CHID1

gene
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Also known as MGC3234FLJ42707SI-CLP

Summary

CHID1 (chitinase domain containing 1, HGNC:28474) is a protein-coding gene on chromosome 11p15.5, encoding Chitinase domain-containing protein 1 (Q9BWS9). Saccharide- and LPS-binding protein with possible roles in pathogen sensing and endotoxin neutralization.

Enables oligosaccharide binding activity. Involved in negative regulation of cytokine production involved in inflammatory response. Located in several cellular components, including late endosome; lysosome; and trans-Golgi network.

Source: NCBI Gene 66005 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 76 total — 1 pathogenic
  • MANE Select transcript: NM_023947

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28474
Approved symbolCHID1
Namechitinase domain containing 1
Location11p15.5
Locus typegene with protein product
StatusApproved
AliasesMGC3234, FLJ42707, SI-CLP
Ensembl geneENSG00000177830
Ensembl biotypeprotein_coding
OMIM615692
Entrez66005

Gene structure

Transcript identifiers

Ensembl transcripts: 66 — 57 protein_coding, 5 nonsense_mediated_decay, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000323578, ENST00000429789, ENST00000436108, ENST00000449825, ENST00000454838, ENST00000524538, ENST00000524832, ENST00000525225, ENST00000525840, ENST00000526714, ENST00000528154, ENST00000528426, ENST00000528521, ENST00000528534, ENST00000528581, ENST00000529539, ENST00000530939, ENST00000531010, ENST00000531859, ENST00000532909, ENST00000533056, ENST00000533059, ENST00000534207, ENST00000534254, ENST00000903752, ENST00000903753, ENST00000903754, ENST00000903755, ENST00000903756, ENST00000903757, ENST00000903758, ENST00000903759, ENST00000903760, ENST00000903761, ENST00000903762, ENST00000903763, ENST00000903764, ENST00000903765, ENST00000903766, ENST00000903767, ENST00000903768, ENST00000903769, ENST00000903770, ENST00000903771, ENST00000903772, ENST00000924111, ENST00000924112, ENST00000924113, ENST00000924114, ENST00000924115, ENST00000924116, ENST00000924117, ENST00000924118, ENST00000924119, ENST00000924120, ENST00000970720, ENST00000970721, ENST00000970722, ENST00000970723, ENST00000970724, ENST00000970725, ENST00000970726, ENST00000970727, ENST00000970728, ENST00000970729, ENST00000970730

RefSeq mRNA: 5 — MANE Select: NM_023947 NM_001142674, NM_001142675, NM_001142676, NM_001142677, NM_023947

CCDS: CCDS44510, CCDS44511, CCDS7722

Canonical transcript exons

ENST00000323578 — 13 exons

ExonStartEnd
ENSE00001958037867859869956
ENSE00002141308910775910810
ENSE00003481765902198902330
ENSE00003535970870121870163
ENSE00003538547899340899401
ENSE00003592892883148883303
ENSE00003594152884068884169
ENSE00003613969902962903111
ENSE00003621317900004900110
ENSE00003624404900936900980
ENSE00003657827904706904859
ENSE00003658118870419870499
ENSE00003693169893427893519

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 97.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.1529 / max 104.0594, expressed in 1813 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
11784728.63601811
1178500.2646103
1178520.073434
1178490.059129
1178530.057514
1178510.023911
1178540.02138
1178480.00762
2060820.00594
1178550.00351

