NCAN

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

Basic information

Region (hg38): 19:19211958-19252233

Previous symbols: [ "CSPG3" ]

Links

ENSG00000130287 ∙ NCBI:1463 ∙ OMIM:600826 ∙ HGNC:2465 ∙ Uniprot:O14594 ∙ 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 NCAN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAN 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					3	3
missense			81	6		87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	81	6	3

Variants in NCAN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-19216964-C-A		not specified	Uncertain significance (Oct 08, 2024)
19-19218917-A-G		not specified	Uncertain significance (Aug 22, 2023)
19-19218921-A-G		not specified	Uncertain significance (Nov 07, 2024)
19-19218926-A-G		not specified	Uncertain significance (Jun 17, 2024)
19-19218930-C-A		not specified	Uncertain significance (Aug 21, 2023)
19-19218932-G-A		not specified	Uncertain significance (Nov 24, 2024)
19-19218958-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-19219038-G-A		not specified	Uncertain significance (Dec 04, 2024)
19-19219086-G-A		not specified	Uncertain significance (Jun 21, 2023)
19-19219086-G-T		not specified	Uncertain significance (Aug 08, 2023)
19-19219092-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-19219104-G-A		not specified	Uncertain significance (Jul 27, 2021)
19-19219152-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-19219155-A-G		not specified	Uncertain significance (Dec 02, 2024)
19-19219163-C-A		not specified	Uncertain significance (Mar 27, 2023)
19-19219200-G-A		not specified	Uncertain significance (Dec 02, 2021)
19-19219213-G-A			Benign (Aug 09, 2018)
19-19219301-C-G		not specified	Uncertain significance (Dec 19, 2022)
19-19219301-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-19224047-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-19224098-A-G		not specified	Uncertain significance (Jul 14, 2021)
19-19224113-G-A		not specified	Uncertain significance (Nov 10, 2024)
19-19224180-C-T		not specified	Uncertain significance (Aug 15, 2024)
19-19224185-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-19224316-A-G		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAN	protein_coding	protein_coding	ENST00000252575	14	40261

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0680	0.932	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	685	776	0.883	0.0000461	8532
Missense in Polyphen		216	295.64	0.73063		3204
Synonymous	0.416	305	314	0.970	0.0000194	2760
Loss of Function	5.00	13	51.9	0.251	0.00000289	554

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000211
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate neuronal adhesion and neurite growth during development by binding to neural cell adhesion molecules (NG-CAM and N-CAM). Chondroitin sulfate proteoglycan; binds to hyaluronic acid.
• Pathway: Spinal Cord Injury;Developmental Biology;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;NCAM signaling for neurite out-growth;L1CAM interactions;NCAM1 interactions;Axon guidance;ECM proteoglycans;Syndecan-3-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.0648
• rvis_EVS: -1.74
• rvis_percentile_EVS: 2.42

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.369
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.573

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncan
• 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;extracellular matrix organization;chondroitin sulfate biosynthetic process;chondroitin sulfate catabolic process;dermatan sulfate biosynthetic process
• Cellular component: extracellular region;Golgi lumen;extracellular matrix;lysosomal lumen
• Molecular function: calcium ion binding;hyaluronic acid binding;carbohydrate binding