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

Summary

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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiethnic meta-analysis of genome-wide association studies in &gt;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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH103203 (e-PCR)
- UniSTS:97536

A009F46 (e-PCR)
- UniSTS:25129

MARC_10213-10214:997278182:1 (e-PCR)
- UniSTS:267068

WI-15777 (e-PCR)
- UniSTS:12123

GDB:375677 (e-PCR)
- UniSTS:157034

GDB:375685 (e-PCR)
- UniSTS:157035

GDB:375688 (e-PCR)
- UniSTS:157036

GDB:375691 (e-PCR)
- UniSTS:157037

G32517 (e-PCR)
- UniSTS:117102

GDB:375697 (e-PCR)
- UniSTS:157039

Pccb (e-PCR), detects polymorphism
- UniSTS:527477

SHGC-64944 (e-PCR)
- UniSTS:41595

SHGC-54603 (e-PCR)
- UniSTS:48803

RH94340 (e-PCR)
- UniSTS:89022

GDB:631802 (e-PCR)
- UniSTS:158429

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 more info	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

EC 6.4.1.3

NP_001171485.1

EC 6.4.1.3

XP_011511175.1

EC 6.4.1.3

XP_054202659.1

EC 6.4.1.3

XP_054202660.1

EC 6.4.1.3

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

NG_008939.1 RefSeqGene

Range

5016..84845

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

136250340..136330169

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060927.1 Alternate T2T-CHM13v2.0

Range

138996153..139070827

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

F8WBI9
XM_054346684.1 → XP_054202659.1 propionyl-CoA carboxylase beta chain, mitochondrial isoform X2

UniProtKB/TrEMBL

E9PEC3