CHIA

protein-coding

chitinase acidic, the group of Chitinases

Gene summary

The protein encoded by this gene degrades chitin, which is found in the cell wall of most fungi as well as in arthropods and some nematodes. The encoded protein can also stimulate interleukin 13 expression, and variations in this gene can lead to asthma susceptibility. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

MANE transcript

NM_201653.4

Inheritance

—

ClinVar variants

U:90B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr1:111,290,851-111,320,566

External References & Databases

Ensembl (ENSG00000134216)

Transcript & Mutation Effects

hg38 • Region Span ~29.7 kb

Loading mutation effect viewer...

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 CHIA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_201653.4. 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				1 clinvar	4 clinvar	5
missense			89 clinvar	6 clinvar	2 clinvar	97
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	90	7	7	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_201653.4	RefSeq	NP_970615.2	11	MANE Select
ENST00000369740.6	Ensembl	ENSP00000358755.1	11	MANE Select
NM_001040623.3	RefSeq	NP_001035713.1	6	Standard
NM_001258001.2	RefSeq	NP_001244930.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
Aminosugars metabolism

Biological Process

polysaccharide catabolic process
immune system process
production of molecular mediator involved in inflammatory response
chitin metabolic process
chitin catabolic process

Molecular Function

chitinase activity
protein binding
chitin binding
kinase binding

Cellular Component

extracellular region
extracellular space
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369740
Coding exons: 11
Length: 29705
Individuals with no LoFs: 123670
Homozygous LoFs: 44
Heterozygous LoFs: 2034
Defined: 125748
p: 0.00830

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.448	294	273	1.08	0.0000145	3127
Missense (PolyPhen)		92	87.031	1.0571		1120
Synonymous	-1.03	122	108	1.13	0.00000661	897
Loss of Function	0.624	22	25.4	0.866	0.00000118	274

Population LoF Frequency

Population	CAF	p-value	Status
African	0.091	0.090	notable
Latino/Admixed American	0.0073	0.0073	notable
Ashkenazi Jewish	0.0058	0.0057	notable
East Asian	0.00022	0.00022	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.0025	0.0025	notable
South Asian	0.0011	0.0011	notable
Other	0.0064	0.0064	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Degrades chitin and chitotriose. May participate in the defense against nematodes, fungi and other pathogens. Plays a role in T-helper cell type 2 (Th2) immune response. Contributes to the response to IL-13 and inflammation in response to IL-13. Stimulates chemokine production by pulmonary epithelial cells. Protects lung epithelial cells against apoptosis and promotes phosphorylation of AKT1. Its function in the inflammatory response and in protecting cells against apoptosis is inhibited by allosamidin, suggesting that the function of this protein depends on carbohydrate binding. {ECO:0000269|PubMed:11085997, ECO:0000269|PubMed:18824549, ECO:0000269|PubMed:19342690, ECO:0000269|PubMed:19435888}.;

Recessive Scores

pRec: 0.217

Intolerance Scores

LoFtool: 0.976
RVIS EVS: 2.09
RVIS percentile EVS: 97.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.541

Gene Damage Prediction

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