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Aliases for CA9 Gene

Aliases for CA9 Gene

  • Carbonic Anhydrase 9 2 3 5
  • Carbonic Anhydrase IX 2 3 4
  • Renal Cell Carcinoma-Associated Antigen G250 3 4
  • RCC-Associated Protein G250 2 3
  • RCC-Associated Antigen G250 3 4
  • Carbonate Dehydratase IX 3 4
  • Carbonic Dehydratase 2 3
  • Membrane Antigen MN 3 4
  • P54/58N 3 4
  • CA-IX 3 4
  • CAIX 3 4
  • PMW1 3 4
  • MN 3 4
  • EC 4
  • G250 4

External Ids for CA9 Gene

Previous GeneCards Identifiers for CA9 Gene

  • GC09P035986
  • GC09P035843
  • GC09P035663
  • GC09P035629

Summaries for CA9 Gene

Entrez Gene Summary for CA9 Gene

  • Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva, and gastric acid. They show extensive diversity in tissue distribution and in their subcellular localization. CA IX is a transmembrane protein and is one of only two tumor-associated carbonic anhydrase isoenzymes known. It is expressed in all clear-cell renal cell carcinoma, but is not detected in normal kidney or most other normal tissues. It may be involved in cell proliferation and transformation. This gene was mapped to 17q21.2 by fluorescence in situ hybridization, however, radiation hybrid mapping localized it to 9p13-p12. [provided by RefSeq, Jun 2014]

GeneCards Summary for CA9 Gene

CA9 (Carbonic Anhydrase 9) is a Protein Coding gene. Diseases associated with CA9 include Clear Cell Renal Cell Carcinoma and Renal Clear Cell Carcinoma. Among its related pathways are Nitrogen metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include carbonate dehydratase activity. An important paralog of this gene is CA14.

UniProtKB/Swiss-Prot for CA9 Gene

  • Reversible hydration of carbon dioxide. Participates in pH regulation. May be involved in the control of cell proliferation and transformation. Appears to be a novel specific biomarker for a cervical neoplasia.

Tocris Summary for CA9 Gene

  • Carbonic anhydrases (EC are zinc-containing enzymes belonging to the lyases family, and are primarily responsible for catalyzing the reversible hydration of carbon dioxide to form bicarbonate (HCO3-) and hydrogen (H+) ions.

Gene Wiki entry for CA9 Gene

Additional gene information for CA9 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CA9 Gene

Genomics for CA9 Gene

GeneHancer (GH) Regulatory Elements for CA9 Gene

Promoters and enhancers for CA9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I035672 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 560.1 +0.9 938 3.9 CTCF MXI1 USF1 FOXA2 SAP130 MAX DMAP1 ZNF48 TEAD3 POLR2A CA9 ARHGEF39 CCDC107
GH09I035726 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.1 +56.6 56559 8.6 YBX1 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D TLN1 CREB3 TMEM8B GBA2 ARHGEF39 TPM2 HMGB3P24 PIGO RN7SL22P ENSG00000228843
GH09I035616 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 11.2 -54.6 -54602 6.4 HDGF PKNOX1 ATF1 SMAD1 RB1 SIN3A BATF RFX5 ETS1 SCRT2 CD72 CCDC107 RN7SL22P ARHGEF39 SIT1 CA9 FAM166B TLN1 CREB3 GBA2
GH09I035634 Enhancer 1.1 Ensembl ENCODE dbSUPER 16.3 -36.6 -36622 6.1 HDGF MEIS2 CEBPG PAX8 BMI1 EGR1 NFATC1 ATF7 IKZF2 RUNX3 ARHGEF39 CA9 CCDC107 CD72 RN7SL22P GBA2 RGP1 MSMP ENSG00000228843 VCP
GH09I035656 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 7 -12.9 -12891 9.9 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ARHGEF39 CCDC107 NPR2 RGP1 PIGO RECK VCP ENSG00000230074 UNC13B CA9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CA9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CA9 gene promoter:

Genomic Locations for CA9 Gene

Genomic Locations for CA9 Gene
7,304 bases
Plus strand

Genomic View for CA9 Gene

Genes around CA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CA9 Gene

Proteins for CA9 Gene

  • Protein details for CA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Carbonic anhydrase 9
    Protein Accession:
    Secondary Accessions:
    • Q5T4R1

    Protein attributes for CA9 Gene

    459 amino acids
    Molecular mass:
    49698 Da
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Forms oligomers linked by disulfide bonds.

    Three dimensional structures from OCA and Proteopedia for CA9 Gene

neXtProt entry for CA9 Gene

Post-translational modifications for CA9 Gene

  • Asn-346 bears high-mannose type glycan structures.
  • Glycosylation at posLast=115115 and Asn346
  • Modification sites at PhosphoSitePlus

Other Protein References for CA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CA9 Gene

Domains & Families for CA9 Gene

Gene Families for CA9 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for CA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the alpha-carbonic anhydrase family.
  • Belongs to the alpha-carbonic anhydrase family.
genes like me logo Genes that share domains with CA9: view

Function for CA9 Gene

Molecular function for CA9 Gene

GENATLAS Biochemistry:
carbonic anhydrase 9,MN/CA antigen expressed in Hela cells and some human carcinomas
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 6.5. {ECO:0000269 PubMed:19805286};
UniProtKB/Swiss-Prot CatalyticActivity:
H(2)CO(3) = CO(2) + H(2)O.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by coumarins, saccharin, sulfonamide derivatives such as acetazolamide (AZA) and Foscarnet (phosphonoformate trisodium salt).
UniProtKB/Swiss-Prot Function:
Reversible hydration of carbon dioxide. Participates in pH regulation. May be involved in the control of cell proliferation and transformation. Appears to be a novel specific biomarker for a cervical neoplasia.
UniProtKB/Swiss-Prot Induction:
By hypoxia.

Enzyme Numbers (IUBMB) for CA9 Gene

Phenotypes From GWAS Catalog for CA9 Gene

Gene Ontology (GO) - Molecular Function for CA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004089 carbonate dehydratase activity TAS,IEA --
GO:0005515 protein binding IPI 26871637
GO:0008270 zinc ion binding IEA --
GO:0016829 lyase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CA9: view
genes like me logo Genes that share phenotypes with CA9: view

Animal Models for CA9 Gene

MGI Knock Outs for CA9:

Animal Model Products

CRISPR Products

miRNA for CA9 Gene

miRTarBase miRNAs that target CA9

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CA9 Gene

Localization for CA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CA9 Gene

Nucleus. Nucleus, nucleolus. Cell membrane; Single-pass type I membrane protein. Cell projection, microvillus membrane; Single-pass type I membrane protein. Note=Found on the surface microvilli and in the nucleus, particularly in nucleolus.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CA9 gene
Compartment Confidence
plasma membrane 5
nucleus 4
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (4)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS,IEA --
genes like me logo Genes that share ontologies with CA9: view

Pathways & Interactions for CA9 Gene

genes like me logo Genes that share pathways with CA9: view

Pathways by source for CA9 Gene

SIGNOR curated interactions for CA9 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002009 morphogenesis of an epithelium IEA --
GO:0006730 one-carbon metabolic process IEA --
GO:0015701 bicarbonate transport TAS --
GO:0033574 response to testosterone IEA --
GO:0042493 response to drug IEA --
genes like me logo Genes that share ontologies with CA9: view

Drugs & Compounds for CA9 Gene

(34) Drugs for CA9 Gene - From: DrugBank, ApexBio, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Benzthiazide Approved Pharma Target, inhibitor 0
Hydroflumethiazide Approved, Investigational Pharma Target, inhibitor 1
Zonisamide Approved, Investigational Pharma Target, inhibitor Antiepileptic with anticonvulsant and mechanistic effect 69
Brinzolamide Approved Pharma CA II inhibitor 63
Dichlorphenamide Approved, Investigational Pharma 2

(13) Additional Compounds for CA9 Gene - From: Novoseek, HMDB, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Carbonic acid
  • Acid of air
  • Aerial acid
  • Bisodium carbonate
  • Calcined
  • Carbonic acid sodium salt

(2) Tocris Compounds for CA9 Gene

Compound Action Cas Number
S4 High affinity and selective CA IX and CA XII inhibitor 1330061-67-0
U 104 Potent carbonic anhydrase (CA) IX and XII inhibitor 178606-66-1

(7) ApexBio Compounds for CA9 Gene

Compound Action Cas Number
Brinzolamide CA II inhibitor 138890-62-7
Chlorothiazide Carbonic anhydrase inhibitor 58-94-6
Dichlorphenamide 120-97-8
Dorzolamide HCl Carbonic anhydrase inhibitor 130693-82-2
Methazolamide Carbonic anhydrase inhibitor 554-57-4
Topiramate GluR5 receptor antagonist,anticonvulsant 97240-79-4
U-104 CAIX inhibitor 178606-66-1
genes like me logo Genes that share compounds with CA9: view

Drug Products

Transcripts for CA9 Gene

Unigene Clusters for CA9 Gene

Carbonic anhydrase IX:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CA9 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11
SP2: -
SP3: -
SP4: -

Relevant External Links for CA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CA9 Gene

mRNA differential expression in normal tissues according to GTEx for CA9 Gene

This gene is overexpressed in Stomach (x37.6).

