Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CS Gene

Aliases for CS Gene

  • Citrate Synthase 2 3 5
  • Citrate (Si)-Synthase 3 4
  • Citrate Synthase, Mitochondrial 3
  • EC 4

External Ids for CS Gene

Previous GeneCards Identifiers for CS Gene

  • GC12M056540
  • GC12P056603
  • GC12M056382
  • GC12M054951
  • GC12M056666
  • GC12M053704

Summaries for CS Gene

Entrez Gene Summary for CS Gene

  • The protein encoded by this gene is a Krebs tricarboxylic acid cycle enzyme that catalyzes the synthesis of citrate from oxaloacetate and acetyl coenzyme A. The enzyme is found in nearly all cells capable of oxidative metablism. This protein is nuclear encoded and transported into the mitochondrial matrix, where the mature form is found. [provided by RefSeq, Jul 2008]

GeneCards Summary for CS Gene

CS (Citrate Synthase) is a Protein Coding gene. Diseases associated with CS include Critical Illness Polyneuropathy and Neuroretinitis. Among its related pathways are Metabolism and Citrate cycle (TCA cycle). Gene Ontology (GO) annotations related to this gene include citrate (Si)-synthase activity.

Additional gene information for CS Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CS Gene

Genomics for CS Gene

GeneHancer (GH) Regulatory Elements for CS Gene

Promoters and enhancers for CS 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
GH12J056298 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.4 -418 4.6 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 GLIS1 ENSG00000257303 IL23A CS BAZ2A ZC3H10 NEMP1 RN7SL809P CDK2 DNAJC14 RPL41
GH12J056286 Promoter 0.7 EPDnew 650.4 +14.3 14328 0.1 CEBPB CEBPG CS GC12M056288 PIR48633 ENSG00000144785
GH12J056204 Enhancer 0.5 ENCODE 11.2 +94.9 94884 1.5 ZNF740 IKZF1 ZNF341 VEZF1 ZFP91 PRDM10 RAD21 SLC39A5 ANKRD52 COQ10A CS PAN2 IL23A ZC3H10 RPL41 SUOX GC12P056196
GH12J056320 Enhancer 0.5 ENCODE 10.9 -20.7 -20727 1 ATF4 CEBPB ATF7 ZNF24 CEBPG APOF CS NABP2 RNF41 SLC39A5 CNPY2 PAN2 GC12P056293
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CS gene promoter:
  • PPAR-alpha
  • Nkx2-5
  • GR
  • GR-alpha

Genomic Locations for CS Gene

Genomic Locations for CS Gene
28,694 bases
Minus strand
28,694 bases
Minus strand

Genomic View for CS Gene

Genes around CS on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CS Gene

Proteins for CS Gene

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

    Protein Symbol:
    Recommended name:
    Citrate synthase, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q71UT9
    • Q7KZH0
    • Q96FZ8
    • Q9BWN8

    Protein attributes for CS Gene

    466 amino acids
    Molecular mass:
    51712 Da
    Quaternary structure:
    • Homodimer.
    • Citrate synthase is found in nearly all cells capable of oxidative metabolism.
    • Sequence=CAE45911.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CS Gene

neXtProt entry for CS Gene

Post-translational modifications for CS Gene

  • Methylated (PubMed:28391595, PubMed:28887308). Trimethylation at Lys-395 by CSKMT decreases citrate synthase activity (PubMed:28887308).
  • Ubiquitination at Lys327 and posLast=103103
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CS Gene

Domains & Families for CS Gene

Gene Families for CS Gene

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

Suggested Antigen Peptide Sequences for CS Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the citrate synthase family.
  • Belongs to the citrate synthase family.
genes like me logo Genes that share domains with CS: view

Function for CS Gene

Molecular function for CS Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA.
GENATLAS Biochemistry:
citrate synthase,mitochondrial,catalyzing the first step of citric acid cycle

