CHIA

chitinase acidic, the group of Chitinases

Basic information

Region (hg38): 1:111290851-111320566

Links

ENSG00000134216 ∙ NCBI:27159 ∙ OMIM:606080 ∙ HGNC:17432 ∙ Uniprot:Q9BZP6 ∙ 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 CHIA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHIA 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					4	4
missense			23	1	3	27
nonsense						0
start loss			1			1
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	8

Variants in CHIA

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

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

Position	Type	Phenotype	Significance	ClinVar
1-111310472-C-T		not specified	Uncertain significance (Feb 17, 2022)
1-111310478-T-G		not specified	Uncertain significance (Jun 21, 2023)
1-111312237-C-T			Benign (Jun 15, 2018)
1-111312238-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-111312286-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-111312303-G-A			Likely benign (Jul 31, 2018)
1-111312333-A-T		not specified	Uncertain significance (Mar 16, 2024)
1-111312370-C-G		not specified	Uncertain significance (Apr 15, 2024)
1-111314543-C-G		not specified	Uncertain significance (Oct 03, 2023)
1-111315282-G-A		not specified	Uncertain significance (Jan 02, 2024)
1-111315301-C-T		not specified	Uncertain significance (Apr 13, 2022)
1-111315337-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-111315400-C-T		not specified	Uncertain significance (May 08, 2024)
1-111315429-G-C			Benign (May 17, 2018)
1-111315431-T-G		not specified	Uncertain significance (Mar 23, 2023)
1-111317715-A-G		not specified	Uncertain significance (Feb 02, 2022)
1-111318017-G-A		not specified	Uncertain significance (Aug 03, 2022)
1-111318082-C-A		not specified	Uncertain significance (Feb 21, 2024)
1-111318516-G-A			Benign (Aug 21, 2018)
1-111318520-A-T		not specified	Uncertain significance (Jul 15, 2021)
1-111318545-T-A		not specified	Uncertain significance (Mar 07, 2024)
1-111318553-T-G		not specified	Uncertain significance (Dec 07, 2021)
1-111318568-C-T		not specified	Uncertain significance (Oct 05, 2022)
1-111318579-C-A			Benign (Jan 08, 2018)
1-111318611-C-T		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHIA	protein_coding	protein_coding	ENST00000369740	11	29705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-13	0.0773	123670	44	2034	125748	0.00830

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.448	294	273	1.08	0.0000145	3127
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0985	0.0975
Ashkenazi Jewish	0.00576	0.00567
East Asian	0.000219	0.000217
Finnish	0.000232	0.000231
European (Non-Finnish)	0.00252	0.00252
Middle Eastern	0.000219	0.000217
South Asian	0.00112	0.00111
Other	0.00638	0.00637

dbNSFP

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}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Aminosugars metabolism (Consensus)

Recessive Scores

• pRec: 0.217

Intolerance Scores

• loftool: 0.976
• rvis_EVS: 2.09
• rvis_percentile_EVS: 97.87

Haploinsufficiency Scores

• pHI: 0.0775
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chia1
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: polysaccharide catabolic process;immune system process;production of molecular mediator involved in inflammatory response;chitin metabolic process;chitin catabolic process;apoptotic process;polysaccharide digestion;positive regulation of chemokine secretion
• Cellular component: extracellular region;extracellular space;cytoplasm
• Molecular function: chitinase activity;protein binding;chitin binding;kinase binding