CHI3L1 chitinase 3 like 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHI3L1provided by HGNC
Official Full Name: chitinase 3 like 1provided by HGNC
Primary source: HGNC:HGNC:1932
See related: Ensembl:ENSG00000133048 MIM:601525; AllianceGenome:HGNC:1932
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GP39; ASRT7; GP-39; YK-40; YKL40; CGP-39; YKL-40; YYL-40; HC-gp39; HCGP-3P; hCGP-39
Summary: Chitinases catalyze the hydrolysis of chitin, which is an abundant glycopolymer found in insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 family of chitinases includes eight human family members. This gene encodes a glycoprotein member of the glycosyl hydrolase 18 family. The protein lacks chitinase activity and is secreted by activated macrophages, chondrocytes, neutrophils and synovial cells. The protein is thought to play a role in the process of inflammation and tissue remodeling. [provided by RefSeq, Sep 2009]
Expression: Biased expression in brain (RPKM 100.8), urinary bladder (RPKM 89.5) and 8 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q32.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (203178931..203186704, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (202441684..202449457, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (203148059..203155832, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional variants of the chitinase 3-like 1 gene are associated with clinicopathologic outcomes and progression of prostate cancer.
Title: Functional variants of the chitinase 3-like 1 gene are associated with clinicopathologic outcomes and progression of prostate cancer.
TIMP1/CHI3L1 facilitates glioma progression and immunosuppression via NF-kappaB activation.
Title: TIMP1/CHI3L1 facilitates glioma progression and immunosuppression via NF-κB activation.
A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1.
Title: A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1.
Association of Plasma YKL-40 With MRI, CSF, and Cognitive Markers of Brain Health and Dementia.
Title: Association of Plasma YKL-40 With MRI, CSF, and Cognitive Markers of Brain Health and Dementia.
Astrocyte biomarkers GFAP and YKL-40 mediate early Alzheimer's disease progression.
Title: Astrocyte biomarkers GFAP and YKL-40 mediate early Alzheimer's disease progression.
An Association of Chitinase-3 Like-Protein-1 With Neuronal Deterioration in Multiple Sclerosis.
Title: An Association of Chitinase-3 Like-Protein-1 With Neuronal Deterioration in Multiple Sclerosis.
Clinical Significance of Chitinase-3-like Protein 1 Gene Expression in Patients With Locally Advanced Gastric Cancer.
Title: Clinical Significance of Chitinase-3-like Protein 1 Gene Expression in Patients With Locally Advanced Gastric Cancer.
The potential roles and mechanisms of Chitinase-3-like-1 in the pathogenesis of type 2-biased airway diseases.
Title: The potential roles and mechanisms of Chitinase-3-like-1 in the pathogenesis of type 2-biased airway diseases.
The tumor-derived cytokine Chi3l1 induces neutrophil extracellular traps that promote T cell exclusion in triple-negative breast cancer.
Title: The tumor-derived cytokine Chi3l1 induces neutrophil extracellular traps that promote T cell exclusion in triple-negative breast cancer.
YKL-40 and the Cellular Metabolic Profile in Parkinson's Disease.
Title: YKL-40 and the Cellular Metabolic Profile in Parkinson's Disease.

Submit: New GeneRIF Correction See all GeneRIFs (536)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Asthma-related traits, susceptibility to, 7 MedGen: C2677770 OMIM: 611960 GeneReviews: Not available	Compare labs
Schizophrenia MedGen: C0036341 OMIM: 181500 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. EBI GWAS Catalog EBI GWAS CatalogPubMed
Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of chitinase 3-like 1 (CHI3L1, cartilage glycoprotein-39) expression by HIV-1 Vpr in Vpr transduced macrophages	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables chitin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chitin binding	IDA Inferred from Direct Assay more info	PubMed
NOT enables chitinase activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables chitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables extracellular matrix structural constituent	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in activation of NF-kappaB-inducing kinase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in carbohydrate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	NAS Non-traceable Author Statement more info	PubMed
involved_in cellular response to tumor necrosis factor	ISS Inferred from Sequence or Structural Similarity more info
involved_in chitin catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IEP Inferred from Expression Pattern more info	PubMed
involved_in lung development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ERK1 and ERK2 cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-8 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of peptidyl-threonine phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to interleukin-1	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to interleukin-6	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to tumor necrosis factor	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
is_active_in extracellular region	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in specific granule lumen	TAS Traceable Author Statement more info

General protein information

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Preferred Names: chitinase-3-like protein 1

Names: 39 kDa synovial protein; cartilage glycoprotein 39; chitinase 3-like 1 (cartilage glycoprotein-39)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_013056.2 RefSeqGene

Range

5000..12773

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001276.4 → NP_001267.2 chitinase-3-like protein 1 precursor

See identical proteins and their annotated locations for NP_001267.2

Status: REVIEWED

Source sequence(s)

AC105940

Consensus CDS

CCDS1435.1

UniProtKB/Swiss-Prot

B2R7B0, P30923, P36222, Q8IVA4, Q96HI7

Related

ENSP00000255409.3, ENST00000255409.8

Conserved Domains (2) summary

cd02872
Location:24 → 380

GH18_chitolectin_chitotriosidase; This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active ...

smart00636
Location:23 → 357

Glyco_18; Glyco_18 domain