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    CLYBL citramalyl-CoA lyase [ Homo sapiens (human) ]

    Gene ID: 171425, updated on 5-Mar-2024

    Summary

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    Official Symbol
    CLYBLprovided by HGNC
    Official Full Name
    citramalyl-CoA lyaseprovided by HGNC
    Primary source
    HGNC:HGNC:18355
    See related
    Ensembl:ENSG00000125246 MIM:609686; AllianceGenome:HGNC:18355
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CLB
    Summary
    Enables (S)-citramalyl-CoA lyase activity; magnesium ion binding activity; and malate synthase activity. Involved in protein homotrimerization and regulation of cobalamin metabolic process. Predicted to be located in mitochondrion. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in kidney (RPKM 2.9), liver (RPKM 2.6) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLYBL in Genome Data Viewer
    Location:
    13q32.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99606690..99909444)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (98817569..99120319)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (100258944..100561698)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1039 Neighboring gene uncharacterized LOC105370332 Neighboring gene Sharpr-MPRA regulatory region 5963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100266847-100267346 Neighboring gene cofilin 1 pseudogene 8 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:100307367-100308566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7957 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:100311497-100312012 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:100313657-100314539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100318072-100318572 Neighboring gene microRNA 4306 Neighboring gene uncharacterized LOC124903199 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100338324-100339081 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100339082-100339840 Neighboring gene Sharpr-MPRA regulatory region 256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100344404-100345161 Neighboring gene CLYBL antisense RNA 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100360371-100360870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100360881-100361877 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100368890-100369679 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100381680-100382597 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100382598-100383514 Neighboring gene CLYBL antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:100398734-100399320 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100400494-100401079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100404341-100405168 Neighboring gene CLYBL antisense RNA 3 Neighboring gene uncharacterized LOC124900342 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100461465-100461966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100461967-100462466 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:100470112-100470282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100485830-100486582 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:100506615-100507814 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100544348-100544902 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100544903-100545456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100545457-100546010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100547191-100547692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100547693-100548192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100552816-100553392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100556702-100557202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100566125-100566624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100565623-100566124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100582975-100583475 Neighboring gene Sharpr-MPRA regulatory region 10052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100608499-100609474 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100609475-100610449 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100626468-100627010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100627011-100627551 Neighboring gene OCT4 hESC enhancer GRCh37_chr13:100631077-100631586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5475 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:100635796-100636995 Neighboring gene Zic family member 2 polyalanine repeat instability region Neighboring gene Zic family member 5 Neighboring gene Zic family member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. Strittmatter L, et al. Hum Mol Genet, 2014 May 1. PMID 24334609, Free PMC Article
    2. Molecular cloning of novel mouse and human putative citrate lyase beta-subunit. Morikawa J, et al. Biochem Biophys Res Commun, 2001 Dec 21. PMID 11741334
    3. The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B(12). Shen H, et al. Cell, 2017 Nov 2. PMID 29056341, Free PMC Article
    4. Genome-wide association study identifies novel loci associated with serum level of vitamin B12 in Chinese men. Lin X, et al. Hum Mol Genet, 2012 Jun 1. PMID 22367966
    5. Mapping the Zap-70 phosphorylation sites on LAT (linker for activation of T cells) required for recruitment and activation of signalling proteins in T cells. Paz PE, et al. Biochem J, 2001 Jun 1. PMID 11368773, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides.
    EBI GWAS Catalog
    Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with serum level of vitamin B12 in Chinese men.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables (S)-citramalyl-CoA lyase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables (S)-citramalyl-CoA lyase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables malate synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of cobalamin metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein homotrimerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cobalamin metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cobalamin metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    citramalyl-CoA lyase, mitochondrial
    Names
    (3S)-malyl-CoA thioesterase
    beta-methylmalate synthase
    citrate lyase beta like
    citrate lyase subunit beta-like protein, mitochondrial
    malate synthase
    NP_001380284.1
    NP_001380285.1
    NP_001380286.1
    NP_001380287.1
    NP_001380288.1
    NP_001380289.1
    NP_001380290.1
    NP_001380291.1
    NP_996531.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001393355.1 → NP_001380284.1  citramalyl-CoA lyase, mitochondrial isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS91830.1
      UniProtKB/TrEMBL
      B4DU60
      Conserved Domains (1) summary
      COG2301
      Location:47 → 303
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    2. NM_001393356.1 → NP_001380285.1  citramalyl-CoA lyase, mitochondrial isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS32002.1
      UniProtKB/Swiss-Prot
      Q5W0F7, Q8N0X4, Q8TDH8
      UniProtKB/TrEMBL
      B4DU60
      Conserved Domains (1) summary
      COG2301
      Location:47 → 337
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    3. NM_001393357.1 → NP_001380286.1  citramalyl-CoA lyase, mitochondrial isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS32002.1
      UniProtKB/Swiss-Prot
      Q5W0F7, Q8N0X4, Q8TDH8
      UniProtKB/TrEMBL
      B4DU60
      Related
      ENSP00000365533.4, ENST00000376355.7
      Conserved Domains (1) summary
      COG2301
      Location:47 → 337
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    4. NM_001393358.1 → NP_001380287.1  citramalyl-CoA lyase, mitochondrial isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS32002.1
      UniProtKB/Swiss-Prot
      Q5W0F7, Q8N0X4, Q8TDH8
      UniProtKB/TrEMBL
      B4DU60
      Related
      ENSP00000509937.1, ENST00000689673.1
      Conserved Domains (1) summary
      COG2301
      Location:47 → 337
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    5. NM_001393359.2 → NP_001380288.1  citramalyl-CoA lyase, mitochondrial isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS32002.1
      UniProtKB/Swiss-Prot
      Q5W0F7, Q8N0X4, Q8TDH8
      UniProtKB/TrEMBL
      B4DU60
      Conserved Domains (1) summary
      COG2301
      Location:47 → 337
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    6. NM_001393360.1 → NP_001380289.1  citramalyl-CoA lyase, mitochondrial isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS91830.1
      UniProtKB/TrEMBL
      B4DU60
      Related
      ENSP00000508871.1, ENST00000693071.1
      Conserved Domains (1) summary
      COG2301
      Location:47 → 303
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    7. NM_001393361.1 → NP_001380290.1  citramalyl-CoA lyase, mitochondrial isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS91830.1
      UniProtKB/TrEMBL
      B4DU60
      Conserved Domains (1) summary
      COG2301
      Location:47 → 303
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    8. NM_001393362.1 → NP_001380291.1  citramalyl-CoA lyase, mitochondrial isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS91830.1
      UniProtKB/TrEMBL
      B4DU60
      Related
      ENSP00000365532.1, ENST00000376354.5
      Conserved Domains (1) summary
      COG2301
      Location:47 → 303
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    9. NM_206808.5 → NP_996531.1  citramalyl-CoA lyase, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_996531.1

      Status: VALIDATED

      Source sequence(s)
      AL137139, AL139035
      Consensus CDS
      CCDS32002.1
      UniProtKB/Swiss-Prot
      Q5W0F7, Q8N0X4, Q8TDH8
      UniProtKB/TrEMBL
      B4DU60
      Related
      ENSP00000342991.4, ENST00000339105.9
      Conserved Domains (1) summary
      COG2301
      Location:47 → 337
      CitE; Citrate lyase beta subunit [Carbohydrate transport and metabolism]

    RNA

    1. NR_104592.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AF428253, AK095506, AL137139, AL139035

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      99606690..99909444
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      98817569..99120319
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N0X4.2 GenPept UniProtKB/Swiss-Prot:Q8N0X4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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