BST1
protein-codingbone marrow stromal cell antigen 1, the group of CD molecules
Gene summary
Bone marrow stromal cell antigen-1 is a stromal cell line-derived glycosylphosphatidylinositol-anchored molecule that facilitates pre-B-cell growth. The deduced amino acid sequence exhibits 33% similarity with CD38. BST1 expression is enhanced in bone marrow stromal cell lines derived from patients with rheumatoid arthritis. The polyclonal B-cell abnormalities in rheumatoid arthritis may be, at least in part, attributed to BST1 overexpression in the stromal cell population. [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 ~35.2 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 BST1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004334.3. 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 | 1 | 3 | ||
| missense | 55 | 4 | 3 | 62 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 58 | 5 | 4 | 67 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004325.2 | 9 | MANE Select | |
| Ensembl | ENSP00000265016.4 | 9 | MANE Select | |
| Ensembl | ENSP00000371783.3 | 10 | Standard | |
| Ensembl | ENSP00000371783.3 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nicotinate and nicotinamide metabolism - Homo sapiens (human)
- Salivary secretion - Homo sapiens (human)
- Pancreatic secretion - Homo sapiens (human)
- Nicotinate and Nicotinamide Metabolism
- NAD+ biosynthetic pathways
Biological Process
- regulation of cell-matrix adhesion
- regulation of cellular extravasation
- humoral immune response
- signal transduction
- positive regulation of cell population proliferation
Molecular Function
- NAD+ nucleosidase activity
- transferase activity
- phosphorus-oxygen lyase activity
- NAD(P)+ nucleosidase activity
- NAD+ nucleotidase, cyclic ADP-ribose generating
Cellular Component
- uropod
- extracellular region
- plasma membrane
- integrin complex
- extrinsic component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000265016
- Coding exons
- 9
- Length
- 35364
- Individuals with no LoFs
- 125621
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 126
- Defined
- 125747
- p
- 0.000501
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.103 | 173 | 169 | 1.02 | 0.00000930 | 2036 |
| Missense (PolyPhen) | 55 | 57.959 | 0.94895 | 738 | ||
| Synonymous | 0.739 | 64 | 72.0 | 0.889 | 0.00000459 | 614 |
| Loss of Function | 0.378 | 17 | 18.8 | 0.906 | 0.00000114 | 189 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0020 | 0.0020 | notable |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.00040 | 0.00040 | rare |
| South Asian | 0.00045 | 0.00039 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Synthesizes the second messagers cyclic ADP-ribose and nicotinate-adenine dinucleotide phosphate, the former a second messenger that elicits calcium release from intracellular stores. May be involved in pre-B-cell growth. {ECO:0000269|PubMed:11866528}.;
Recessive Scores
- pRec
- 0.198
Intolerance Scores
- LoFtool
- 0.853
- RVIS EVS
- 0.86
- RVIS percentile EVS
- 88.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.515
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |