BCAN

brevican, the group of C-type lectin domain containing|V-set domain containing|Sushi domain containing|Hyalectan proteoglycans

Basic information

Region (hg38): 1:156641390-156659532

Links

ENSG00000132692 ∙ NCBI:63827 ∙ OMIM:600347 ∙ HGNC:23059 ∙ Uniprot:Q96GW7 ∙ 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 BCAN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAN 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				2	1	3
missense			70	6	2	78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	8	3

Variants in BCAN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-156646073-C-T		not specified	Uncertain significance (Jul 22, 2024)
1-156646125-T-C		not specified	Likely benign (Feb 07, 2023)
1-156646806-C-A		not specified	Uncertain significance (Jun 11, 2024)
1-156646965-C-T		not specified	Uncertain significance (Aug 05, 2024)
1-156646993-G-A		not specified	Uncertain significance (Jun 14, 2023)
1-156646999-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-156647013-G-C		not specified	Uncertain significance (Jan 17, 2024)
1-156647022-C-G		not specified	Benign (Mar 29, 2016)
1-156647094-C-T		not specified	Uncertain significance (Mar 12, 2024)
1-156647099-C-A		not specified	Uncertain significance (Mar 20, 2024)
1-156647119-G-T		not specified	Uncertain significance (Jan 05, 2022)
1-156647133-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-156647538-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-156647541-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-156647546-G-A		not specified	Uncertain significance (Sep 21, 2023)
1-156647582-C-G		not specified	Uncertain significance (Sep 25, 2024)
1-156648017-G-A		not specified	Uncertain significance (Aug 12, 2024)
1-156648066-C-T		not specified	Uncertain significance (Jun 07, 2023)
1-156651462-C-T		not specified	Uncertain significance (Oct 06, 2022)
1-156651473-G-A		not specified	Uncertain significance (Sep 23, 2023)
1-156651488-T-G		not specified	Uncertain significance (Mar 19, 2024)
1-156651509-G-T		not specified	Uncertain significance (Jun 25, 2024)
1-156651515-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-156651515-G-C		not specified	Uncertain significance (Jul 17, 2023)
1-156651543-C-G		not specified	Uncertain significance (Nov 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAN	protein_coding	protein_coding	ENST00000329117	13	18143

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000176	1.00	125692	0	55	125747	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.834	496	551	0.900	0.0000333	5744
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000273
Ashkenazi Jewish	0.00	0.00
East Asian	0.00145	0.00131
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.00145	0.00131
South Asian	0.0000983	0.0000980
Other	0.000192	0.000163

dbNSFP

Source: dbNSFP

• 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.
• Pathway: Spinal Cord Injury;Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate biosynthesis;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Extracellular matrix organization;Metabolism;Integrin;Degradation of the extracellular matrix;ECM proteoglycans (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.734
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.58

Haploinsufficiency Scores

• pHI: 0.281
• hipred: Y
• hipred_score: 0.541
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.825

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcan
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: skeletal system development;cell adhesion;central nervous system development;hippocampus development;extracellular matrix organization;chondroitin sulfate biosynthetic process;chondroitin sulfate catabolic process;dermatan sulfate biosynthetic process;synapse maturation
• Cellular component: extracellular region;Golgi lumen;extracellular matrix;anchored component of membrane;lysosomal lumen;glutamatergic synapse
• Molecular function: hyaluronic acid binding;carbohydrate binding