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Aliases for CHI3L2 Gene

Aliases for CHI3L2 Gene

  • Chitinase 3 Like 2 2 3 5
  • Chondrocyte Protein 39 3 4
  • YKL-39 3 4
  • Chitinase-3-Like Protein 2 3
  • Chitinase 3-Like 2 2
  • CHIL2 3
  • YKL39 3

External Ids for CHI3L2 Gene

Previous GeneCards Identifiers for CHI3L2 Gene

  • GC01P112186
  • GC01P110642
  • GC01P110872
  • GC01P111069
  • GC01P111482
  • GC01P111571
  • GC01P111770
  • GC01P109641

Summaries for CHI3L2 Gene

Entrez Gene Summary for CHI3L2 Gene

  • The protein encoded by this gene is similar to bacterial chitinases but lacks chitinase activity. The encoded protein is secreted and is involved in cartilage biogenesis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for CHI3L2 Gene

CHI3L2 (Chitinase 3 Like 2) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include carbohydrate binding and chitin binding. An important paralog of this gene is CHIT1.

UniProtKB/Swiss-Prot for CHI3L2 Gene

  • Lectin that binds chitooligosaccharides and other glycans with high affinity, but not heparin. Has no chitinase activity.

Additional gene information for CHI3L2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHI3L2 Gene

Genomics for CHI3L2 Gene

GeneHancer (GH) Regulatory Elements for CHI3L2 Gene

Promoters and enhancers for CHI3L2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J111212 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 688 +21.0 20976 19.3 HDGF PKNOX1 FOXA2 SMAD1 FEZF1 YBX1 ZNF2 IRF4 YY1 ZNF213 CHI3L2 DDX20 LOC105378903 ENSG00000232240 PIFO ATP5PB WDR77 OVGP1 DENND2D CEPT1
GH01J111189 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 14.5 -2.7 -2671 16.6 HDGF PKNOX1 FOXA2 SMAD1 IRF4 ZNF766 ZNF207 ZNF143 FOS CEBPZ DENND2D PIR46223 DRAM2 CEPT1 CHI3L2 DDX20 CD53 ENSG00000243960 LRIF1 RAP1A
GH01J111234 Enhancer 1 ENCODE dbSUPER 30.2 +35.5 35535 3.9 ELF3 FOXA2 ARID4B SIN3A DNMT3B THRB RARA RCOR1 CREM GATAD2B CHI3L2 DENND2D ENSG00000232240 LOC105378903 OVGP1 ATP5PB WDR77 CHIAP1
GH01J111138 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.1 -60.0 -60045 4.5 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 DRAM2 CEPT1 DDX20 DENND2D ENSG00000243960 CHI3L2 RBM15 OVGP1 RBM15-AS1 ENSG00000272982
GH01J111242 Enhancer 0.6 dbSUPER 27.3 +42.6 42616 1.9 ELF3 SOX5 SOX13 HMG20A RARA TEAD3 BCL6 KDM1A FOXP1 CHI3L2 DENND2D OVGP1 CHIAP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHI3L2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHI3L2 gene promoter:
  • Tal-1
  • E47
  • AML1a
  • Ik-3
  • LCR-F1
  • NF-AT

Genomic Locations for CHI3L2 Gene

Genomic Locations for CHI3L2 Gene
42,670 bases
Plus strand
42,670 bases
Plus strand

Genomic View for CHI3L2 Gene

Genes around CHI3L2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHI3L2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHI3L2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHI3L2 Gene

Proteins for CHI3L2 Gene

  • Protein details for CHI3L2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chitinase-3-like protein 2
    Protein Accession:
    Secondary Accessions:
    • A6NNY3
    • B4DPR7
    • Q15749
    • Q15783
    • Q5VUV7
    • Q96F97

    Protein attributes for CHI3L2 Gene

    390 amino acids
    Molecular mass:
    43501 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAB04534.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAC50597.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CHI3L2 Gene

    Alternative splice isoforms for CHI3L2 Gene


neXtProt entry for CHI3L2 Gene

Post-translational modifications for CHI3L2 Gene

  • Glycosylation at Asn35
  • Ubiquitination at posLast=384384, posLast=345345, Lys340, posLast=329329, and posLast=199199
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CHI3L2 Gene

Domains & Families for CHI3L2 Gene

Gene Families for CHI3L2 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for CHI3L2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the glycosyl hydrolase 18 family.
  • Belongs to the glycosyl hydrolase 18 family.
genes like me logo Genes that share domains with CHI3L2: view

Function for CHI3L2 Gene

Molecular function for CHI3L2 Gene

UniProtKB/Swiss-Prot Function:
Lectin that binds chitooligosaccharides and other glycans with high affinity, but not heparin. Has no chitinase activity.
GENATLAS Biochemistry:
chitinase 3-like 2,expressed in chondrocytes,synovial cell,lung,heart

Phenotypes From GWAS Catalog for CHI3L2 Gene

Gene Ontology (GO) - Molecular Function for CHI3L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004568 NOT chitinase activity IDA 22742450
GO:0008061 chitin binding IDA 22742450
GO:0016787 hydrolase activity IEA --
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with CHI3L2: view
genes like me logo Genes that share phenotypes with CHI3L2: view

Animal Model Products

CRISPR Products

miRNA for CHI3L2 Gene

miRTarBase miRNAs that target CHI3L2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHI3L2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CHI3L2 Gene

