CHI3L1

chitinase 3 like 1, the group of Chitinases

Basic information

Region (hg38): 1:203178931-203186704

Links

ENSG00000133048 ∙ NCBI:1116 ∙ OMIM:601525 ∙ HGNC:1932 ∙ Uniprot:P36222 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHI3L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHI3L1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	2	2

Variants in CHI3L1

This is a list of pathogenic ClinVar variants found in the CHI3L1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-203179449-G-A		not specified	Uncertain significance (May 26, 2024)
1-203179509-A-C		not specified	Uncertain significance (Mar 22, 2023)
1-203179515-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-203179557-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-203179768-T-C		not specified	Uncertain significance (Jun 27, 2023)
1-203179774-C-A		not specified	Uncertain significance (Jun 13, 2024)
1-203179790-A-G		not specified	Uncertain significance (Mar 28, 2023)
1-203179822-G-C		not specified	Uncertain significance (Apr 18, 2023)
1-203179835-C-T		not specified	Uncertain significance (Jun 13, 2024)
1-203179862-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-203180544-C-T		not specified	Uncertain significance (May 29, 2024)
1-203180582-A-G		not specified	Uncertain significance (Dec 13, 2022)
1-203180585-G-C		not specified	Uncertain significance (Dec 05, 2022)
1-203180597-A-G		not specified	Uncertain significance (Jul 09, 2021)
1-203180634-T-G		not specified	Uncertain significance (Feb 27, 2023)
1-203180641-C-T			Benign (May 21, 2018)
1-203181184-C-A		not specified	Uncertain significance (Dec 21, 2023)
1-203181184-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-203181202-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-203181235-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-203181247-T-C		not specified	Uncertain significance (Aug 08, 2023)
1-203181257-A-G		not specified	Uncertain significance (Mar 15, 2024)
1-203182740-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-203182778-C-T		not specified	Likely benign (Aug 04, 2023)
1-203182779-G-A		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHI3L1	protein_coding	protein_coding	ENST00000255409	10	7819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000111	0.949	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.579	253	228	1.11	0.0000134	2514
Missense in Polyphen		86	80.826	1.064		1006
Synonymous	-1.28	109	93.2	1.17	0.00000608	749
Loss of Function	1.82	11	19.7	0.558	9.27e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000248
Ashkenazi Jewish	0.00	0.00
East Asian	0.00262	0.00256
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.00262	0.00256
South Asian	0.0000653	0.0000653
Other	0.000194	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Carbohydrate-binding lectin with a preference for chitin. Has no chitinase activity. May play a role in tissue remodeling and in the capacity of cells to respond to and cope with changes in their environment. Plays a role in T-helper cell type 2 (Th2) inflammatory response and IL-13-induced inflammation, regulating allergen sensitization, inflammatory cell apoptosis, dendritic cell accumulation and M2 macrophage differentiation. Facilitates invasion of pathogenic enteric bacteria into colonic mucosa and lymphoid organs. Mediates activation of AKT1 signaling pathway and subsequent IL8 production in colonic epithelial cells. Regulates antibacterial responses in lung by contributing to macrophage bacterial killing, controlling bacterial dissemination and augmenting host tolerance. Also regulates hyperoxia-induced injury, inflammation and epithelial apoptosis in lung. {ECO:0000269|PubMed:16472595, ECO:0000269|PubMed:19414556, ECO:0000269|PubMed:20558631, ECO:0000269|PubMed:9492324}.
• Disease: DISEASE: Asthma-related traits 7 (ASRT7) [MIM:611960]: Asthma- related traits include clinical symptoms of asthma, such as coughing, wheezing, dyspnea, bronchial hyperresponsiveness as assessed by methacholine challenge test, serum IgE levels, atopy and atopic dermatitis. {ECO:0000269|PubMed:18403759}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:17160890, ECO:0000269|PubMed:20051317}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Mammary gland development pathway - Involution (Stage 4 of 4);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.349

Intolerance Scores

• loftool: 0.727
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.98

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.203
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.563

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chil1
• Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;apoptotic process;inflammatory response;activation of NF-kappaB-inducing kinase activity;response to mechanical stimulus;positive regulation of peptidyl-threonine phosphorylation;lung development;response to tumor necrosis factor;neutrophil degranulation;positive regulation of angiogenesis;cartilage development;positive regulation of protein kinase B signaling;positive regulation of ERK1 and ERK2 cascade;response to interleukin-1;response to interleukin-6;cellular response to interleukin-1;cellular response to tumor necrosis factor;interleukin-8 secretion
• Cellular component: extracellular region;extracellular space;cytoplasm;endoplasmic reticulum;extracellular matrix;specific granule lumen;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: chitinase activity;extracellular matrix structural constituent;protein binding;chitin binding;carbohydrate binding