BST2
protein-codingbone marrow stromal cell antigen 2, the group of CD molecules
Gene summary
Bone marrow stromal cells are involved in the growth and development of B-cells. The specific function of the protein encoded by the bone marrow stromal cell antigen 2 is undetermined; however, this protein may play a role in pre-B-cell growth and in rheumatoid arthritis. [provided by RefSeq, Jul 2008]
MANE transcript
NM_004335.4
Inheritance
—
ClinVar variants
U:23B:3
Top phenotype
—
gnomAD constraint
pLI —, LoF o/e 0.72
Max pathogenic AF
—
Genomic locus
chr19:17,402,939-17,405,630
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.7 kbLoading mutation effect viewer...
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 BST2 variants in ClinVar
not specifiedTotal: 20
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004335.4. 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 | 1 | ||||
| missense | 17 | 2 | 19 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 23 | 3 | 0 | 26 |
Loading ClinVar variants...
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
Showing 4 of 24 transcripts
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004326.1 | 4 | MANE Select | |
| Ensembl | ENSP00000252593.6 | 4 | MANE Select | |
| Ensembl | ENSP00000505650.1 | 2 | Standard | |
| Ensembl | ENSP00000530240.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ebola Virus Pathway on Host
- Ebola Virus Pathway on Host
- Neutrophil degranulation
- Cytokine Signaling in Immune system
- Innate Immune System
Biological Process
- negative regulation of plasmacytoid dendritic cell cytokine production
- humoral immune response
- cell-cell signaling
- multicellular organism development
- cell population proliferation
Molecular Function
- RNA binding
- protein binding
- metalloendopeptidase inhibitor activity
- identical protein binding
- protein homodimerization activity
Cellular Component
- cytoplasm
- multivesicular body
- Golgi apparatus
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000252593
- Coding exons
- 4
- Length
- 2710
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125740
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.708 | 88 | 109 | 0.809 | 0.00000621 | 1154 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000065 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000028 | 0.000026 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.0942
Intolerance Scores
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.776
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |