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    PCCB propionyl-CoA carboxylase subunit beta [ Homo sapiens (human) ]

    Gene ID: 5096, updated on 7-Apr-2024

    Summary

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    Official Symbol
    PCCBprovided by HGNC
    Official Full Name
    propionyl-CoA carboxylase subunit betaprovided by HGNC
    Primary source
    HGNC:HGNC:8654
    See related
    Ensembl:ENSG00000114054 MIM:232050; AllianceGenome:HGNC:8654
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    The protein encoded by this gene is a subunit of the propionyl-CoA carboxylase (PCC) enzyme, which is involved in the catabolism of propionyl-CoA. PCC is a mitochondrial enzyme that probably acts as a dodecamer of six alpha subunits and six beta subunits. This gene encodes the beta subunit of PCC. Defects in this gene are a cause of propionic acidemia type II (PA-2). Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in liver (RPKM 38.7), kidney (RPKM 36.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3q22.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (136250340..136330169)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (138996153..139070827)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (135969182..136049011)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:135876195-135876694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:135906825-135907326 Neighboring gene CRIPTO pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:135907961-135908462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20580 Neighboring gene hESC enhancers GRCh37_chr3:135914134-135914880 and GRCh37_chr3:135914881-135915627 Neighboring gene Sharpr-MPRA regulatory region 3094 Neighboring gene MSL complex subunit 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:135942902-135943448 Neighboring gene ribosomal protein L31 pseudogene 23 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:135968821-135969687 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:136015730-136016305 Neighboring gene STAG1 cohesin complex component Neighboring gene RNA, U6 small nuclear 1284, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20586 Neighboring gene RNY4 pseudogene 4

    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. Novel variants of the PCCB gene in Chinese patients with propionic acidemia. Yang X, et al. Clin Chim Acta, 2021 Aug. PMID 33798502
    2. Gene diagnosis and pedigree analysis of two Han ethnicity families with propionic acidemia in Fujian. Chen Y, et al. Medicine (Baltimore), 2021 Mar 12. PMID 33725819, Free PMC Article
    3. Biochemical phenotype and its relationship to treatment in 16 individuals with PCCB c.1606A > G (p.Asn536Asp) variant propionic acidemia. Wenger O, et al. Mol Genet Metab, 2020 Nov. PMID 33127324
    4. Autism in patients with propionic acidemia. Witters P, et al. Mol Genet Metab, 2016 Dec. PMID 27825584
    5. Functional analysis of PCCB mutations causing propionic acidemia based on expression studies in deficient human skin fibroblasts. Pérez-Cerdá C, et al. Biochim Biophys Acta, 2003 May 20. PMID 12757933

    See all (105) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A common benign intronic deletion masking a pathogenic deep intronic PCCB variant - genome sequencing and RNA studies to the rescue.
      Title: A common benign intronic deletion masking a pathogenic deep intronic PCCB variant - genome sequencing and RNA studies to the rescue.
    2. Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways.
      Title: Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways.
    3. Novel variants of the PCCB gene in Chinese patients with propionic acidemia.
      Title: Novel variants of the PCCB gene in Chinese patients with propionic acidemia.
    4. Biochemical phenotype and its relationship to treatment in 16 individuals with PCCB c.1606A > G (p.Asn536Asp) variant propionic acidemia.
      Title: Biochemical phenotype and its relationship to treatment in 16 individuals with PCCB c.1606A > G (p.Asn536Asp) variant propionic acidemia.
    5. Functional Analysis of the PCCA and PCCB Gene Variants Predicted to Affect Splicing.
      Title: Functional Analysis of the PCCA and PCCB Gene Variants Predicted to Affect Splicing.
    6. Gene diagnosis and pedigree analysis of two Han ethnicity families with propionic acidemia in Fujian.
      Title: Gene diagnosis and pedigree analysis of two Han ethnicity families with propionic acidemia in Fujian.
    7. his work represents a large-scale update on pathogenic mutations in the PCCA and PCCB genes causing Propionic acidemia (PA), and confirms previous reports indicating a major causative role of mutation-induced protein destabilization
      Title: Identification of 34 novel mutations in propionic acidemia: Functional characterization of missense variants and phenotype associations.
    8. Recurrent lactic acid elevations were present in six out of the eight patients. Five of the eight patients were diagnosed with Autism Spectrum Disorder, four of them had pathogenic variants in PCCB
      Title: Autism in patients with propionic acidemia.
    9. we identified seven novel genetic variants: p.Leu549Pro, p.Glu564*, p.Leu641Pro in MUT, p.Tyr206Cys in PCCB, p.His194Arg, p.Val298Met in BCKDHA and p.Glu286_Met290del in BCKDHB gene. In silico and/or eukaryotic expression studies confirmed pathogenic effect of all novel genetic variants
      Title: Molecular and phenotypic characteristics of seven novel mutations causing branched-chain organic acidurias.
    10. The majority of patients had mutations in the PCCA gene (18/25). A total of 26 mutations were noted: 20 in the PCCA gene and 6 in PCCB gene. Seventeen mutations were novel (14 in PCCA and 3 in PCCB).
      Title: Seventeen Novel Mutations in PCCA and PCCB Genes in Indian Propionic Acidemia Patients, and Their Outcomes.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    Associated conditions

