathogenic ClinVar variants found in the BST2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-17403709-C-G | not specified | Uncertain significance (Mar 28, 2024) | ||
| 19-17403751-C-T | not specified | Uncertain significance (May 30, 2024) | ||
| 19-17403763-C-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 19-17404403-G-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 19-17405410-C-T | not specified | Uncertain significance (Sep 14, 2023) | ||
| 19-17405512-G-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 19-17405521-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
| 19-17405539-T-C | not specified | Uncertain significance (Apr 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BST2 | protein_coding | protein_coding | ENST00000252593 | 4 | 2710 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000425 | 0.664 | 125733 | 0 | 7 | 125740 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.708 | 88 | 109 | 0.809 | 0.00000621 | 1154 |
| Missense in Polyphen | 24 | 38.296 | 0.62669 | 422 | ||
| Synonymous | 1.59 | 35 | 49.2 | 0.712 | 0.00000313 | 369 |
| Loss of Function | 0.752 | 6 | 8.34 | 0.719 | 3.95e-7 | 98 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000654 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000276 | 0.0000264 |
| Middle Eastern | 0.0000654 | 0.0000544 |
| South Asian | 0.000102 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: IFN-induced antiviral host restriction factor which efficiently blocks the release of diverse mammalian enveloped viruses by directly tethering nascent virions to the membranes of infected cells. Acts as a direct physical tether, holding virions to the cell membrane and linking virions to each other. The tethered virions can be internalized by endocytosis and subsequently degraded or they can remain on the cell surface. In either case, their spread as cell-free virions is restricted. Its target viruses belong to diverse families, including retroviridae: human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV-2), simian immunodeficiency viruses (SIVs), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FIV), prototype foamy virus (PFV), Mason- Pfizer monkey virus (MPMV), human T-cell leukemia virus type 1 (HTLV-1), Rous sarcoma virus (RSV) and murine leukemia virus (MLV), flavivirideae: hepatitis C virus (HCV), filoviridae: ebola virus (EBOV) and marburg virus (MARV), arenaviridae: lassa virus (LASV) and machupo virus (MACV), herpesviridae: kaposis sarcoma- associated herpesvirus (KSHV), rhabdoviridae: vesicular stomatitis virus (VSV), orthomyxoviridae: influenza A virus, and paramyxoviridae: nipah virus. Can inhibit cell surface proteolytic activity of MMP14 causing decreased activation of MMP15 which results in inhibition of cell growth and migration. Can stimulate signaling by LILRA4/ILT7 and consequently provide negative feedback to the production of IFN by plasmacytoid dendritic cells in response to viral infection (PubMed:19564354, PubMed:26172439). Plays a role in the organization of the subapical actin cytoskeleton in polarized epithelial cells. Isoform 1 and isoform 2 are both effective viral restriction factors but have differing antiviral and signaling activities (PubMed:23028328, PubMed:26172439). Isoform 2 is resistant to HIV-1 Vpu-mediated degradation and restricts HIV-1 viral budding in the presence of Vpu (PubMed:23028328, PubMed:26172439). Isoform 1 acts as an activator of NF-kappa-B and this activity is inhibited by isoform 2 (PubMed:23028328). {ECO:0000269|PubMed:18200009, ECO:0000269|PubMed:18342597, ECO:0000269|PubMed:19036818, ECO:0000269|PubMed:19179289, ECO:0000269|PubMed:19564354, ECO:0000269|PubMed:19879838, ECO:0000269|PubMed:20399176, ECO:0000269|PubMed:20419159, ECO:0000269|PubMed:20686043, ECO:0000269|PubMed:20940320, ECO:0000269|PubMed:20943977, ECO:0000269|PubMed:21529378, ECO:0000269|PubMed:21621240, ECO:0000269|PubMed:22065321, ECO:0000269|PubMed:22520941, ECO:0000269|PubMed:23028328, ECO:0000269|PubMed:26172439}.;
- Pathway
- Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Neutrophil degranulation;Cytokine Signaling in Immune system;Innate Immune System;Immune System;Interferon alpha/beta signaling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.0942
Intolerance Scores
- loftool
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.360
- hipred
- N
- hipred_score
- 0.153
- ghis
- 0.559
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.776
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Bst2
- Phenotype
- cellular phenotype; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of plasmacytoid dendritic cell cytokine production;humoral immune response;cell-cell signaling;multicellular organism development;cell population proliferation;response to virus;negative regulation of endopeptidase activity;negative regulation of cell growth;negative regulation of cell migration;regulation of actin cytoskeleton organization;response to interferon-gamma;response to interferon-alpha;response to interferon-beta;B cell activation;positive regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;negative regulation of viral genome replication;innate immune response;defense response to virus;type I interferon signaling pathway;negative regulation of intracellular transport of viral material
- Cellular component
- cytoplasm;multivesicular body;Golgi apparatus;cytosol;plasma membrane;integral component of plasma membrane;cell surface;membrane;apical plasma membrane;anchored component of membrane;azurophil granule membrane;membrane raft;extracellular exosome
- Molecular function
- RNA binding;protein binding;metalloendopeptidase inhibitor activity;identical protein binding;protein homodimerization activity