CHI3L2

protein-coding

chitinase 3 like 2, the group of Chitinases

Gene 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]

MANE transcript

NM_004000.3

Inheritance

—

ClinVar variants

U:62B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr1:111,200,771-111,243,440

External References & Databases

Ensembl (ENSG00000064886)

Transcript & Mutation Effects

hg38 • Region Span ~42.7 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 CHI3L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004000.3. 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			2 clinvar	2 clinvar	1 clinvar	5
missense			57 clinvar	2 clinvar		59
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	62	4	1	67

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004000.3	RefSeq	NP_003991.2	10	MANE Select
ENST00000369748.9	Ensembl	ENSP00000358763.4	10	MANE Select
NM_001025197.1	RefSeq	NP_001020368.1	9	Standard
NM_001025199.2	RefSeq	NP_001020370.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

carbohydrate metabolic process

Molecular Function

chitinase activity
chitin binding
carbohydrate binding

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000445067
Coding exons: 10
Length: 42670
Individuals with no LoFs: 125622
Homozygous LoFs: 1
Heterozygous LoFs: 125
Defined: 125748
p: 0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.427	223	206	1.08	0.00000959	2564
Missense (PolyPhen)		72	75.881	0.94886		1012
Synonymous	-1.61	96	78.0	1.23	0.00000377	731
Loss of Function	-0.0238	21	20.9	1.01	8.82e-7	256

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0018	0.0018	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.00014	0.000092	rare
European (Non-Finnish)	0.00035	0.00033	rare
South Asian	0.00044	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Lectin that binds chitooligosaccharides and other glycans with high affinity, but not heparin. Has no chitinase activity. {ECO:0000269|PubMed:22742450}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.945
RVIS EVS: 0.15
RVIS percentile EVS: 64.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.456

Gene Damage Prediction

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