NCAN

protein-coding

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

Gene summary

Neurocan is a chondroitin sulfate proteoglycan thought to be involved in the modulation of cell adhesion and migration.[supplied by OMIM, Jul 2002]

Previous symbols:

CSPG3

MANE transcript

NM_004386.3

Inheritance

—

ClinVar variants

U:203B:15

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr19:19,211,958-19,252,233

External References & Databases

Ensembl (ENSG00000130287)

Transcript & Mutation Effects

hg38 • Region Span ~40.3 kb

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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 NCAN variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 210

not providedTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Developmental dyslexiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004386.3. 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 clinvar	3 clinvar	4
missense			202 clinvar	11 clinvar		213
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	203	12	3	218

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004386.3	RefSeq	NP_004377.2	14	MANE Select
ENST00000252575.11	Ensembl	ENSP00000252575.4	14	MANE Select
ENST00000588231.1	Ensembl	ENSP00000465599.3	4	Standard
ENST00000910089.1	Ensembl	ENSP00000580148.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spinal Cord Injury
Developmental Biology
Metabolism of carbohydrates
A tetrasaccharide linker sequence is required for GAG synthesis
Heparan sulfate/heparin (HS-GAG) metabolism

Biological Process

skeletal system development
cell adhesion
central nervous system development
extracellular matrix organization
chondroitin sulfate biosynthetic process

Molecular Function

calcium ion binding
hyaluronic acid binding
carbohydrate binding

Cellular Component

extracellular region
Golgi lumen
extracellular matrix
lysosomal lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252575
Coding exons: 14
Length: 40261
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.16	685	776	0.883	0.0000461	8532
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000066	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.165

Intolerance Scores

LoFtool: 0.0648
RVIS EVS: -1.74
RVIS percentile EVS: 2.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.573

Gene Damage Prediction

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