Top tissues by expression

254 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225597.86gold quality
body of pancreasUBERON:000115097.27gold quality
right testisUBERON:000453497.05gold quality
left testisUBERON:000453396.81gold quality
pancreasUBERON:000126496.14gold quality
right lobe of liverUBERON:000111496.07gold quality
adenohypophysisUBERON:000219696.00gold quality
right adrenal gland cortexUBERON:003582796.00gold quality
islet of LangerhansUBERON:000000695.97gold quality
right uterine tubeUBERON:000130295.89gold quality
right adrenal glandUBERON:000123395.86gold quality
left adrenal glandUBERON:000123495.81gold quality
left adrenal gland cortexUBERON:003582595.61gold quality
spleenUBERON:000210695.59gold quality
right coronary arteryUBERON:000162595.56gold quality
right ovaryUBERON:000211895.36gold quality
pituitary glandUBERON:000000795.32gold quality
left ovaryUBERON:000211995.32gold quality
testisUBERON:000047395.16gold quality
right atrium auricular regionUBERON:000663194.92gold quality
gall bladderUBERON:000211094.87gold quality
descending thoracic aortaUBERON:000234594.72gold quality
minor salivary glandUBERON:000183094.71gold quality
body of stomachUBERON:000116194.67gold quality
adrenal cortexUBERON:000123594.64gold quality
thoracic aortaUBERON:000151594.63gold quality
adrenal glandUBERON:000236994.63gold quality
ascending aortaUBERON:000149694.59gold quality
left coronary arteryUBERON:000162694.59gold quality
endocervixUBERON:000045894.56gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-5061yes27.39
E-ANND-3yes17.99
E-CURD-112no3.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting CHID1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-444799.8567.812900
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-317599.6566.302031
HSA-MIR-715099.6266.801322
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-486-3P99.5166.821901
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-3191-3P99.4563.94356
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-6751-3P98.4466.35835
HSA-MIR-1199-5P98.4466.51829
HSA-MIR-473697.9665.891287
HSA-MIR-6810-3P97.9664.571023
HSA-MIR-66597.6065.641781
HSA-MIR-425397.4865.11692
HSA-MIR-6862-5P97.4864.84713
HSA-MIR-5699-5P97.3667.031014
HSA-MIR-7106-3P97.3365.33644

Literature-anchored findings (GeneRIF, showing 8)

  • The crystals of SI-CLP belong to the space group P3(2)21 with unit cell parameters a=b=99.79 A, c=250.53 A, alpha=beta=90 degrees, gamma=120 degrees. (PMID:19275751)
  • Structure of human stabilin-1 interacting chitinase-like protein (SI-CLP) reveals a saccharide-binding cleft with lower sugar-binding selectivity. (PMID:20724479)
  • stabilin-1-interacting chitinase-like protein functions as a regulator of the inflammatory response in rheumatoid arthritis by macrophages. (PMID:24470346)
  • This review comprehensively analyzes recent data about expression pattern, and involvement of human YKL-40, YKL-39 and SI-CLP in cancer. [review] (PMID:26733160)
  • These results indicate that CHID1 positively regulates RLR antiviral signal, revealing the novel mechanism of the RIG-I antiviral signaling pathway. (PMID:31106867)
  • CHID1 Is a Novel Prognostic Marker of Non-Small Cell Lung Cancer. (PMID:33466316)
  • Brain CHID1 Expression Correlates with NRGN and CALB1 in Healthy Subjects and AD Patients. (PMID:33924468)
  • Chitinase domain containing 1 increase is associated with low survival rate and M0 macrophages infiltrates in colorectal cancer patients. (PMID:35932496)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriochid1ENSDARG00000069673
mus_musculusChid1ENSMUSG00000025512
rattus_norvegicusChid1ENSRNOG00000063613
drosophila_melanogasterCG8460FBGN0031996
caenorhabditis_elegansWBGENE00019980

Paralogs (6): CHI3L2 (ENSG00000064886), OVGP1 (ENSG00000085465), CTBS (ENSG00000117151), CHI3L1 (ENSG00000133048), CHIT1 (ENSG00000133063), CHIA (ENSG00000134216)

Protein

Protein identifiers

Chitinase domain-containing protein 1Q9BWS9 (reviewed: Q9BWS9)

Alternative names: Stabilin-1-interacting chitinase-like protein

All UniProt accessions (14): E9PI70, E9PIP0, E9PJ91, E9PJL0, E9PKF1, E9PPA0, E9PPH0, E9PQZ0, E9PRL3, Q9BWS9, H0YC89, H0YCC4, H0YDL6, H0YEA3

UniProt curated annotations — full annotation on UniProt →

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).

