CHIT1

chitinase 1, the group of Chitinases

Basic information

Region (hg38): 1:203212827-203273641

Links

ENSG00000133063 ∙ NCBI:1118 ∙ OMIM:600031 ∙ HGNC:1936 ∙ Uniprot:Q13231 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Chitotriosidase deficiency	AR	General	Variants may have implications for monitoring (including related to therapy) in Gaucher disease; Testing relevant to Gaucher disease, if necessary, would be tested as part of care	Biochemical	8132768; 9748235; 16972172; 17464953; 17693102; 15900564; 15528158; 22959626

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHIT1 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			3	18	3	24
missense			37	6	30	73
nonsense			2	1		3
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region				5	3	8
non coding			19	6	2	27
Total	0	0	64	31	36

Variants in CHIT1

This is a list of pathogenic ClinVar variants found in the CHIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-203216107-G-A		Chitotriosidase deficiency	Uncertain significance (Jun 14, 2016)
1-203216135-T-G		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216146-G-C		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216160-A-G		Chitotriosidase deficiency	Uncertain significance (Jan 12, 2018)
1-203216290-G-C		Chitotriosidase deficiency	Uncertain significance (Jan 12, 2018)
1-203216355-A-C		Chitotriosidase deficiency	Benign (Jan 12, 2018)
1-203216439-C-T		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216486-C-T		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216609-C-G		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216651-G-A		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216746-T-C		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216765-T-G		Chitotriosidase deficiency	Uncertain significance (Jan 12, 2018)
1-203216770-G-A		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216790-C-T		Chitotriosidase deficiency	Uncertain significance (Jan 12, 2018)
1-203216804-C-T		Chitotriosidase deficiency	Uncertain significance (Apr 27, 2017)
1-203216832-G-A		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216914-G-C		not specified	Uncertain significance (Apr 22, 2022)
1-203216932-C-A		Chitotriosidase deficiency	Benign (May 06, 2021)
1-203216934-T-C		Chitotriosidase deficiency	Uncertain significance (Jan 13, 2018)
1-203216938-G-C		Chitotriosidase deficiency • not specified	Uncertain significance (Feb 28, 2023)
1-203216939-G-A		Chitotriosidase deficiency	Conflicting classifications of pathogenicity (Jan 12, 2024)
1-203216940-G-A		Chitotriosidase deficiency	Conflicting classifications of pathogenicity (Nov 28, 2021)
1-203216946-T-C		Chitotriosidase deficiency	Likely benign (Aug 30, 2023)
1-203216964-C-T		Chitotriosidase deficiency	Conflicting classifications of pathogenicity (Jan 15, 2024)
1-203216965-G-A		Chitotriosidase deficiency	Conflicting classifications of pathogenicity (Nov 18, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHIT1	protein_coding	protein_coding	ENST00000367229	11	60815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.17e-16	0.0159	123431	60	2257	125748	0.00926

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.191	265	256	1.03	0.0000153	3037
Missense in Polyphen		104	94.746	1.0977		1236
Synonymous	-0.856	115	104	1.11	0.00000655	903
Loss of Function	0.222	24	25.2	0.952	0.00000120	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0902	0.0902
Ashkenazi Jewish	0.00655	0.00657
East Asian	0.000273	0.000272
Finnish	0.00618	0.00616
European (Non-Finnish)	0.00431	0.00430
Middle Eastern	0.000273	0.000272
South Asian	0.00258	0.00255
Other	0.00636	0.00621

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Degrades chitin, chitotriose and chitobiose. May participate in the defense against nematodes and other pathogens. Isoform 3 has no enzymatic activity. {ECO:0000269|PubMed:7592832, ECO:0000269|PubMed:7836450}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;Neutrophil degranulation;Digestion of dietary carbohydrate;Innate Immune System;Immune System;Aminosugars metabolism;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.264

Intolerance Scores

• loftool: 0.923
• rvis_EVS: 1.05
• rvis_percentile_EVS: 91.32

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chit1
• Phenotype: immune system phenotype

Gene ontology

• Biological process: polysaccharide catabolic process;chitin catabolic process;immune response;response to bacterium;neutrophil degranulation;polysaccharide digestion
• Cellular component: extracellular region;extracellular space;lysosome;specific granule lumen;tertiary granule lumen
• Molecular function: hydrolase activity, hydrolyzing O-glycosyl compounds;chitinase activity;chitin binding;endochitinase activity