CHID1

chitinase domain containing 1, the group of Chitinases

Basic information

Region (hg38): 11:867859-915058

Links

ENSG00000177830 ∙ NCBI:66005 ∙ OMIM:615692 ∙ HGNC:28474 ∙ Uniprot:Q9BWS9 ∙ 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 CHID1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHID1 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						0
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in CHID1

This is a list of pathogenic ClinVar variants found in the CHID1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-869893-C-T		not specified	Uncertain significance (Mar 12, 2024)
11-869943-C-T		not specified	Uncertain significance (Mar 04, 2024)
11-870141-C-T		not specified	Uncertain significance (Jul 11, 2023)
11-870144-C-T		not specified	Uncertain significance (May 23, 2023)
11-883151-G-A		not specified	Uncertain significance (Apr 23, 2024)
11-883155-C-T		not specified	Uncertain significance (Dec 14, 2023)
11-883188-C-T		not specified	Uncertain significance (May 23, 2024)
11-884087-C-T		not specified	Uncertain significance (Feb 02, 2022)
11-884117-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-884146-G-A		not specified	Uncertain significance (Nov 09, 2022)
11-884165-C-T		not specified	Uncertain significance (Jun 28, 2022)
11-893472-G-A		not specified	Uncertain significance (Nov 18, 2022)
11-899349-T-C		not specified	Uncertain significance (Jun 05, 2023)
11-899380-C-T		not specified	Uncertain significance (Mar 28, 2023)
11-899389-C-A		not specified	Uncertain significance (Mar 14, 2023)
11-899389-C-T		not specified	Uncertain significance (Mar 31, 2023)
11-902207-C-T		not specified	Uncertain significance (Sep 27, 2022)
11-902234-T-A		not specified	Uncertain significance (Jan 23, 2023)
11-902240-G-A		not specified	Uncertain significance (May 01, 2024)
11-902277-C-A		not specified	Likely benign (Dec 16, 2023)
11-902982-C-T		not specified	Uncertain significance (Apr 01, 2024)
11-902990-G-A		not specified	Uncertain significance (Apr 27, 2022)
11-903107-T-C		not specified	Uncertain significance (Dec 12, 2023)
11-904719-G-A		not specified	Uncertain significance (Mar 25, 2024)
11-904723-T-C		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHID1	protein_coding	protein_coding	ENST00000454838	13	47702

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000138	0.992	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.928	210	251	0.835	0.0000162	2699
Missense in Polyphen		42	58.374	0.7195		675
Synonymous	-0.203	110	107	1.02	0.00000722	825
Loss of Function	2.35	12	24.6	0.488	0.00000129	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000610	0.000598
Middle Eastern	0.0000544	0.0000544
South Asian	0.000294	0.000294
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Saccharide- and LPS-binding protein with possible roles in pathogen sensing and endotoxin neutralization. Ligand-binding specificity relates to the length of the oligosaccharides, with preference for chitotetraose (in vitro). {ECO:0000269|PubMed:20724479}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.825
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.179
• hipred: N
• hipred_score: 0.289
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.291

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chid1

Gene ontology

• Biological process: platelet degranulation;carbohydrate metabolic process;innate immune response;negative regulation of cytokine production involved in inflammatory response
• Cellular component: extracellular region;extracellular space;nucleus;lysosome;late endosome;trans-Golgi network;membrane;lysosomal lumen;extracellular exosome
• Molecular function: protein binding;chitin binding;oligosaccharide binding