Subunit / interactions. Interacts with STAB1.

Subcellular location. Secreted. Lysosome.

Tissue specificity. Expressed in cells of monocytic, T, B and epithelial origin.

Induction. Up-regulated by IL4/interleukin-4 and dexamethasone in the macrophages. Up-regulated by glucocorticoid.

Similarity. Belongs to the glycosyl hydrolase 18 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9BWS9-11yes
Q9BWS9-22
Q9BWS9-33

RefSeq proteins (5): NP_001136146, NP_001136147, NP_001136148, NP_001136149, NP_076436* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001223Glyco_hydro18_catDomain
IPR011583Chitinase_II/V-like_catDomain
IPR017853GH_hydrolase_sfHomologous_superfamily
IPR029070Chitinase_insertion_sfHomologous_superfamily

Pfam: PF00704

UniProt features (52 total): helix 16, strand 16, mutagenesis site 6, turn 6, splice variant 2, sequence variant 2, signal peptide 1, chain 1, sequence conflict 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3BXWX-RAY DIFFRACTION2.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BWS9-F191.610.86

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (6):

PositionPhenotype
261significantly decreased carbohydrate binding.
277no noticeable effect.
302significantly decreased carbohydrate binding.
84significantly decreased carbohydrate binding.
88significantly decreased carbohydrate binding.
110significantly decreased carbohydrate binding.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-114608Platelet degranulation

MSigDB gene sets: 114 (showing top): GOBP_INFLAMMATORY_RESPONSE, REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION, AP4_Q6, CAGCTG_AP4_Q5, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOCC_TRANS_GOLGI_NETWORK, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_PRODUCTION_OF_MOLECULAR_MEDIATOR_INVOLVED_IN_INFLAMMATORY_RESPONSE, GOBP_CYTOKINE_PRODUCTION, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, AACTTT_UNKNOWN, GOBP_NEGATIVE_REGULATION_OF_CYTOKINE_PRODUCTION, CETS1P54_01, GOCC_LYSOSOMAL_LUMEN, GOCC_VACUOLAR_LUMEN

GO Biological Process (4): carbohydrate metabolic process (GO:0005975), innate immune response (GO:0045087), negative regulation of cytokine production involved in inflammatory response (GO:1900016), immune system process (GO:0002376)

GO Molecular Function (3): chitin binding (GO:0008061), oligosaccharide binding (GO:0070492), protein binding (GO:0005515)

GO Cellular Component (10): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), nucleus (GO:0005634), lysosome (GO:0005764), late endosome (GO:0005770), trans-Golgi network (GO:0005802), endomembrane system (GO:0012505), membrane (GO:0016020), lysosomal lumen (GO:0043202), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Response to elevated platelet cytosolic Ca2+1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
primary metabolic process1
immune response1
defense response to symbiont1
negative regulation of cytokine production1
cytokine production involved in inflammatory response1
regulation of cytokine production involved in inflammatory response1
biological_process1
carbohydrate derivative binding1
carbohydrate binding1
binding1
intracellular membrane-bounded organelle1
lytic vacuole1
endosome1
Golgi apparatus subcompartment1
vacuole1
plasma membrane1
lysosome1
vacuolar lumen1
extracellular vesicle1

Protein interactions and networks

STRING

1055 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CHID1STAB1Q9NY15840
CHID1CHI3L2Q15782745
CHID1CHIT1Q13231683
CHID1CHIAQ9BZP6665
CHID1CHI3L1P30923599
CHID1OVGP1Q12889565
CHID1SLC35A3Q9Y2D2488
CHID1SLC35D2Q76EJ3473
CHID1SLC35B4Q969S0453
CHID1TIMM21Q9BVV7433
CHID1CHIC1Q5VXU3427
CHID1CNDP1Q96KN2402
CHID1RAB29O14966396
CHID1CNDP2Q96KP4388
CHID1SLC35B3Q9H1N7375

