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Aliases for PDXDC1 Gene

Aliases for PDXDC1 Gene

  • Pyridoxal Dependent Decarboxylase Domain Containing 1 2 3 5
  • Pyridoxal-Dependent Decarboxylase Domain-Containing Protein 1 3
  • EC 56
  • EC 4.1.1.- 4
  • KIAA0251 4
  • EC 4.1.1 56
  • LP8165 3

External Ids for PDXDC1 Gene

Previous GeneCards Identifiers for PDXDC1 Gene

  • GC16P014978
  • GC16P015068
  • GC16P014770

Summaries for PDXDC1 Gene

GeneCards Summary for PDXDC1 Gene

PDXDC1 (Pyridoxal Dependent Decarboxylase Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include pyridoxal phosphate binding and carboxy-lyase activity.

Additional gene information for PDXDC1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDXDC1 Gene

Genomics for PDXDC1 Gene

GeneHancer (GH) Regulatory Elements for PDXDC1 Gene

Promoters and enhancers for PDXDC1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I014973 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 554.2 +0.7 730 2.8 PKNOX1 CLOCK ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PDXDC1 NPIPA2 ENSG00000183458 NPIPA3 NPIPA1 PARN LOC100505915 NPIPA5 ENSG00000261819 BFAR
GH16I014997 Promoter/Enhancer 0.8 EPDnew dbSUPER 550.3 +23.2 23172 0.1 ZNF121 PIR39802 PDXDC1 RRN3 LOC728138 GC16P014859
GH16I014095 Enhancer 1.1 Ensembl ENCODE 18.3 -877.7 -877684 3.8 CLOCK FOXA2 ZNF493 ZFP64 ZNF133 NEUROD1 FEZF1 ZNF213 FOS ZNF202 LOC100505915 PARN ENSG00000183458 RRN3 NPIPA3 NPIPA1 NPIPA2 ERCC4 BFAR PDXDC1
GH16I015487 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.8 +516.6 516582 7.6 PKNOX1 SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A YY1 ZNF766 FOS LOC100505915 PARN RRN3 C16orf45 PKD1P6 PKD1P1 BFAR ENSG00000183458 PDXDC1 ENSG00000207425
GH16I015575 Enhancer 1.5 FANTOM5 ENCODE dbSUPER 9.8 +602.0 602035 2.6 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT DMAP1 YY1 POLR2B ZNF766 PARN ENSG00000263335 BFAR LOC100505915 RRN3 PKD1P6 PKD1P1 ENSG00000183458 C16orf45 PDXDC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDXDC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDXDC1 gene promoter:

Genomic Locations for PDXDC1 Gene

Genomic Locations for PDXDC1 Gene
164,759 bases
Plus strand

Genomic View for PDXDC1 Gene

Genes around PDXDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDXDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDXDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDXDC1 Gene

Proteins for PDXDC1 Gene

  • Protein details for PDXDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pyridoxal-dependent decarboxylase domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • B4DR55
    • B4DSL3
    • E7EMH5
    • E7EPL4
    • H3BNZ1
    • O00236
    • Q4F6X7
    • Q6PID7
    • Q86YF1
    • Q8N4Q9
    • Q8TBS5

    Protein attributes for PDXDC1 Gene

    788 amino acids
    Molecular mass:
    86707 Da
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    No Data Available
    • Sequence=AAH33748.1; Type=Frameshift; Positions=369; Evidence={ECO:0000305}; Sequence=AAZ14099.1; Type=Frameshift; Positions=369; Evidence={ECO:0000305}; Sequence=BAA19780.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PDXDC1 Gene


neXtProt entry for PDXDC1 Gene

Selected DME Specific Peptides for PDXDC1 Gene


Post-translational modifications for PDXDC1 Gene

No Post-translational modifications

Domains & Families for PDXDC1 Gene

Gene Families for PDXDC1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PDXDC1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the group II decarboxylase family.
  • Belongs to the group II decarboxylase family.
genes like me logo Genes that share domains with PDXDC1: view

