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Aliases for PCCA Gene

Aliases for PCCA Gene

  • Propionyl-CoA Carboxylase Alpha Subunit 2 3 5
  • EC 4 58
  • Propionyl Coenzyme A Carboxylase, Alpha Polypeptide 2
  • Propanoyl-CoA:Carbon Dioxide Ligase Subunit Alpha 4
  • PCCase Subunit Alpha 4
  • EC 6.4.1 58

External Ids for PCCA Gene

Previous GeneCards Identifiers for PCCA Gene

  • GC13P099101
  • GC13P095128
  • GC13P099577
  • GC13P098439
  • GC13P099539
  • GC13P100741
  • GC13P081336

Summaries for PCCA Gene

Entrez Gene Summary for PCCA Gene

  • The protein encoded by this gene is the alpha subunit of the heterodimeric mitochondrial enzyme Propionyl-CoA carboxylase. PCCA encodes the biotin-binding region of this enzyme. Mutations in either PCCA or PCCB (encoding the beta subunit) lead to an enzyme deficiency resulting in propionic acidemia. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

GeneCards Summary for PCCA Gene

PCCA (Propionyl-CoA Carboxylase Alpha Subunit) is a Protein Coding gene. Diseases associated with PCCA include Propionicacidemia and Pcca-Related Propionic Acidemia. Among its related pathways are Metabolism and HIV Life Cycle. GO annotations related to this gene include enzyme binding and biotin carboxylase activity. An important paralog of this gene is MCCC1.

Additional gene information for PCCA Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCCA Gene

Genomics for PCCA Gene

Regulatory Elements for PCCA Gene

Enhancers for PCCA Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13H100098 1.2 Ensembl ENCODE 5.7 +11.1 11089 3.5 ELF3 FOXA2 FEZF1 RAD21 RARA YY1 ZNF366 ATF7 ZNF202 ZNF362 PCCA ASNSP3 GC13P100113 PIR44331
GH13H100049 0.6 ENCODE 4.6 -38.2 -38225 2 ZFHX2 POLR2A ZNF547 GFI1B PRDM10 ZNF18 PCCA GC13M100051 GC13P100038
GH13H099955 0.8 FANTOM5 dbSUPER 1.2 -133.1 -133134 0.3 ZNF202 EZH2 ETS1 ZIC5 ZIC2 PCCA LOC101927437 GC13P099922
GH13H100088 1.3 ENCODE dbSUPER 0.7 +0.4 357 2.3 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 SP3 PCCA PIR44331 GC13P100113
GH13H100108 0.3 FANTOM5 0.4 +19.3 19340 0.2 GC13P100113 PIR44331 PCCA
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCCA on UCSC Golden Path with GeneCards custom track

Promoters for PCCA Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000065153 86 2200 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 SP3

Genomic Locations for PCCA Gene

Genomic Locations for PCCA Gene
441,423 bases
Plus strand

Genomic View for PCCA Gene

Genes around PCCA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCCA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCCA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCCA Gene

Proteins for PCCA Gene

  • Protein details for PCCA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Propionyl-CoA carboxylase alpha chain, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B4DKY8
    • B4DPF9
    • C9JPQ8
    • Q15979
    • Q8WXQ7

    Protein attributes for PCCA Gene

    728 amino acids
    Molecular mass:
    80059 Da
    Name=biotin; Xref=ChEBI:CHEBI:57586;
    Quaternary structure:
    • Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.
    • Sequence=AAA60035.1; Type=Frameshift; Positions=374, 378, 380, 395; Evidence={ECO:0000305}; Sequence=AAH00140.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAK61392.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAA32763.1; Type=Frameshift; Positions=23; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCCA Gene

    Alternative splice isoforms for PCCA Gene


neXtProt entry for PCCA Gene

Selected DME Specific Peptides for PCCA Gene


Post-translational modifications for PCCA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for PCCA Gene

Gene Families for PCCA Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCCA: view

No data available for UniProtKB/Swiss-Prot for PCCA Gene

Function for PCCA Gene

Molecular function for PCCA Gene

GENATLAS Biochemistry:
propionyl-CoA carboxylase,alpha polypeptide,biotin-dependent,mitochondrial conversion of propionyl CoA to methylmalonyl CoA,branched chain valine,isoleucine catabolism,energy pathway
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + propanoyl-CoA + HCO(3)(-) = ADP + phosphate + (S)-methylmalonyl-CoA.

