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

Gene ID: 5096, updated on 2-Nov-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
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Genomic context

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See PCCB in Genome Data Viewer
Location:
3q22.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (136250340..136330169)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (138996153..139070827)
RS_2024_09 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 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. Human propionyl-CoA carboxylase beta subunit gene: exon-intron definition and mutation spectrum in Spanish and Latin American propionic acidemia patients. Rodríguez-Pombo P, et al. Am J Hum Genet, 1998 Aug. PMID 9683601, Free PMC Article
  2. Novel variants of the PCCB gene in Chinese patients with propionic acidemia. Yang X, et al. Clin Chim Acta, 2021 Aug. PMID 33798502
  3. 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
  4. 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
  5. Autism in patients with propionic acidemia. Witters P, et al. Mol Genet Metab, 2016 Dec. PMID 27825584

See all (117) 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)

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
  
located_in mitochondrion HTP PubMed 
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_2024_08

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

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