Protein differential expression in normal tissues from HIPED for CA9 Gene

This gene is overexpressed in Stomach (44.6) and Gallbladder (14.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CA9 Gene

NURSA nuclear receptor signaling pathways regulating expression of CA9 Gene:


SOURCE GeneReport for Unigene cluster for CA9 Gene:


mRNA Expression by UniProt/SwissProt for CA9 Gene:

Tissue specificity: Expressed primarily in carcinoma cells lines. Expression is restricted to very few normal tissues and the most abundant expression is found in the epithelial cells of gastric mucosa.

Evidence on tissue expression from TISSUES for CA9 Gene

  • Intestine(4.5)
  • Stomach(3.6)
  • Gall bladder(2.4)
  • Kidney(2)
genes like me logo Genes that share expression patterns with CA9: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CA9 Gene

Orthologs for CA9 Gene

This gene was present in the common ancestor of animals.

Orthologs for CA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CA9 33 34
  • 99.34 (n)
(Canis familiaris)
Mammalia CA9 33 34
  • 85.98 (n)
(Bos Taurus)
Mammalia CA9 33 34
  • 84.94 (n)
(Rattus norvegicus)
Mammalia Car9 33
  • 80.69 (n)
(Mus musculus)
Mammalia Car9 33 16 34
  • 79.62 (n)
(Monodelphis domestica)
Mammalia CA9 34
  • 63 (a)
(Gallus gallus)
Aves CA9 33 34
  • 55.05 (n)
(Anolis carolinensis)
Reptilia CA9 34
  • 57 (a)
(Danio rerio)
Actinopterygii ca9 33 34
  • 48.08 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013402 33
  • 48.4 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6074 35
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8628 34
  • 17 (a)
Species where no ortholog for CA9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CA9 Gene

Gene Tree for CA9 (if available)
Gene Tree for CA9 (if available)

Paralogs for CA9 Gene

Paralogs for CA9 Gene

(5) SIMAP similar genes for CA9 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CA9: view

Variants for CA9 Gene

Sequence variations from dbSNP and Humsavar for CA9 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000059538 -- 35,679,586(+) G/C intron_variant
rs1000405272 -- 35,673,190(+) AAAAAAA/AAAAAA upstream_transcript_variant
rs1000492441 -- 35,675,416(+) C/G intron_variant
rs1000964737 -- 35,673,534(+) A/T upstream_transcript_variant
rs1001097048 -- 35,673,860(+) C/T genic_upstream_transcript_variant, non_coding_transcript_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CA9 Gene

Variant ID Type Subtype PubMed ID
nsv1125318 OTHER inversion 24896259
nsv466385 CNV loss 19166990
nsv614166 CNV loss 21841781
nsv6528 CNV insertion 18451855

Variation tolerance for CA9 Gene

Residual Variation Intolerance Score: 36.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.33; 92.64% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CA9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CA9 Gene

Disorders for CA9 Gene

MalaCards: The human disease database

(19) MalaCards diseases for CA9 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
clear cell renal cell carcinoma
  • clear-cell metastatic renal cell carcinoma
renal clear cell carcinoma
  • clear cell carcinoma of kidney
kidney cancer
  • malignant neoplasm of kidney except pelvis
renal cell carcinoma, nonpapillary
  • rcc
- elite association - COSMIC cancer census association via MalaCards
Search CA9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CA9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CA9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CA9 Gene

Publications for CA9 Gene

  1. CA9 gene: single nucleotide polymorphism predicts metastatic renal cell carcinoma prognosis. (PMID: 19539328) de Martino M … Belldegrun AS (The Journal of urology 2009) 3 22 44 58
  2. Cloning and characterization of MN, a human tumor-associated protein with a domain homologous to carbonic anhydrase and a putative helix-loop-helix DNA binding segment. (PMID: 8084592) Pastorek J … Stanbridge EJ (Oncogene 1994) 3 4 22 58
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  4. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PMID: 20819778) Zhang X … Wu X (Carcinogenesis 2010) 3 44 58
  5. Molecular biomarkers for advanced renal cell carcinoma: implications for prognosis and therapy. (PMID: 18976937) Kim HS … Lim HY (Urologic oncology 2010) 3 22 58

Products for CA9 Gene

Sources for CA9 Gene

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