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

Aliases for CLYBL Gene

Aliases for CLYBL Gene

  • Citrate Lyase Beta Like 2 3 5
  • Beta-Methylmalate Synthase 3 4
  • Malate Synthase 3 4
  • CLB 3 4
  • Citrate Lyase Subunit Beta-Like Protein, Mitochondrial 3
  • Citrate Lyase Beta-Like 4
  • EC 2.3.3.- 4
  • EC 4

External Ids for CLYBL Gene

Previous GeneCards Identifiers for CLYBL Gene

  • GC13P098619
  • GC13P094646
  • GC13P099096
  • GC13P097956
  • GC13P099056
  • GC13P100258
  • GC13P081019

Summaries for CLYBL Gene

GeneCards Summary for CLYBL Gene

CLYBL (Citrate Lyase Beta Like) is a Protein Coding gene. Diseases associated with CLYBL include Dermatophytosis. GO annotations related to this gene include lyase activity.

UniProtKB/Swiss-Prot for CLYBL Gene

  • Mitochondrial malate and beta-methylmalate synthase, which may be involved in vitamin B12 metabolism (Probable). Acts both as a malate synthase, converting glyoxylate and acetyl-CoA to malate. Also acts as a beta-methylmalate synthase by mediating conversion of glyoxylate and propionyl-CoA to beta-methylmalate (PubMed:24334609).

Additional gene information for CLYBL Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLYBL Gene

Genomics for CLYBL Gene

Regulatory Elements for CLYBL Gene

Enhancers for CLYBL Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13H099655 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.9 +51.2 51234 5.3 PKNOX1 FOXA2 ATF1 ZSCAN4 SIN3A ZNF2 RAD21 RARA RFX5 YY1 ZIC5 CLYBL ZIC2 LINC00449 MIR4306 GC13P099679
GH13H099685 2.6 VISTA Ensembl ENCODE dbSUPER 5.4 +81.8 81836 6.1 ELF3 PKNOX1 TAL1 BATF ZNF2 TCF12 ZNF316 CTBP1 GATA2 POLR2A CLYBL DOCK9-AS2 CLYBL-AS2 GC13P099679
GH13H099541 1.1 Ensembl ENCODE 11.9 -63.8 -63841 2.4 HDGF TBL1XR1 BMI1 BATF RFX5 ATF7 ETV6 RUNX3 IKZF2 CREM CLYBL TM9SF2 GC13M099538 RNY3P6 GC13M099563
GH13H099605 1.1 ENCODE 6.4 -0.3 -264 2.4 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 GPR18 CLYBL TM9SF2 LOC105370332 GC13M099598
GH13H099614 1 Ensembl ENCODE 5.8 +8.0 8037 0.6 CTCF TFAP4 MXI1 SAP130 ARID4B MAX DMAP1 KMT2B RAD21 RARA CLYBL MIR4306
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLYBL on UCSC Golden Path with GeneCards custom track

Promoters for CLYBL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000065117 36 1401 PKNOX1 FOXA2 MLX ARID4B FEZF1 DMAP1 ZNF2 YY1 ZNF143 SP3

Genomic Locations for CLYBL Gene

Genomic Locations for CLYBL Gene
302,796 bases
Plus strand

Genomic View for CLYBL Gene

Genes around CLYBL on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CLYBL Gene

Proteins for CLYBL Gene

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

    Protein Symbol:
    Recommended name:
    Citrate lyase subunit beta-like protein, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q5W0F7
    • Q8TDH8

    Protein attributes for CLYBL Gene

    340 amino acids
    Molecular mass:
    37359 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CLYBL Gene


neXtProt entry for CLYBL Gene

Post-translational modifications for CLYBL Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLYBL Gene

Domains & Families for CLYBL Gene

Gene Families for CLYBL Gene

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

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HpcH/HpaI aldolase family. Citrate lyase beta subunit-like subfamily.
  • Belongs to the HpcH/HpaI aldolase family. Citrate lyase beta subunit-like subfamily.
genes like me logo Genes that share domains with CLYBL: view

Function for CLYBL Gene

Molecular function for CLYBL Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.6 mM for glyoxylate (with acetyl-CoA as cosubstrate) {ECO:0000269 PubMed:24334609}; KM=1.2 mM for glyoxylate (with propionyl-CoA as cosubstrate) {ECO:0000269 PubMed:24334609}; KM=74 uM for acetyl-CoA {ECO:0000269 PubMed:24334609}; KM=23 uM for propionyl-CoA {ECO:0000269 PubMed:24334609}; Note=kcat is 0.12 sec(-1) for malate synthase reaction. kcat is 0.09 sec(-1) for beta-methylmalate synthase reaction. {ECO:0000269 PubMed:24334609};
UniProtKB/Swiss-Prot CatalyticActivity:
Acetyl-CoA + H(2)O + glyoxylate = (S)-malate + CoA.
UniProtKB/Swiss-Prot CatalyticActivity:
Propionyl-CoA + H(2)O + glyoxylate = beta-methylmalate + CoA.
UniProtKB/Swiss-Prot Function:
Mitochondrial malate and beta-methylmalate synthase, which may be involved in vitamin B12 metabolism (Probable). Acts both as a malate synthase, converting glyoxylate and acetyl-CoA to malate. Also acts as a beta-methylmalate synthase by mediating conversion of glyoxylate and propionyl-CoA to beta-methylmalate (PubMed:24334609).

Enzyme Numbers (IUBMB) for CLYBL Gene

Phenotypes From GWAS Catalog for CLYBL Gene

Gene Ontology (GO) - Molecular Function for CLYBL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 24334609
GO:0003824 catalytic activity IEA --
GO:0004474 malate synthase activity IEA,IDA 24334609
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CLYBL: view

Phenotypes for CLYBL Gene

genes like me logo Genes that share phenotypes with CLYBL: view

Animal Model Products

CRISPR Products

miRNA for CLYBL Gene

miRTarBase miRNAs that target CLYBL

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLYBL Gene

Localization for CLYBL Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLYBL Gene


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 CLYBL gene
Compartment Confidence
mitochondrion 4
cytoskeleton 3
peroxisome 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CLYBL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CLYBL: view

Pathways & Interactions for CLYBL Gene

SuperPathways for CLYBL Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLYBL Gene


No data available for Pathways by source and SIGNOR curated interactions for CLYBL Gene

Drugs & Compounds for CLYBL Gene

(3) Drugs for CLYBL Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
acetic acid Approved Nutra Full agonist, Agonist 115
Citric Acid Vet_approved Nutra Agonist, Activator 1200
Magnesium Nutra 0
genes like me logo Genes that share compounds with CLYBL: view

Transcripts for CLYBL Gene

Unigene Clusters for CLYBL Gene

Citrate lyase beta like:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for CLYBL Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLYBL Gene

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

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

This gene is overexpressed in Liver (x5.0).

Protein differential expression in normal tissues from HIPED for CLYBL Gene

This gene is overexpressed in Liver, secretome (29.2) and Liver (6.5).

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

Protein tissue co-expression partners for CLYBL Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLYBL Gene:


SOURCE GeneReport for Unigene cluster for CLYBL Gene:


Evidence on tissue expression from TISSUES for CLYBL Gene

  • Liver(4.3)
  • Skin(4.3)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with CLYBL: 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 CLYBL Gene

Orthologs for CLYBL Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CLYBL Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLYBL 33 34
  • 99.51 (n)
(Canis familiaris)
Mammalia CLYBL 33 34
  • 89.51 (n)
(Mus musculus)
Mammalia Clybl 33 16 34
  • 86.62 (n)
(Rattus norvegicus)
Mammalia Clybl 33
  • 86.22 (n)
(Bos Taurus)
Mammalia CLYBL 33 34
  • 82.59 (n)
(Monodelphis domestica)
Mammalia CLYBL 34
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia CLYBL 34
  • 79 (a)
(Gallus gallus)
Aves CLYBL 33 34
  • 78.21 (n)
(Anolis carolinensis)
Reptilia CLYBL 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clybl 33
  • 72.82 (n)
(Danio rerio)
Actinopterygii clybl 33 33 34
  • 67.2 (n)
(Caenorhabditis elegans)
Secernentea CELE_C01G10.7 33
  • 52.01 (n)
C01G10.7 35 34
  • 47 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU02734 33
  • 45.2 (n)
Species where no ortholog for CLYBL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for CLYBL Gene

Gene Tree for CLYBL (if available)
Gene Tree for CLYBL (if available)

Paralogs for CLYBL Gene

(3) SIMAP similar genes for CLYBL Gene using alignment to 6 proteins:

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

No data available for Paralogs for CLYBL Gene

Variants for CLYBL Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for CLYBL Gene

The loss-of-function polymorphism (rs41281112) changes Arg-259 to a premature stop codon, leading to loss of the protein product, may be associated with reduction of circulating vitamin B12.

Sequence variations from dbSNP and Humsavar for CLYBL Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs1000022 -- 99,808,965(+) GTTCA(C/T)GTCCT intron-variant
rs1000022782 -- 99,854,772(+) TCTCC(A/G)CTTTC intron-variant
rs1000026668 -- 99,894,195(+) ACCCG(C/T)GTCTC intron-variant, utr-variant-3-prime
rs1000042738 -- 99,768,071(+) AGATT(C/T)TCCCC intron-variant
rs1000055201 -- 99,847,098(+) GTTGT(A/G)AACAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv832696 CNV gain 17160897
nsv821675 CNV loss 15273396
nsv510360 OTHER sequence alteration 20534489
nsv1047981 CNV gain 25217958
nsv1045800 CNV loss 25217958
nsv1043076 CNV gain 25217958
esv3633334 CNV loss 21293372
esv3550973 CNV deletion 23714750
esv34003 CNV loss 18971310
esv2747875 CNV deletion 23290073
esv2668346 CNV deletion 23128226
dgv345n67 CNV gain 20364138

Variation tolerance for CLYBL Gene

Residual Variation Intolerance Score: 53.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.26; 81.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLYBL Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

Disorders for CLYBL Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLYBL Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
  • tinea
- elite association - COSMIC cancer census association via MalaCards
Search CLYBL in MalaCards View complete list of genes associated with diseases

Relevant External Links for CLYBL

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLYBL: view

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

Publications for CLYBL Gene

  1. CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. (PMID: 24334609) Strittmatter L … Mootha VK (Human molecular genetics 2014) 3 4 60
  2. Genome-wide association study identifies novel loci associated with serum level of vitamin B12 in Chinese men. (PMID: 22367966) Lin X … Sun J (Human molecular genetics 2012) 3 45 60
  3. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 45 60
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  5. Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. (PMID: 18821565) Lasky-Su J … Faraone SV (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 45 60

Products for CLYBL Gene

Sources for CLYBL Gene

Loading form....