BCAN
protein-codingbrevican, the group of C-type lectin domain containing|V-set domain containing|Sushi domain containing|Hyalectan proteoglycans
Gene summary
This gene encodes a member of the lectican family of chondroitin sulfate proteoglycans that is specifically expressed in the central nervous system. This protein is developmentally regulated and may function in the formation of the brain extracellular matrix. This protein is highly expressed in gliomas and may promote the growth and cell motility of brain tumor cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.1 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 BCAN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021948.5. 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 | 3 | 1 | 5 | ||
| missense | 135 | 6 | 2 | 143 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 137 | 9 | 3 | 149 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_068767.3 | 13 | MANE Select | |
| Ensembl | ENSP00000331210.4 | 13 | MANE Select | |
| RefSeq | NP_940819.1 | 7 | Standard | |
| Ensembl | ENSP00000354925.5 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Spinal Cord Injury
- Metabolism of carbohydrates
- A tetrasaccharide linker sequence is required for GAG synthesis
- Heparan sulfate/heparin (HS-GAG) metabolism
- Chondroitin sulfate biosynthesis
Biological Process
- skeletal system development
- cell adhesion
- central nervous system development
- hippocampus development
- extracellular matrix organization
Molecular Function
- hyaluronic acid binding
- carbohydrate binding
Cellular Component
- extracellular region
- Golgi lumen
- extracellular matrix
- anchored component of membrane
- lysosomal lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000329117
- Coding exons
- 13
- Length
- 18143
- Individuals with no LoFs
- 125692
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 55
- Defined
- 125747
- p
- 0.000219
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.834 | 496 | 551 | 0.900 | 0.0000333 | 5744 |
| Missense (PolyPhen) | 189 | 252.56 | 0.74833 | 2586 | ||
| Synonymous | 0.154 | 233 | 236 | 0.987 | 0.0000145 | 1951 |
| Loss of Function | 3.48 | 17 | 41.1 | 0.414 | 0.00000218 | 447 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.000089 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0014 | 0.0013 | notable |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00019 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in the terminally differentiating and the adult nervous system during postnatal development. Could stabilize interactions between hyaluronan (HA) and brain proteoglycans.;
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- LoFtool
- 0.734
- RVIS EVS
- -1.06
- RVIS percentile EVS
- 7.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.825
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |