CHI3L2 chitinase 3 like 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHI3L2provided by HGNC
Official Full Name: chitinase 3 like 2provided by HGNC
Primary source: HGNC:HGNC:1933
See related: Ensembl:ENSG00000064886 MIM:601526; AllianceGenome:HGNC:1933
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: CHIL2; YKL39; YKL-39
Summary: 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]
Expression: Biased expression in appendix (RPKM 55.9), salivary gland (RPKM 27.1) and 11 other tissues See more
Orthologs: all
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Genomic context

Location:: 1p13.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (111227659..111243440)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (111241751..111258269)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (111770281..111786062)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

M2 macrophage marker CHI3L2 could serve as a potential prognostic and immunological biomarker in glioma by integrated single-cell and bulk RNA-Seq analysis.
Title: M2 macrophage marker CHI3L2 could serve as a potential prognostic and immunological biomarker in glioma by integrated single-cell and bulk RNA-Seq analysis.
An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes.
Title: An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 (CHI3L2) as a potential mediator of B12 deficiency in adipocytes.
Chitinase 3-Like 2.
Title: Chitinase 3-Like 2.
IL-2, IL-6 and chitinase 3-like 2 might predict early relapse activity in multiple sclerosis.
Title: IL-2, IL-6 and chitinase 3-like 2 might predict early relapse activity in multiple sclerosis.
Circular RNA circ-CHI3L1.2 modulates cisplatin resistance of osteosarcoma cells via the miR-340-5p/LPAATbeta axis.
Title: Circular RNA circ-CHI3L1.2 modulates cisplatin resistance of osteosarcoma cells via the miR-340-5p/LPAATβ axis.
Lack of association of CD44-rs353630 and CHI3L2-rs684559 with pancreatic ductal adenocarcinoma survival.
Title: Lack of association of CD44-rs353630 and CHI3L2-rs684559 with pancreatic ductal adenocarcinoma survival.
Comprehensive Analysis of CD163 as a Prognostic Biomarker and Associated with Immune Infiltration in Glioblastoma Multiforme.
Title: Comprehensive Analysis of CD163 as a Prognostic Biomarker and Associated with Immune Infiltration in Glioblastoma Multiforme.
YKL-39 as a Potential New Target for Anti-Angiogenic Therapy in Cancer.
Title: YKL-39 as a Potential New Target for Anti-Angiogenic Therapy in Cancer.
Results find that expression of CHI3L2 in tumor cells of conventional small renal cell carcinomas defines a group of patients at high risk for postoperative progression.
Title: M2 Macrophage Marker Chitinase 3-Like 2 (CHI3L2) Associates With Progression of Conventional Renal Cell Carcinoma.
In patients with breast cancer who received anthracycline-containing NAC the absence of clinical response is associated with the presence of M2+ macrophage phenotype (YKL-39-CCL18 + or YKL-39 + CCL18-) based on TOP2a overexpression data.
Title: Expression of M2 macrophage markers YKL-39 and CCL18 in breast cancer is associated with the effect of neoadjuvant chemotherapy.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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

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
Tat	tat	Microarray analysis indicates HIV-1 Tat-induced upregulation of chitinase 3-like 2 (CHI3L2) in primary human brain microvascular endothelial cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-75289 (e-PCR)
- UniSTS:22640

AL034262 (e-PCR)
- UniSTS:94083

SHGC-75295 (e-PCR)
- UniSTS:15265

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

Process	Evidence Code	Pubs
involved_in carbohydrate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in chitin catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in extracellular region	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	HDA more info	PubMed

General protein information

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Preferred Names: chitinase-3-like protein 2

Names: chondrocyte protein 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.

mRNA and Protein(s)

NM_001025197.1 → NP_001020368.1 chitinase-3-like protein 2 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

BM787868, BQ181849, U58514

Consensus CDS

CCDS30803.1

UniProtKB/TrEMBL

Q53FH2

Related

ENSP00000358759.2, ENST00000369744.6

Conserved Domains (2) summary

cd02872
Location:19 → 377

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:18 → 355

Glyco_18; Glyco_18 domain
NM_001025199.2 → NP_001020370.1 chitinase-3-like protein 2 isoform c

See identical proteins and their annotated locations for NP_001020370.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.

Source sequence(s)

BQ181849, U58514, U58515

Consensus CDS

CCDS41367.1

UniProtKB/TrEMBL

Q53FH2

Related

ENSP00000437086.1, ENST00000466741.5

Conserved Domains (2) summary

cd02872
Location:2 → 308

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:3 → 286

Glyco_18; Glyco_18 domain
NM_004000.3 → NP_003991.2 chitinase-3-like protein 2 isoform a precursor

See identical proteins and their annotated locations for NP_003991.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

BG698401, BQ181849, U58514

Consensus CDS

CCDS30802.1

UniProtKB/Swiss-Prot

A6NNY3, B4DPR7, Q15749, Q15782, Q15783, Q5VUV7, Q96F97

UniProtKB/TrEMBL

Q53FH2

Related

ENSP00000358763.4, ENST00000369748.9

Conserved Domains (1) summary

cd02872
Location:29 → 387

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 ...