IntAct

57 interactions, top by confidence:

ABTypeScore
C1QTNF9C1QTNF9Bpsi-mi:“MI:0914”(association)0.780
B3GNT3PGRMC1psi-mi:“MI:0914”(association)0.670
C1orf54EXTL3psi-mi:“MI:0914”(association)0.530
GPIHBP1ADAM10psi-mi:“MI:0914”(association)0.530
CHID1HSPA5psi-mi:“MI:0915”(physical association)0.400
repUQCRBpsi-mi:“MI:0914”(association)0.350
PLXNB2psi-mi:“MI:0914”(association)0.350
TMEM106AQSOX1psi-mi:“MI:0914”(association)0.350
KLK15SPINT1psi-mi:“MI:0914”(association)0.350
PDGFRAGXYLT2psi-mi:“MI:0914”(association)0.350
CLEC12BGXYLT2psi-mi:“MI:0914”(association)0.350
CCL3KRBA1psi-mi:“MI:0914”(association)0.350
PSCAMETTL15psi-mi:“MI:0914”(association)0.350
ST14LIPT2psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
GPIHBP1SAC3D1psi-mi:“MI:0914”(association)0.350
C1QTNF7AGRNpsi-mi:“MI:0914”(association)0.350
TMEM25NME4psi-mi:“MI:0914”(association)0.350
HPNTOR1Apsi-mi:“MI:0914”(association)0.350
PCDHB3ESYT2psi-mi:“MI:0914”(association)0.350
TMEM106ATMEM131Lpsi-mi:“MI:0914”(association)0.350
LY86TMEM131Lpsi-mi:“MI:0914”(association)0.350
P2RX2TMEM131Lpsi-mi:“MI:0914”(association)0.350
ASIC4TMEM131Lpsi-mi:“MI:0914”(association)0.350
TMEM87APOTEFpsi-mi:“MI:0914”(association)0.350
NCR3POTEFpsi-mi:“MI:0914”(association)0.350
PI15psi-mi:“MI:0914”(association)0.350
MFAP4QSOX1psi-mi:“MI:0914”(association)0.350
DPEP2QSOX1psi-mi:“MI:0914”(association)0.350
PRG2QSOX1psi-mi:“MI:0914”(association)0.350

BioGRID (92): CHID1 (Affinity Capture-MS), CHID1 (Co-fractionation), GAA (Co-fractionation), MAN2B1 (Co-fractionation), CHID1 (Proximity Label-MS), CHID1 (Affinity Capture-MS), CHID1 (Co-fractionation), CHID1 (Co-fractionation), CHID1 (Proximity Label-MS), CHID1 (Affinity Capture-RNA), CHID1 (Proximity Label-MS), CHID1 (Proximity Label-MS), CHID1 (Proximity Label-MS), CHID1 (Proximity Label-MS), CHID1 (Proximity Label-MS)

ESM2 similar proteins: A0JPQ9, O14657, O14672, O19015, O35598, P09958, P16098, P23188, P23377, P58780, P82993, Q01458, Q01460, Q08169, Q0JJD4, Q10741, Q10743, Q10RB4, Q1L8D2, Q28193, Q29LW1, Q29NU5, Q4V8H8, Q58D55, Q5EAB4, Q5GF25, Q5RFF6, Q66IL0, Q68EX9, Q6NXH2, Q6ZJJ0, Q7SYK0, Q7Z1Z1, Q8BH64, Q8MLZ7, Q8MX31, Q8MX32, Q8MX40, Q8T0R7, Q922Q9

