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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 Subunit Beta-Like Protein 4
  • Citramalyl-CoA Lyase, Mitochondrial 3
  • Citrate Lyase Beta-Like 4
  • EC 4.1.3.25 4
  • EC 2.3.3.- 4
  • EC 2.3.3.9 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 Cutaneous Mycosis and Dermatophytosis. Gene Ontology (GO) annotations related to this gene include lyase activity.

UniProtKB/Swiss-Prot for CLYBL Gene

  • Mitochondrial citramalyl-CoA lyase indirectly involved in the vitamin B12 metabolism (PubMed:29056341). Converts citramalyl-CoA into acetyl-CoA and pyruvate in the C5-dicarboxylate catabolism pathway (PubMed:29056341). The C5-dicarboxylate catabolism pathway is required to detoxify itaconate, a vitamin B12-poisoning metabolite (PubMed:29056341). Also acts as a malate synthase in vitro, converting glyoxylate and acetyl-CoA to malate (PubMed:24334609, PubMed:29056341). Also acts as a beta-methylmalate synthase in vitro, by mediating conversion of glyoxylate and propionyl-CoA to beta-methylmalate (PubMed:24334609, PubMed:29056341). Also has very weak citramalate synthase activity in vitro (PubMed:24334609, PubMed:29056341).

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

GeneHancer (GH) Regulatory Elements for CLYBL Gene

Promoters and enhancers for CLYBL Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J099605 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 656.4 -0.3 -264 2.4 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF213 CLYBL LOC105370332 GPR18 TM9SF2 GC13M099598
GH13J099655 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 9.9 +51.2 51233 5.3 PKNOX1 FOXA2 ZSCAN4 SIN3A ZNF2 RAD21 RARA RFX5 YY1 ETS1 ZIC5 CLYBL ZIC2 LINC00449 MIR4306 GC13P099679
GH13J099541 Enhancer 1 Ensembl ENCODE 11.9 -63.8 -63840 2.4 HDGF STAT5A BMI1 BATF IRF4 ATF7 ETV6 BCLAF1 IKZF2 RUNX3 CLYBL TM9SF2 RNY3P6 GC13M099538 GC13M099563
GH13J099685 Enhancer 1.8 VISTA UCNEbase Ensembl ENCODE dbSUPER 5.4 +81.8 81835 6.1 ELF3 PKNOX1 BATF ZNF2 IRF4 ETS1 TCF12 GATA2 CREM CEBPB CLYBL DOCK9-DT CLYBL-AS2 GC13P099679
GH13J099614 Enhancer 0.9 Ensembl ENCODE 5.8 +8.0 8037 0.6 CTCF TFAP4 MXI1 SAP130 ARID4B MAX DMAP1 KMT2B RAD21 RARA CLYBL MIR4306
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLYBL on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLYBL gene promoter:
  • FOXO1a
  • FOXO1
  • FOXC1
  • SEF-1 (1)
  • TBP
  • C/EBPalpha
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for CLYBL Gene

Genomic Locations for CLYBL Gene
chr13:99,606,664-99,909,459
(GRCh38/hg38)
Size:
302,796 bases
Orientation:
Plus strand
chr13:100,258,919-100,549,388
(GRCh37/hg19)
Size:
290,470 bases
Orientation:
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:
    Q8N0X4-CLYBL_HUMAN
    Recommended name:
    Citramalyl-CoA lyase, mitochondrial
    Protein Accession:
    Q8N0X4
    Secondary Accessions:
    • Q5W0F7
    • Q8TDH8

    Protein attributes for CLYBL Gene

    Size:
    340 amino acids
    Molecular mass:
    37359 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homotrimer.

    Three dimensional structures from OCA and Proteopedia for CLYBL Gene

    Alternative splice isoforms for CLYBL Gene

    UniProtKB/Swiss-Prot:

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

Q8N0X4

UniProtKB/Swiss-Prot:

CLYBL_HUMAN :
  • Belongs to the HpcH/HpaI aldolase family. Citrate lyase beta subunit-like subfamily.
Family:
  • 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 Function:
Mitochondrial citramalyl-CoA lyase indirectly involved in the vitamin B12 metabolism (PubMed:29056341). Converts citramalyl-CoA into acetyl-CoA and pyruvate in the C5-dicarboxylate catabolism pathway (PubMed:29056341). The C5-dicarboxylate catabolism pathway is required to detoxify itaconate, a vitamin B12-poisoning metabolite (PubMed:29056341). Also acts as a malate synthase in vitro, converting glyoxylate and acetyl-CoA to malate (PubMed:24334609, PubMed:29056341). Also acts as a beta-methylmalate synthase in vitro, by mediating conversion of glyoxylate and propionyl-CoA to beta-methylmalate (PubMed:24334609, PubMed:29056341). Also has very weak citramalate synthase activity in vitro (PubMed:24334609, PubMed:29056341).
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 CatalyticActivity:
(3S)-citramalyl-CoA = acetyl-CoA + pyruvate.
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=28.7 uM for propionyl-CoA (for beta-methylmalate synthase) {ECO:0000269 PubMed:29056341}; KM=57.3 uM for acetyl-CoA (for malate synthase) {ECO:0000269 PubMed:29056341}; KM=25 uM for acetyl-CoA (for citramalate synthase) {ECO:0000269 PubMed:29056341}; KM=23 uM for (3S)-citramalyl-CoA (for citramalyl-CoA lyase) {ECO:0000269 PubMed:29056341}; 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 (PubMed:24334609). kcat is 0.09 sec(-1) for beta-methylmalate synthase reaction (PubMed:24334609). kcat is 0.135 sec(-1) for beta-methylmalate synthase reaction (PubMed:29056341). kcat is 0.146 sec(-1) for malate synthase reaction (PubMed:29056341). kcat is 0.08 sec(-1) for citramalate synthase reaction (PubMed:29056341). kcat is 14.1 sec(-1) for citramalyl-CoA lyase reaction (PubMed:29056341). {ECO:0000269 PubMed:24334609, ECO:0000269 PubMed:29056341};

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 IDA,IEA 24334609
GO:0016740 transferase activity IEA --
GO:0016829 lyase activity IEA --
genes like me logo Genes that share ontologies with CLYBL: view
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

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

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

Mitochondrion.

Subcellular locations from

COMPARTMENTS
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

GO ID Qualified GO term Evidence PubMed IDs
GO:0070207 protein homotrimerization IDA 29056341
GO:0106064 regulation of cobalamin metabolic process IDA 29056341
genes like me logo Genes that share ontologies with CLYBL: view

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 116
Citric Acid Approved, Vet_approved Nutra Agonist, Activator 1243
Magnesium Approved Nutra 0
genes like me logo Genes that share compounds with CLYBL: view

Transcripts for CLYBL Gene

mRNA/cDNA for CLYBL Gene

Unigene Clusters for CLYBL Gene

Citrate lyase beta like:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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

No ASD Table

Relevant External Links for CLYBL Gene

GeneLoc Exon Structure for
CLYBL
ECgene alternative splicing isoforms for
CLYBL

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, 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:

CLYBL

SOURCE GeneReport for Unigene cluster for CLYBL Gene:

Hs.655642

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
chimpanzee
(Pan troglodytes)
Mammalia CLYBL 34 33
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CLYBL 34 33
  • 89.51 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Clybl 16 34 33
  • 86.62 (n)
rat
(Rattus norvegicus)
Mammalia Clybl 33
  • 86.22 (n)
cow
(Bos Taurus)
Mammalia CLYBL 34 33
  • 82.59 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLYBL 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLYBL 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLYBL 34 33
  • 78.21 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLYBL 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clybl 33
  • 72.82 (n)
zebrafish
(Danio rerio)
Actinopterygii clybl 34 33 33
  • 67.2 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea CELE_C01G10.7 33
  • 52.01 (n)
C01G10.7 34 35
  • 45 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
OneToOne
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

ENSEMBL:
Gene Tree for CLYBL (if available)
TreeFam:
Gene Tree for CLYBL (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLYBL: view image

Paralogs for CLYBL Gene

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

  • CLYBL_HUMAN
  • B4DU60_HUMAN
  • Q5JVB9_HUMAN
  • Q5JVC0_HUMAN
  • Q5JVC1_HUMAN
  • Q5JVC2_HUMAN
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

CLYBL_HUMAN-Q8N0X4
The protein is absent in 2.7% of the human population due to a loss-of-function polymorphism (rs41281112) that changes Arg-259 to a premature stop codon, leading to loss of the protein product (PubMed:23754956, PubMed:24334609). This polymorphism is associated with reduction of circulating vitamin B12 (PubMed:23754956, PubMed:24334609). The reduction of circulating vitamin B12 is caused by accumulation of citramalyl-CoA, an intermediate in the C5-dicarboxylate metabolic pathway that includes itaconate (PubMed:29056341). Itaconate acting as a vitamin B12-poisoning metabolite that inactivates the mitochondrial methylglutaconyl-CoA hydratase (AUH) enzyme (PubMed:29056341).

Sequence variations from dbSNP and Humsavar for CLYBL Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs1000022 -- 99,808,965(+) C/T intron_variant
rs1000022782 -- 99,854,772(+) G/A intron_variant
rs1000026668 -- 99,894,195(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000042738 -- 99,768,071(+) C/T intron_variant
rs1000055201 -- 99,847,098(+) G/A intron_variant

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

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

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)

Additional Variant Information for CLYBL Gene

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

SNP Genotyping and Copy Number Assay Products

Disorders for CLYBL Gene

MalaCards: The human disease database

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

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

Additional Disease Information for CLYBL

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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. The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. (PMID: 29056341) Shen H … Mootha VK (Cell 2017) 3 4 58
  2. 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 58
  3. 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 44 58
  4. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 44 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 CLYBL Gene

Sources for CLYBL Gene

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