Enzyme Numbers (IUBMB) for PCCA Gene

Phenotypes From GWAS Catalog for PCCA Gene

Gene Ontology (GO) - Molecular Function for PCCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004075 biotin carboxylase activity IEA --
GO:0004658 propionyl-CoA carboxylase activity TAS,IEA --
GO:0005524 ATP binding IEA --
GO:0009374 biotin binding TAS 3460076
genes like me logo Genes that share ontologies with PCCA: view
genes like me logo Genes that share phenotypes with PCCA: view

Human Phenotype Ontology for PCCA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PCCA Gene

MGI Knock Outs for PCCA:

Animal Model Products

Clone Products

  • Addgene plasmids for PCCA

No data available for Transcription Factor Targets and HOMER Transcription for PCCA Gene

Localization for PCCA Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCCA Gene

Mitochondrion matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PCCA gene
Compartment Confidence
mitochondrion 5
cytosol 5

Gene Ontology (GO) - Cellular Components for PCCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PCCA: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCCA Gene

Pathways & Interactions for PCCA Gene

genes like me logo Genes that share pathways with PCCA: view

UniProtKB/Swiss-Prot P05165-PCCA_HUMAN

  • Pathway: Metabolic intermediate metabolism; propanoyl-CoA degradation; succinyl-CoA from propanoyl-CoA: step 1/3.

Gene Ontology (GO) - Biological Process for PCCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006768 biotin metabolic process TAS --
GO:0019626 short-chain fatty acid catabolic process TAS --
genes like me logo Genes that share ontologies with PCCA: view

No data available for SIGNOR curated interactions for PCCA Gene

Drugs & Compounds for PCCA Gene

(6) Drugs for PCCA Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Biotin Approved Nutra Target 49
Phosphoric acid Approved Pharma 0
Propanoyl-CoA Experimental Pharma 0
spermidine Experimental Pharma Antagonist, Pore Blocker 0
ATP Nutra Agonist 0

(8) Additional Compounds for PCCA Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
Carbonic acid
  • Acid of air
  • Aerial acid
  • Bisodium carbonate
  • Calcined
  • Carbonic acid sodium salt
  • (R)-methylmalonyl-CoA
  • (R)-methylmalonyl-Coenzyme A
  • (S)-2-Methyl-3-Oxopropanoyl-Coa
  • (S)-methyl-malonyl-CoA
  • (S)-methyl-malonyl-Coenzyme A
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
  • (S)-Methylmalonyl-CoA
  • (S)-Methylmalonyl-Coenzyme A
genes like me logo Genes that share compounds with PCCA: view

Transcripts for PCCA Gene

Unigene Clusters for PCCA Gene

Propionyl CoA carboxylase, alpha polypeptide:
Representative Sequences:

Clone Products

  • Addgene plasmids for PCCA

Alternative Splicing Database (ASD) splice patterns (SP) for PCCA Gene

No ASD Table

Relevant External Links for PCCA Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCCA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCCA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCCA Gene

This gene is overexpressed in Liver (x4.4).

Protein differential expression in normal tissues from HIPED for PCCA Gene

This gene is overexpressed in Kidney (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCCA Gene

Protein tissue co-expression partners for PCCA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCCA Gene:


SOURCE GeneReport for Unigene cluster for PCCA Gene:


Evidence on tissue expression from TISSUES for PCCA Gene

  • Kidney(4.6)
  • Liver(4.6)
  • Nervous system(3.4)
  • Adrenal gland(2.1)
  • Pancreas(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PCCA Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • ear
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • adrenal gland
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • stomach
  • pelvis
  • rectum
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood
  • bone marrow
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • sweat gland
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with PCCA: view

No data available for mRNA Expression by UniProt/SwissProt for PCCA Gene

Orthologs for PCCA Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PCCA Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCCA 33 34
  • 99.5 (n)
(Canis familiaris)
Mammalia PCCA 33 34
  • 92.4 (n)
(Bos Taurus)
Mammalia PCCA 33 34
  • 89.19 (n)
(Monodelphis domestica)
Mammalia PCCA 34
  • 87 (a)
(Mus musculus)
Mammalia Pcca 33 16 34
  • 86.74 (n)
(Rattus norvegicus)
Mammalia Pcca 33
  • 86.58 (n)
(Ornithorhynchus anatinus)
Mammalia PCCA 34
  • 81 (a)
(Gallus gallus)
Aves PCCA 33 34
  • 81.93 (n)
(Anolis carolinensis)
Reptilia PCCA 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcca 33
  • 76.57 (n)
Str.11243 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.25798 33
(Danio rerio)
Actinopterygii pcca 33 34
  • 69.59 (n)
Dr.23782 33
(Caenorhabditis elegans)
Secernentea pcca-1 33 34
  • 59.29 (n)
F27D9.5 35
  • 58 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DUR1,2 34
  • 12 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 58 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4365 33
Species where no ortholog for PCCA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PCCA Gene

Gene Tree for PCCA (if available)
Gene Tree for PCCA (if available)

Paralogs for PCCA Gene

Paralogs for PCCA Gene

(4) SIMAP similar genes for PCCA Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with PCCA: view