Diamond homologs: A0JPQ9, Q54G42, Q5EAB4, Q5RFF6, Q66IL0, Q68EX9, Q7SYK0, Q922Q9, Q9BWS9, P37531

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

76 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance54
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1808628GRCh37/hg19 11p15.5(chr11:461373-2157956)x4Pathogenic

SpliceAI

3003 predictions. Top by Δscore:

VariantEffectΔscore
11:870117:GCAC:Gdonor_loss1.0000
11:870118:CA:Cdonor_loss1.0000
11:870119:A:ACdonor_gain1.0000
11:870119:A:AGdonor_loss1.0000
11:870120:C:CCdonor_gain1.0000
11:870120:CCTT:Cdonor_gain1.0000
11:870159:GGCTC:Gacceptor_gain1.0000
11:870161:CTC:Cacceptor_gain1.0000
11:870162:TC:Tacceptor_gain1.0000
11:870163:CC:Cacceptor_gain1.0000
11:870164:C:CCacceptor_gain1.0000
11:870415:TCA:Tdonor_loss1.0000
11:870416:CACTT:Cdonor_loss1.0000
11:870417:A:ACdonor_gain1.0000
11:870417:ACTT:Adonor_gain1.0000
11:870418:C:CTdonor_gain1.0000
11:870418:CT:Cdonor_gain1.0000
11:870418:CTT:Cdonor_gain1.0000
11:870418:CTTC:Cdonor_gain1.0000
11:870420:T:TAdonor_gain1.0000
11:870495:TGTAC:Tacceptor_gain1.0000
11:870497:TAC:Tacceptor_gain1.0000
11:870498:AC:Aacceptor_gain1.0000
11:870499:CC:Cacceptor_gain1.0000
11:870500:C:CAacceptor_loss1.0000
11:884066:A:ACdonor_gain1.0000
11:884067:C:CTdonor_gain1.0000
11:884067:CTG:Cdonor_gain1.0000
11:884165:CGGTC:Cacceptor_gain1.0000
11:884168:TC:Tacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000075417 (11:880567 G>A), RS1000113020 (11:893442 G>A), RS1000118894 (11:886972 C>T), RS1000188214 (11:891354 T>A,G), RS1000215750 (11:877439 GTCTC>G,GTCTCTC), RS1000240364 (11:917176 G>A), RS1000295247 (11:899716 C>T), RS1000363576 (11:904461 T>G), RS1000385292 (11:897408 G>A), RS1000416172 (11:904180 C>G), RS1000436990 (11:902581 G>A), RS1000444226 (11:871697 G>A), RS1000450014 (11:894751 G>A), RS1000628612 (11:868466 C>T), RS1000653503 (11:873992 T>C)

Disease associations

OMIM: gene MIM:615692 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST002625_2Chronic bronchitis and chronic obstructive pulmonary disease5.000000e-08
GCST010988_457Adult body size3.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects expression, decreases expression, affects cotreatment, increases abundance, increases expression3
bisphenol Aincreases expression, affects cotreatment, affects methylation, decreases methylation2
Arsenicaffects methylation, affects cotreatment, increases abundance, increases expression2
Dexamethasonedecreases reaction, affects cotreatment, increases expression2
aristolochic acid Idecreases expression1
bisphenol Faffects cotreatment, increases expression1
tremortindecreases expression1
beta-lapachoneincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
aflatoxin B2increases methylation1
di-n-butylphosphoric acidaffects expression1
K 7174decreases expression1
Fulvestrantaffects cotreatment, affects methylation, decreases methylation1
Benzo(a)pyreneaffects methylation1
Cisplatindecreases expression1
Dinitrochlorobenzeneaffects binding1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Leadaffects splicing1
Manganeseaffects cotreatment, increases abundance, increases expression1
Rotenoneincreases expression1
Smokedecreases expression1
Thiramdecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Aflatoxin B1decreases expression1
Cadmium Chloridedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E8NRLN229-CHID1Cancer cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): chronic bronchitis