    Description Tests
    Propionic acidemia
    MedGen: C0268579 OMIM: 606054 GeneReviews: Propionic Acidemia
    		Compare labs

    EBI GWAS Catalog

    Description
    Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts.
    EBI GWAS Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp451E113

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables propionyl-CoA carboxylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables propionyl-CoA carboxylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in branched-chain amino acid metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in fatty acid metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in short-chain fatty acid catabolic process IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of catalytic complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    propionyl-CoA carboxylase beta chain, mitochondrial
    Names
    PCCase subunit beta
    propanoyl-CoA:carbon dioxide ligase subunit beta
    propionyl CoA carboxylase, beta polypeptide
    propionyl Coenzyme A carboxylase, beta polypeptide
    propionyl-CoA carboxylase beta subunit
    NP_000523.2
    NP_001171485.1
    XP_011511175.1
    XP_054202659.1
    XP_054202660.1

    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.

    Genomic

    1. NG_008939.1 RefSeqGene

      Range
      5016..84845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000532.5 → NP_000523.2  propionyl-CoA carboxylase beta chain, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_000523.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      BC013768, DA090969
      Consensus CDS
      CCDS3089.1
      UniProtKB/Swiss-Prot
      B7Z2Z4, P05166, Q16813, Q96CX0
      UniProtKB/TrEMBL
      E7ETT1
      Related
      ENSP00000251654.4, ENST00000251654.9
      Conserved Domains (1) summary
      COG4799
      Location:37 → 539
      MmdA; Acetyl-CoA carboxylase, carboxyltransferase component [Lipid transport and metabolism]

    2. NM_001178014.2 → NP_001171485.1  propionyl-CoA carboxylase beta chain, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_001171485.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is longer compared to isoform 1.
      Source sequence(s)
      AC069524, AK295312
      Consensus CDS
      CCDS54643.1
      UniProtKB/TrEMBL
      A0A1B2JLU8
      Related
      ENSP00000419027.1, ENST00000469217.5
      Conserved Domains (2) summary
      COG4799
      Location:37 → 559
      MmdA; Acetyl-CoA carboxylase, carboxyltransferase component [Lipid transport and metabolism]
      cl23717
      Location:63 → 230
      crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      136250340..136330169
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011512873.2 → XP_011511175.1  propionyl-CoA carboxylase beta chain, mitochondrial isoform X1

      UniProtKB/TrEMBL
      F8WBI9
      Related
      ENSP00000417937.1, ENST00000484181.5
      Conserved Domains (2) summary
      COG4799
      Location:37 → 362
      MmdA; Acetyl-CoA carboxylase, carboxyltransferase component [Lipid transport and metabolism]
      cl23717
      Location:63 → 210
      crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      138996153..139070827
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346685.1 → XP_054202660.1  propionyl-CoA carboxylase beta chain, mitochondrial isoform X1

    2. XM_054346684.1 → XP_054202659.1  propionyl-CoA carboxylase beta chain, mitochondrial isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P05166.3 GenPept UniProtKB/Swiss-Prot:P05166

    Gene LinkOut

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

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