Function for PDXDC1 Gene

Enzyme Numbers (IUBMB) for PDXDC1 Gene

Phenotypes From GWAS Catalog for PDXDC1 Gene

Gene Ontology (GO) - Molecular Function for PDXDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016829 lyase activity IEA --
GO:0016831 carboxy-lyase activity IEA --
GO:0030170 pyridoxal phosphate binding IEA --
GO:0045296 cadherin binding IDA 25468996
genes like me logo Genes that share ontologies with PDXDC1: view

Phenotypes for PDXDC1 Gene

genes like me logo Genes that share phenotypes with PDXDC1: view

Animal Model Products

miRNA for PDXDC1 Gene

miRTarBase miRNAs that target PDXDC1

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDXDC1 Gene

Localization for PDXDC1 Gene

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 PDXDC1 gene
Compartment Confidence
golgi apparatus 5
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (4)
  • Vesicles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDXDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with PDXDC1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PDXDC1 Gene

Pathways & Interactions for PDXDC1 Gene

SuperPathways for PDXDC1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDXDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0019752 carboxylic acid metabolic process IEA --
genes like me logo Genes that share ontologies with PDXDC1: view

No data available for Pathways by source and SIGNOR curated interactions for PDXDC1 Gene

Drugs & Compounds for PDXDC1 Gene

(1) Drugs for PDXDC1 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
genes like me logo Genes that share compounds with PDXDC1: view

Transcripts for PDXDC1 Gene

Unigene Clusters for PDXDC1 Gene

Pyridoxal-dependent decarboxylase domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDXDC1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b
SP2: - -

Relevant External Links for PDXDC1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDXDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDXDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDXDC1 Gene

This gene is overexpressed in Bone (26.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDXDC1 Gene

Protein tissue co-expression partners for PDXDC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDXDC1 Gene:


SOURCE GeneReport for Unigene cluster for PDXDC1 Gene:


Evidence on tissue expression from TISSUES for PDXDC1 Gene

  • Nervous system(4.9)
  • Liver(4.6)
  • Lung(4.4)
  • Bone marrow(4.2)
  • Intestine(2.7)
genes like me logo Genes that share expression patterns with PDXDC1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDXDC1 Gene

Orthologs for PDXDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDXDC1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDXDC1 33 34
  • 98.97 (n)
(Canis familiaris)
Mammalia PDXDC1 33 34
  • 87.35 (n)
(Bos Taurus)
Mammalia PDXDC1 33 34
  • 86.3 (n)
(Mus musculus)
Mammalia Pdxdc1 33 16 34
  • 85.56 (n)
(Rattus norvegicus)
Mammalia Pdxdc1 33
  • 84.84 (n)
(Ornithorhynchus anatinus)
Mammalia PDXDC1 34
  • 70 (a)
(Monodelphis domestica)
Mammalia PDXDC1 34
  • 68 (a)
(Gallus gallus)
Aves PDXDC1 33 34
  • 71.1 (n)
(Anolis carolinensis)
Reptilia PDXDC1 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdxdc1 33
  • 67.5 (n)
(Danio rerio)
Actinopterygii pdxdc1 33 34
  • 64.68 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000861 33
  • 43.98 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG1486 33 34
  • 43.96 (n)
(Caenorhabditis elegans)
Secernentea C14H10.3 33 34
  • 44.01 (n)
Species where no ortholog for PDXDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PDXDC1 Gene

Gene Tree for PDXDC1 (if available)
Gene Tree for PDXDC1 (if available)

Paralogs for PDXDC1 Gene Pseudogenes for PDXDC1 Gene

genes like me logo Genes that share paralogs with PDXDC1: view

No data available for Paralogs for PDXDC1 Gene

Variants for PDXDC1 Gene

Sequence variations from dbSNP and Humsavar for PDXDC1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000007371 -- 15,032,331(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000038947 -- 15,107,822(+) A/C genic_downstream_transcript_variant, intron_variant
rs1000043521 -- 15,125,949(+) G/T genic_downstream_transcript_variant, intron_variant
rs1000050810 -- 15,087,395(+) C/A genic_downstream_transcript_variant, intron_variant
rs1000091517 -- 15,135,686(+) G/A/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PDXDC1 Gene

