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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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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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