CHI3L2

chitinase 3 like 2, the group of Chitinases

Basic information

Region (hg38): 1:111200770-111243440

Links

ENSG00000064886 ∙ NCBI:1117 ∙ OMIM:601526 ∙ HGNC:1933 ∙ Uniprot:Q15782 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHI3L2 gene.

• Inborn genetic diseases (20 variants)
• not provided (4 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHI3L2 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	1	2
missense			19		2	21
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	21	1	3

Variants in CHI3L2

This is a list of pathogenic ClinVar variants found in the CHI3L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-111227760-C-A		not specified	Uncertain significance (Jul 09, 2021)
1-111229869-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-111229879-G-A		not specified	Uncertain significance (Dec 14, 2021)
1-111230756-C-G		not specified	Uncertain significance (Nov 13, 2023)
1-111230789-C-T		not specified	Uncertain significance (Sep 19, 2022)
1-111230861-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-111230897-A-G		not specified	Uncertain significance (Apr 08, 2022)
1-111230935-C-T			Likely benign (Apr 26, 2018)
1-111231255-T-A		not specified	Uncertain significance (Feb 28, 2023)
1-111231281-T-C		not specified	Uncertain significance (Nov 01, 2022)
1-111234907-G-A		not specified	Likely benign (Dec 20, 2023)
1-111234963-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-111235001-G-A		not specified	Likely benign (Dec 11, 2023)
1-111235676-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-111235708-G-A			Benign (Mar 29, 2018)
1-111235744-C-G		not specified	Uncertain significance (Feb 10, 2022)
1-111236062-A-G		not specified	Uncertain significance (Jul 12, 2023)
1-111236119-G-T		not specified	Uncertain significance (Jun 14, 2023)
1-111236130-G-A		not specified	Uncertain significance (Apr 08, 2023)
1-111238768-T-C		not specified	Uncertain significance (Oct 25, 2022)
1-111238787-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-111238804-A-T		not specified	Uncertain significance (Jul 05, 2023)
1-111238879-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-111238913-G-C		not specified	Uncertain significance (Oct 24, 2023)
1-111241358-C-T		not specified	Uncertain significance (Dec 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHI3L2	protein_coding	protein_coding	ENST00000445067	10	42670

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.99e-14	0.0158	125622	1	125	125748	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.427	223	206	1.08	0.00000959	2564
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00295	0.00295
Ashkenazi Jewish	0.00	0.00
East Asian	0.000279	0.000272
Finnish	0.000142	0.0000924
European (Non-Finnish)	0.000348	0.000334
Middle Eastern	0.000279	0.000272
South Asian	0.000443	0.000425
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.215
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.456

Gene Damage Prediction

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

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: extracellular region;extracellular space
• Molecular function: chitinase activity;chitin binding;carbohydrate binding