CHID1
protein-codingchitinase domain containing 1, the group of Chitinases
Gene summary
Enables oligosaccharide binding activity. Involved in negative regulation of cytokine production involved in inflammatory response. Located in several cellular components, including late endosome; obsolete extracellular space; and trans-Golgi network. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.2 kbGenCC 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 CHID1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_023947.4. 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 | 1 | ||||
| missense | 58 | 4 | 62 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 64 | 4 | 0 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_076436.3 | 12 | MANE Select | |
| Ensembl | ENSP00000325055.8 | 12 | MANE Select | |
| RefSeq | NP_001136146.1 | 12 | Standard | |
| RefSeq | NP_001136147.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Platelet degranulation
- Response to elevated platelet cytosolic Ca2+
- Platelet activation, signaling and aggregation
- Hemostasis
Biological Process
- platelet degranulation
- carbohydrate metabolic process
- innate immune response
- negative regulation of cytokine production involved in inflammatory response
Molecular Function
- protein binding
- chitin binding
- oligosaccharide binding
Cellular Component
- extracellular region
- extracellular space
- nucleus
- lysosome
- late endosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000454838
- Coding exons
- 13
- Length
- 47702
- Individuals with no LoFs
- 125659
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 89
- Defined
- 125748
- p
- 0.000354
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.928 | 210 | 251 | 0.835 | 0.0000162 | 2699 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00061 | 0.00060 | rare |
| South Asian | 0.00029 | 0.00029 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.825
- RVIS EVS
- -0.18
- RVIS percentile EVS
- 40.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.291
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |