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Aliases for PDHX Gene

Aliases for PDHX Gene

  • Pyruvate Dehydrogenase Complex Component X 2 3 5
  • Dihydrolipoamide Dehydrogenase-Binding Protein Of Pyruvate Dehydrogenase Complex 3 4
  • Lipoyl-Containing Pyruvate Dehydrogenase Complex Component X 3 4
  • E3BP 3 4
  • PDX1 3 4
  • ProX 3 4
  • Pyruvate Dehydrogenase Complex, Lipoyl-Containing Component X 3
  • Pyruvate Dehydrogenase Complex, E3-Binding Protein Subunit 3
  • Pyruvate Dehydrogenase Protein X Component, Mitochondrial 3
  • E3-Binding Protein 4
  • DLDBP 3
  • PDHXD 3
  • OPDX 3

External Ids for PDHX Gene

Previous GeneCards Identifiers for PDHX Gene

  • GC11P034977
  • GC11P034902
  • GC11P034636

Summaries for PDHX Gene

Entrez Gene Summary for PDHX Gene

  • The pyruvate dehydrogenase (PDH) complex is located in the mitochondrial matrix and catalyzes the conversion of pyruvate to acetyl coenzyme A. The PDH complex thereby links glycolysis to Krebs cycle. The PDH complex contains three catalytic subunits, E1, E2, and E3, two regulatory subunits, E1 kinase and E1 phosphatase, and a non-catalytic subunit, E3 binding protein (E3BP). This gene encodes the E3 binding protein subunit; also known as component X of the pyruvate dehydrogenase complex. This protein tethers E3 dimers to the E2 core of the PDH complex. Defects in this gene are a cause of pyruvate dehydrogenase deficiency which results in neurological dysfunction and lactic acidosis in infancy and early childhood. This protein is also a minor antigen for antimitochondrial antibodies. These autoantibodies are present in nearly 95% of patients with the autoimmune liver disease primary biliary cirrhosis (PBC). In PBC, activated T lymphocytes attack and destroy epithelial cells in the bile duct where this protein is abnormally distributed and overexpressed. PBC eventually leads to cirrhosis and liver failure. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]

GeneCards Summary for PDHX Gene

PDHX (Pyruvate Dehydrogenase Complex Component X) is a Protein Coding gene. Diseases associated with PDHX include Pyruvate Dehydrogenase E3-Binding Protein Deficiency and Lactic Acidosis. Among its related pathways are Metabolism and Signaling by Retinoic Acid. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring acyl groups. An important paralog of this gene is DLAT.

UniProtKB/Swiss-Prot for PDHX Gene

  • Required for anchoring dihydrolipoamide dehydrogenase (E3) to the dihydrolipoamide transacetylase (E2) core of the pyruvate dehydrogenase complexes of eukaryotes. This specific binding is essential for a functional PDH complex.

Gene Wiki entry for PDHX Gene

Additional gene information for PDHX Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDHX Gene

Genomics for PDHX Gene

GeneHancer (GH) Regulatory Elements for PDHX Gene

Promoters and enhancers for PDHX Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J034914 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 672.9 +1.0 1016 4.5 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 APIP PDHX ENSG00000271369 CAT MIR1343
GH11J035006 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 19.4 +95.0 94977 9.8 PKNOX1 STAT5A BMI1 FEZF1 BATF IRF4 RAD21 RFX5 SCRT2 ZNF207 GC11M035009 APIP CD44 PDHX LOC100507144 MIR1343 PAMR1 GC11P034975
GH11J035137 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.1 +226.7 226737 10.4 HDGF SIN3A YBX1 IRF4 GLIS2 ZNF143 ATF7 FOS RUNX3 MCM3 CD44 LOC100507144 APIP PDHX GC11P035210
GH11J034908 Enhancer 1 Ensembl ENCODE 21.6 -5.8 -5759 3.5 FOXA2 DNMT3B RAD21 YY1 EGR1 SCRT2 FOS RXRA ZBTB25 CEBPB APIP PDHX MIR1343 EHF GC11M034882
GH11J034975 Enhancer 1.1 Ensembl ENCODE dbSUPER 19.1 +61.6 61604 4.4 FOXA2 JUN YY1 GATA3 POLR2A FOSL2 HOMEZ MAFK TCF7L2 RXRA APIP PDHX MIR1343 GC11P034975 GC11M035009
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDHX on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDHX gene promoter:
  • ER-alpha
  • CUTL1
  • RORalpha1
  • Brachyury
  • IRF-7A
  • IRF-2
  • AREB6
  • GATA-3
  • GATA-2
  • GATA-1

Genomic Locations for PDHX Gene

Genomic Locations for PDHX Gene
chr11:34,915,829-35,020,591
(GRCh38/hg38)
Size:
104,763 bases
Orientation:
Plus strand
chr11:34,937,376-35,042,138
(GRCh37/hg19)
Size:
104,763 bases
Orientation:
Plus strand

Genomic View for PDHX Gene

Genes around PDHX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PDHX Gene

Proteins for PDHX Gene

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

    Protein Symbol:
    O00330-ODPX_HUMAN
    Recommended name:
    Pyruvate dehydrogenase protein X component, mitochondrial
    Protein Accession:
    O00330
    Secondary Accessions:
    • B4DW62
    • D3DR11
    • E9PB14
    • E9PBP7
    • O60221
    • Q96FV8
    • Q99783

    Protein attributes for PDHX Gene

    Size:
    501 amino acids
    Molecular mass:
    54122 Da
    Quaternary structure:
    • Part of the inner core of the multimeric pyruvate dehydrogenase complex that is composed of about 48 DLAT and 12 PDHX molecules (PubMed:14638692, PubMed:20361979). This core binds multiple copies of pyruvate dehydrogenase (subunits PDH1A and PDHB, E1), dihydrolipoamide acetyltransferase (DLAT, E2) and lipoamide dehydrogenase (DLD, E3) (PubMed:14638692). Interacts with SIRT4 (PubMed:25525879). Interacts with DLD (PubMed:20385101, PubMed:16263718, PubMed:16442803, PubMed:20160912, PubMed:20361979).

    Three dimensional structures from OCA and Proteopedia for PDHX Gene

    Alternative splice isoforms for PDHX Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDHX Gene

Post-translational modifications for PDHX Gene

  • Delipoylated at Lys-97 by SIRT4, delipoylation decreases the PHD complex activity.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDHX Gene

Domains & Families for PDHX Gene

Gene Families for PDHX Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PDHX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O00330

UniProtKB/Swiss-Prot:

ODPX_HUMAN :
  • Belongs to the 2-oxoacid dehydrogenase family.
Family:
  • Belongs to the 2-oxoacid dehydrogenase family.
genes like me logo Genes that share domains with PDHX: view

Function for PDHX Gene

Molecular function for PDHX Gene

UniProtKB/Swiss-Prot Function:
Required for anchoring dihydrolipoamide dehydrogenase (E3) to the dihydrolipoamide transacetylase (E2) core of the pyruvate dehydrogenase complexes of eukaryotes. This specific binding is essential for a functional PDH complex.

Phenotypes From GWAS Catalog for PDHX Gene

Gene Ontology (GO) - Molecular Function for PDHX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16263718
GO:0016746 transferase activity, transferring acyl groups IEA --
GO:0034604 contributes_to pyruvate dehydrogenase (NAD+) activity IDA 9242632
genes like me logo Genes that share ontologies with PDHX: view
genes like me logo Genes that share phenotypes with PDHX: view

Human Phenotype Ontology for PDHX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDHX

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for PDHX Gene

Localization for PDHX Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDHX Gene

Mitochondrion matrix.

Subcellular locations from

COMPARTMENTS
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 PDHX gene
Compartment Confidence
mitochondrion 5
plasma membrane 3
nucleus 3
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDHX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
GO:0045254 pyruvate dehydrogenase complex IDA 9242632
genes like me logo Genes that share ontologies with PDHX: view

Pathways & Interactions for PDHX Gene

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

Gene Ontology (GO) - Biological Process for PDHX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006090 pyruvate metabolic process TAS --
GO:0008152 metabolic process IEA --
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate TAS --
GO:0034641 cellular nitrogen compound metabolic process TAS --
GO:0061732 mitochondrial acetyl-CoA biosynthetic process from pyruvate IC 9242632
genes like me logo Genes that share ontologies with PDHX: view

No data available for SIGNOR curated interactions for PDHX Gene

Drugs & Compounds for PDHX Gene

(13) Drugs for PDHX Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Gimeracil Approved Pharma Dihydropyrimidine dehydrogenase inhibitor 0
Mycophenolate mofetil Approved, Investigational Pharma IMPDH inhibitor 987
Stiripentol Approved Pharma An LDH inhibitor 9
Trilostane Approved, Investigational, Vet_approved, Withdrawn Pharma 2
Lipoic Acid Approved, Investigational Nutra 0

(4) Additional Compounds for PDHX Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PDHX: view

Transcripts for PDHX Gene

mRNA/cDNA for PDHX Gene

Unigene Clusters for PDHX Gene

Pyruvate dehydrogenase complex, component X:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDHX

Clone Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c
SP1: - - -
SP2: - - - - - - - - -
SP3: - -
SP4:

Relevant External Links for PDHX Gene

GeneLoc Exon Structure for
PDHX
ECgene alternative splicing isoforms for
PDHX

Expression for PDHX Gene

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

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

This gene is overexpressed in Muscle - Skeletal (x4.7) and Heart - Left Ventricle (x4.4).

Protein differential expression in normal tissues from HIPED for PDHX Gene

This gene is overexpressed in Heart (22.6) and Brain (6.0).

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



Protein tissue co-expression partners for PDHX Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDHX Gene:

PDHX

SOURCE GeneReport for Unigene cluster for PDHX Gene:

Hs.502315

Evidence on tissue expression from TISSUES for PDHX Gene

  • Nervous system(4.9)
  • Liver(4.4)
  • Muscle(2.6)
  • Heart(2.5)
  • Kidney(2.5)
  • Stomach(2.2)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • eyelid
  • face
  • forehead
  • head
  • mouth
  • skull
Thorax:
  • chest wall
  • rib
  • rib cage
  • sternum
Limb:
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with PDHX: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for PDHX Gene

Orthologs for PDHX Gene

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

Orthologs for PDHX Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDHX 34 33
  • 99.67 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PDHX 34 33
  • 90.02 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LOC517402 33
  • 88.96 (n)
PDHX 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdhx 16 34 33
  • 83.43 (n)
oppossum
(Monodelphis domestica)
Mammalia PDHX 34
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDHX 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDHX 34 33
  • 72.79 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 79 (a)
OneToMany
-- 34
  • 52 (a)
OneToMany
-- 34
  • 49 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia pdhx 33
  • 63.89 (n)
zebrafish
(Danio rerio)
Actinopterygii pdhx 34 33
  • 58.68 (n)
OneToOne
zgc66110 33
fruit fly
(Drosophila melanogaster)
Insecta CG5261 34
  • 34 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C30H6.7 34
  • 37 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LAT1 34
  • 32 (a)
OneToOne
PDX1 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5274 34
  • 46 (a)
OneToOne
Species where no ortholog for PDHX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • rat (Rattus norvegicus)
  • 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 PDHX Gene

ENSEMBL:
Gene Tree for PDHX (if available)
TreeFam:
Gene Tree for PDHX (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDHX: view image

Paralogs for PDHX Gene

Paralogs for PDHX Gene

(1) SIMAP similar genes for PDHX Gene using alignment to 4 proteins:

  • ODPX_HUMAN
  • E9PLU0_HUMAN
  • E9PRI6_HUMAN
  • H0YD97_HUMAN
genes like me logo Genes that share paralogs with PDHX: view

Variants for PDHX Gene

Sequence variations from dbSNP and Humsavar for PDHX Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1049306 benign, not specified, Pyruvate dehydrogenase complex deficiency 34,916,722(+) C/T coding_sequence_variant, intron_variant, missense_variant
rs1049307 benign, not specified, Pyruvate dehydrogenase complex deficiency 34,916,763(+) T/C/G coding_sequence_variant, intron_variant, synonymous_variant
rs1049333 likely-benign, Pyruvate dehydrogenase complex deficiency 34,996,062(+) T/C 3_prime_UTR_variant
rs112032820 benign, Pyruvate dehydrogenase complex deficiency 34,916,527(+) C/G/T 5_prime_UTR_variant, intron_variant
rs113073242 benign, Pyruvate dehydrogenase complex deficiency 34,916,454(+) A/G 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv2759817 CNV loss 17122850
esv34511 CNV loss 17911159
esv3579474 CNV loss 25503493
nsv1042014 CNV loss 25217958
nsv1055116 CNV gain 25217958
nsv437715 CNV loss 16327808
nsv437716 CNV loss 16327808
nsv518924 CNV loss 19592680
nsv825836 CNV loss 20364138
nsv832119 CNV gain 17160897

Variation tolerance for PDHX Gene

Residual Variation Intolerance Score: 85.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.57; 86.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDHX Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PDHX Gene

MalaCards: The human disease database

(7) MalaCards diseases for PDHX Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PDHX in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ODPX_HUMAN
  • Pyruvate dehydrogenase E3-binding protein deficiency (PDHXD) [MIM:245349]: A metabolic disorder characterized by decreased activity of the pyruvate dehydrogenase complex without observable reduction in the activities of enzymes E1, E2, or E3. Clinical features include hypotonia and psychomotor retardation. {ECO:0000269 PubMed:9399911}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for PDHX Gene

severe developmental delay and mental retardation

Additional Disease Information for PDHX

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

Publications for PDHX Gene

  1. Detection of a homozygous four base pair deletion in the protein X gene in a case of pyruvate dehydrogenase complex deficiency. (PMID: 9467010) Ling M … Robinson BH (Human molecular genetics 1998) 2 3 4 22 58
  2. How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex. (PMID: 16263718) Ciszak EM … Patel MS (The Journal of biological chemistry 2006) 3 4 22 58
  3. Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex. (PMID: 16442803) Brautigam CA … Chuang DT (Structure (London, England : 1993) 2006) 3 4 22 58
  4. Organization of the cores of the mammalian pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and their capacities to bind the E1 and E3 components. (PMID: 14638692) Hiromasa Y … Roche TE (The Journal of biological chemistry 2004) 3 4 22 58
  5. Dihydrolipoamide dehydrogenase-binding protein of the human pyruvate dehydrogenase complex. DNA-derived amino acid sequence, expression, and reconstitution of the pyruvate dehydrogenase complex. (PMID: 9242632) Harris RA … Popov KM (The Journal of biological chemistry 1997) 3 4 22 58

Products for PDHX Gene

Sources for PDHX Gene

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