Enzyme Numbers (IUBMB) for CS Gene

Phenotypes From GWAS Catalog for CS Gene

Gene Ontology (GO) - Molecular Function for CS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0004108 citrate (Si)-synthase activity TAS,IEA --
GO:0016740 transferase activity IEA --
GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer IEA --
genes like me logo Genes that share ontologies with CS: view
genes like me logo Genes that share phenotypes with CS: view

Animal Models for CS Gene

MGI Knock Outs for CS:
  • Cs Cs<tm1.1(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for CS

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CS

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

Localization for CS Gene

Subcellular locations from UniProtKB/Swiss-Prot for CS Gene

Mitochondrion matrix.

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 CS gene
Compartment Confidence
extracellular 5
mitochondrion 5
nucleus 5
cytoskeleton 2
peroxisome 2
cytosol 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA 21630459
GO:0005739 mitochondrion IDA --
GO:0005759 mitochondrial matrix TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CS: view

Pathways & Interactions for CS Gene

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

UniProtKB/Swiss-Prot O75390-CISY_HUMAN

  • Pathway: Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 1/2.

Gene Ontology (GO) - Biological Process for CS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IDA 9543345
GO:0006099 tricarboxylic acid cycle IEA,TAS --
GO:0006101 citrate metabolic process IEA --
genes like me logo Genes that share ontologies with CS: view

No data available for SIGNOR curated interactions for CS Gene

Drugs & Compounds for CS Gene

(41) Drugs for CS Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Citric Acid Approved, Vet_approved Nutra Agonist, Activator, Target 1243
Water Approved Pharma 0
Alpha-Fluoro-Carboxymethyldethia Coenzyme a Complex Experimental Pharma Target 0
Malate Ion Experimental Pharma Target 0
Nitromethyldethia Coenzyme A Experimental Pharma Target 0

(43) Additional Compounds for CS Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • AcCoA
  • Acetyl coenzyme A
  • S-Acetyl-CoA
  • S-Acetyl-coenzyme A
  • Ac-CoA
Oxalacetic acid
  • 2-Oxobutanedioic acid
  • 2-Oxosuccinic acid
  • 3-Carboxy-3-oxopropanoic acid
  • keto-Succinic acid
  • Ketosuccinic acid
genes like me logo Genes that share compounds with CS: view

Transcripts for CS Gene

mRNA/cDNA for CS Gene

Unigene Clusters for CS Gene

Citrate synthase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CS

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

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d · 5e ^ 6a · 6b · 6c · 6d ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ·
SP1: - - - - - - -
SP2: - - -
SP3: - - - - - -
SP5: - - - - - -
SP6: - - - - - - - -
SP7: - -
SP8: - - - - - - - - - - -
SP9: - - - - - -
SP10: - - - - - - - - - - -
SP11: - - - - - - - - - - - -
SP12: - - - - - - - - - - - - - -
SP13: - - - -
SP14: -
SP15: - - - -

ExUns: 13c ^ 14 ^ 15 ^ 16 ^ 17

Relevant External Links for CS Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CS Gene

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

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

This gene is overexpressed in Heart - Left Ventricle (x4.6) and Muscle - Skeletal (x4.5).

Protein differential expression in normal tissues from HIPED for CS Gene

This gene is overexpressed in Heart (8.7).

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

Protein tissue co-expression partners for CS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CS Gene:


SOURCE GeneReport for Unigene cluster for CS Gene:


Evidence on tissue expression from TISSUES for CS Gene

  • Nervous system(5)
  • Heart(4.7)
  • Liver(4.7)
  • Muscle(3.9)
  • Lung(3.6)
  • Intestine(3.3)
  • Blood(3)
  • Eye(3)
  • Kidney(3)
  • Skin(3)
  • Pancreas(2.5)
genes like me logo Genes that share expression patterns with CS: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CS Gene