Variants for PCCA Gene

Sequence variations from dbSNP and Humsavar for PCCA Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs118169528 other, Propionic acidemia type I (PA-1) [MIM:606054] 100,368,504(+) CAACT(G/T)GGAGC intron-variant, nc-transcript-variant, reference, missense
rs121964958 Pathogenic, Propionic acidemia type I (PA-1) [MIM:606054] 100,301,512(+) GGAAA(A/T)GATCC intron-variant, nc-transcript-variant, reference, missense
rs141371306 Propionic acidemia type I (PA-1) [MIM:606054] 100,111,886(+) CATGT(C/T)GGGTG nc-transcript-variant, upstream-variant-2KB, reference, missense
rs202247814 Pathogenic, Propionic acidemia type I (PA-1) [MIM:606054] 100,155,090(+) CCCAA(A/G)CTGTG nc-transcript-variant, reference, missense, utr-variant-5-prime
rs202247815 Pathogenic, Propionic acidemia type I (PA-1) [MIM:606054] 100,209,354(+) TTTCA(C/T)TGGAC nc-transcript-variant, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for PCCA Gene

Variant ID Type Subtype PubMed ID
nsv977273 CNV duplication 23825009
nsv977272 CNV duplication 23825009
nsv832698 CNV loss 17160897
nsv832697 CNV loss 17160897
nsv7247 OTHER inversion 18451855
nsv526668 CNV gain 19592680
nsv523329 CNV loss 19592680
nsv518301 CNV loss 19592680
nsv509512 CNV insertion 20534489
nsv507729 OTHER sequence alteration 20534489
nsv507728 OTHER sequence alteration 20534489
nsv474342 CNV novel sequence insertion 20440878
nsv473298 CNV novel sequence insertion 20440878
nsv1134345 CNV deletion 24896259
nsv1120424 CNV deletion 24896259
nsv1069769 CNV deletion 25765185
nsv1037571 CNV loss 25217958
nsv1037414 CNV loss 25217958
esv3892435 CNV loss 25118596
esv3892434 CNV loss 25118596
esv3633346 CNV loss 21293372
esv3633345 CNV loss 21293372
esv3633344 CNV loss 21293372
esv3633343 CNV loss 21293372
esv3633341 CNV loss 21293372
esv3633340 CNV loss 21293372
esv3582760 CNV gain 25503493
esv3408110 CNV duplication 20981092
esv3364634 CNV insertion 20981092
esv3308710 CNV mobile element insertion 20981092
esv3303042 CNV tandem duplication 20981092
esv2747880 CNV deletion 23290073
esv2747879 CNV deletion 23290073
esv2747878 CNV deletion 23290073
esv2747877 CNV deletion 23290073
esv2671626 CNV deletion 23128226
esv2669958 CNV deletion 23128226
esv2668656 CNV deletion 23128226
esv2634464 CNV deletion 19546169
esv2490241 CNV deletion 19546169
dgv577e212 CNV loss 25503493

Variation tolerance for PCCA Gene

Residual Variation Intolerance Score: 11.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.79; 58.18% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCCA Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCCA Gene

Disorders for PCCA Gene

MalaCards: The human disease database

(7) MalaCards diseases for PCCA Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • propionic acidemia
pcca-related propionic acidemia
  • pcca-related propionicacidemia
bile duct adenocarcinoma
methylmalonic acidemia
  • methylmalonic acidemia, cbla type
multiple carboxylase deficiency
  • mcd
- elite association - COSMIC cancer census association via MalaCards
Search PCCA in MalaCards View complete list of genes associated with diseases


  • Propionic acidemia type I (PA-1) [MIM:606054]: Life-threatening disease characterized by episodic vomiting, lethargy and ketosis, neutropenia, periodic thrombocytopenia, hypogammaglobulinemia, developmental retardation, and intolerance to protein. {ECO:0000269 PubMed:10101253, ECO:0000269 PubMed:10329019, ECO:0000269 PubMed:12559849, ECO:0000269 PubMed:15059621}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for PCCA Gene

hyperglycinemia,ketotic,propionic acidemia A

Relevant External Links for PCCA

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PCCA: view

Publications for PCCA Gene

  1. Mutation spectrum of the PCCA and PCCB genes in Japanese patients with propionic acidemia. (PMID: 15059621) Yang X … Ohura T (Molecular genetics and metabolism 2004) 3 4 22 60
  2. Propionic acidemia: identification of twenty-four novel mutations in Europe and North America. (PMID: 12559849) Pérez B … Ugarte M (Molecular genetics and metabolism 2003) 3 4 22 60
  3. Functional characterization of PCCA mutations causing propionic acidemia. (PMID: 12385775) Clavero S … Desviat LR (Biochimica et biophysica acta 2002) 3 22 25 60
  4. Structure of the PCCA gene and distribution of mutations causing propionic acidemia. (PMID: 11592820) Campeau E … Gravel RA (Molecular genetics and metabolism 2001) 3 4 22 60
  5. Genetic heterogeneity in propionic acidemia patients with alpha-subunit defects. Identification of five novel mutations, one of them causing instability of the protein. (PMID: 10101253) Richard E … Ugarte M (Biochimica et biophysica acta 1999) 3 4 22 60

Products for PCCA Gene

  • Addgene plasmids for PCCA

Sources for PCCA Gene

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