Localization for CHI3L2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHI3L2 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHI3L2 gene
Compartment Confidence
extracellular 5
mitochondrion 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CHI3L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IBA --
GO:0005615 extracellular space HDA,TAS 16502470
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with CHI3L2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CHI3L2 Gene

Pathways & Interactions for CHI3L2 Gene

SuperPathways for CHI3L2 Gene

No Data Available

Interacting Proteins for CHI3L2 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 23)
Selected Interacting proteins: ENSP00000358763 Q15782-CH3L2_HUMAN for CHI3L2 Gene via STRING IID

Gene Ontology (GO) - Biological Process for CHI3L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IEA --
GO:0006032 NOT chitin catabolic process IBA --
genes like me logo Genes that share ontologies with CHI3L2: view

No data available for Pathways by source and SIGNOR curated interactions for CHI3L2 Gene

Drugs & Compounds for CHI3L2 Gene

(2) Drugs for CHI3L2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
N-Acetyl-D-glucosamine Approved, Investigational Nutra 0
genes like me logo Genes that share compounds with CHI3L2: view

Transcripts for CHI3L2 Gene

Unigene Clusters for CHI3L2 Gene

Chitinase 3-like 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHI3L2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHI3L2 Gene

No ASD Table

Relevant External Links for CHI3L2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CHI3L2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CHI3L2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CHI3L2 Gene

This gene is overexpressed in Minor Salivary Gland (x8.2) and Lung (x4.4).

Protein differential expression in normal tissues from HIPED for CHI3L2 Gene

This gene is overexpressed in Salivary gland (44.8), Synovial fluid (8.0), and Breast (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CHI3L2 Gene

Protein tissue co-expression partners for CHI3L2 Gene

NURSA nuclear receptor signaling pathways regulating expression of CHI3L2 Gene:


SOURCE GeneReport for Unigene cluster for CHI3L2 Gene:


mRNA Expression by UniProt/SwissProt for CHI3L2 Gene:

Tissue specificity: Highest expression in chondrocytes, followed by synoviocytes, lung and heart. Not detected in spleen, pancreas, and liver. May also be expressed in developing brain and placenta.

Evidence on tissue expression from TISSUES for CHI3L2 Gene

  • Nervous system(4.4)
  • Blood(2.4)
  • Lung(2.4)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with CHI3L2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CHI3L2 Gene

Orthologs for CHI3L2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CHI3L2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CHI3L2 34 33
  • 99.4 (n)
(Bos Taurus)
Mammalia CHI3L2 34 33
  • 87.99 (n)
(Monodelphis domestica)
Mammalia CHI3L2 34
  • 62 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 36 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 48 (a)
-- 34
  • 45 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG2989 35
  • 40 (a)
CG9357 35
  • 38 (a)
Cht3 35
  • 37 (a)
CG10531 35
  • 37 (a)
Cht1 35
  • 36 (a)
Cht2 35
  • 34 (a)
CG3044 35
  • 29 (a)
Chit 35
  • 26 (a)
Idgf4 35
  • 26 (a)
Cht7 34
  • 17 (a)
(Caenorhabditis elegans)
Secernentea cht-1 34
  • 24 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CTS2 34
  • 19 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8046 34
  • 21 (a)
Species where no ortholog for CHI3L2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for CHI3L2 Gene

Gene Tree for CHI3L2 (if available)
Gene Tree for CHI3L2 (if available)
Evolutionary constrained regions (ECRs) for CHI3L2: view image

Paralogs for CHI3L2 Gene

Paralogs for CHI3L2 Gene

(5) SIMAP similar genes for CHI3L2 Gene using alignment to 10 proteins:

  • E9PP75_HUMAN
  • E9PR52_HUMAN
  • H0YD88_HUMAN
  • H0YE91_HUMAN
  • H0YEJ1_HUMAN Pseudogenes for CHI3L2 Gene

genes like me logo Genes that share paralogs with CHI3L2: view

Variants for CHI3L2 Gene

Sequence variations from dbSNP and Humsavar for CHI3L2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs13721 benign, not specified 111,241,360(+) C/A/T coding_sequence_variant, missense_variant, synonymous_variant
rs1000119976 -- 111,235,174(+) C/T intron_variant
rs1000289785 -- 111,235,466(+) T/C intron_variant
rs1000414696 -- 111,240,956(+) A/G intron_variant
rs1000596071 -- 111,236,450(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CHI3L2 Gene

Variant ID Type Subtype PubMed ID
nsv10639 CNV gain 18304495
nsv463250 CNV loss 19166990
nsv547535 CNV loss 21841781

Variation tolerance for CHI3L2 Gene

Residual Variation Intolerance Score: 89.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.67; 72.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHI3L2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHI3L2 Gene

Disorders for CHI3L2 Gene

Additional Disease Information for CHI3L2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CHI3L2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CHI3L2 Gene

Publications for CHI3L2 Gene

  1. Isolation and sequence of a novel human chondrocyte protein related to mammalian members of the chitinase protein family. (PMID: 8702629) Hu B … Price PA (The Journal of biological chemistry 1996) 2 3 4 22 58
  2. Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties. (PMID: 22742450) Schimpl M … van Aalten DM (The Biochemical journal 2012) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Enhanced expression of the human chitinase 3-like 2 gene (YKL-39) but not chitinase 3-like 1 gene (YKL-40) in osteoarthritic cartilage. (PMID: 12435396) Steck E … Richter W (Biochemical and biophysical research communications 2002) 3 22 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for CHI3L2 Gene

Sources for CHI3L2 Gene

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