Orthologs for CS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CS Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CS 33
  • 99.57 (n)
(Canis familiaris)
Mammalia CS 34 33
  • 93.28 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 93 (a)
-- 34
  • 90 (a)
(Bos Taurus)
Mammalia CS 34 33
  • 92.92 (n)
(Mus musculus)
Mammalia Csl 34
  • 90 (a)
Cs 16 34 33
  • 88.74 (n)
(Rattus norvegicus)
Mammalia Cs 33
  • 89.45 (n)
(Gallus gallus)
Aves CS 34 33
  • 77.78 (n)
(Anolis carolinensis)
Reptilia CS 34
  • 88 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cs 33
  • 77.83 (n)
Str.1513 33
(Danio rerio)
Actinopterygii cs 34
  • 88 (a)
LOC100536541 33
  • 77.19 (n)
wufb58e04 33
fruit fly
(Drosophila melanogaster)
Insecta CG3861 35
  • 73 (a)
kdn 34 33
  • 66.29 (n)
CG14740 35
  • 54 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012048 33
  • 67.56 (n)
(Caenorhabditis elegans)
Secernentea T20G5.2 35
  • 68 (a)
cts-1 34 33
  • 61.78 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CIT2 34 33
  • 57.67 (n)
CIT1 36
thale cress
(Arabidopsis thaliana)
eudicotyledons ATCS 33
  • 61.71 (n)
(Glycine max)
eudicotyledons Gma.16706 33
(Oryza sativa)
Liliopsida Os02g0194100 33
  • 60.47 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 70 (a)
Cin.5369 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5369 33
Species where no ortholog for CS 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CS Gene

Gene Tree for CS (if available)
Gene Tree for CS (if available)
Evolutionary constrained regions (ECRs) for CS: view image

Paralogs for CS Gene

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

No data available for Paralogs for CS Gene

Variants for CS Gene

Sequence variations from dbSNP and Humsavar for CS Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000006386 -- 56,291,495(-) AGGAGG/AGGAGGAGG intron_variant
rs1000066329 -- 56,283,441(-) C/T intron_variant
rs1000131674 -- 56,276,382(-) C/A/T intron_variant
rs1000322159 -- 56,290,768(-) G/A intron_variant
rs1000330693 -- 56,296,926(-) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
nsv482992 CNV gain+loss 15286789

Variation tolerance for CS Gene

Residual Variation Intolerance Score: 59.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.32; 7.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CS Gene

Human Gene Mutation Database (HGMD)
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 CS Gene

Disorders for CS Gene

MalaCards: The human disease database

(12) MalaCards diseases for CS Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
critical illness polyneuropathy
  • polyneuropathy, critical illness
  • focal retinitis and retinochoroiditis, juxtapapillary
cat-scratch disease
  • oroya fever
cerebral creatine deficiency syndrome 2
  • ccds2
  • bartonella infectious disease
- elite association - COSMIC cancer census association via MalaCards
Search CS in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CS

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 CS: view

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

Publications for CS Gene

  1. Single nucleotide polymorphisms in succinate dehydrogenase subunits and citrate synthase genes: association results for impaired spermatogenesis. (PMID: 17298551) Bonache S … Larriba S (International journal of andrology 2007) 3 22 44 58
  2. [Cloning and tissue expression pattern analysis of the human citrate synthase cDNA]. (PMID: 12549038) Liu Q … Zhao SY (Shi yan sheng wu xue bao 2000) 3 4 22 58
  3. Human METTL12 is a mitochondrial methyltransferase that modifies citrate synthase. (PMID: 28391595) Rhein VF … Walker JE (FEBS letters 2017) 3 4 58
  4. Uncovering human METTL12 as a mitochondrial methyltransferase that modulates citrate synthase activity through metabolite-sensitive lysine methylation. (PMID: 28887308) Małecki J … Falnes PØ (The Journal of biological chemistry 2017) 3 4 58
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58

Products for CS Gene

  • Invitrogen Antibodies for CS (AFLGC-CS)

Sources for CS Gene

Loading form....