Variant ID Type Subtype PubMed ID
esv3570354 CNV gain 25503493
esv3582039 CNV loss 25503493
esv3584701 CNV loss 24956385
esv3584925 CNV gain 24956385
esv3638020 CNV loss 21293372
esv3446644 CNV duplication 20981092
esv3437667 CNV duplication 20981092
esv3430780 CNV duplication 20981092
esv3430647 CNV duplication 20981092
esv3430066 CNV duplication 20981092
esv3418750 CNV duplication 20981092
esv3414261 CNV duplication 20981092
esv3413987 CNV duplication 20981092
esv3409568 CNV duplication 20981092
esv3405700 CNV duplication 20981092
esv3385246 CNV duplication 20981092
esv3378041 CNV duplication 20981092
esv3366485 CNV insertion 20981092
esv3360897 CNV duplication 20981092
esv3360432 CNV duplication 20981092
esv3337075 CNV duplication 20981092
esv32598 CNV gain 17666407
esv29939 CNV gain 18421352
esv2914901 CNV duplication 24192839
esv2913790 CNV duplication 24192839
esv2762254 CNV gain+loss 21179565
esv2760416 CNV gain+loss 21179565
esv2758632 CNV gain+loss 17122850
esv2714014 CNV deletion 23290073
esv2676791 CNV deletion 23128226
esv26385 CNV loss 19812545
esv2631582 CNV gain 19546169
esv2602193 CNV loss 19546169
esv23670 CNV loss 19812545
esv1168353 CNV deletion 17803354
esv1004883 CNV gain 20482838
dgv793e212 CNV loss 25503493
dgv4922n54 CNV loss 21841781
dgv4921n54 CNV loss 21841781
dgv4920n54 CNV loss 21841781
dgv4919n54 CNV loss 21841781
dgv482e214 CNV gain 21293372
dgv481e214 CNV gain 21293372
dgv480e214 CNV gain 21293372
dgv462n67 CNV gain 20364138
dgv344n27 CNV loss 19166990
dgv2n1 OTHER inversion 15895083
dgv2770n100 CNV loss 25217958
dgv2769n100 CNV gain+loss 25217958
dgv2768n100 CNV loss 25217958
dgv2767n100 CNV gain 25217958
dgv2766n100 CNV gain 25217958
dgv2765n100 CNV gain 25217958
dgv2764n100 CNV gain 25217958
dgv2763n100 CNV loss 25217958
dgv2762n100 CNV gain+loss 25217958
dgv2761n100 CNV loss 25217958
dgv2760n100 CNV loss 25217958
dgv2759n100 CNV gain+loss 25217958
dgv2757n100 CNV gain+loss 25217958
dgv2756n100 CNV loss 25217958
dgv2755n100 CNV gain 25217958
dgv2753n100 CNV loss 25217958
dgv2752n100 CNV gain+loss 25217958
dgv2750n100 CNV loss 25217958
dgv2749n100 CNV gain 25217958
dgv2747n100 CNV loss 25217958
dgv2746n100 CNV gain+loss 25217958
dgv2745n100 CNV gain 25217958
dgv2744n100 CNV loss 25217958
dgv2742n100 CNV gain 25217958
dgv2741n100 CNV gain+loss 25217958
dgv2740n100 CNV loss 25217958
dgv2738n100 CNV gain 25217958
dgv1502e59 CNV duplication 20981092
dgv1501e59 CNV duplication 20981092
dgv1500e59 CNV duplication 20981092
dgv11n31 CNV gain 19718026
dgv112n111 CNV duplication 26073780
dgv111n111 CNV duplication 26073780
nsv984375 CNV duplication 23825009
nsv984266 CNV duplication 23825009
nsv984265 CNV duplication 23825009
nsv984264 CNV duplication 23825009
nsv978191 CNV duplication 23825009
nsv977911 CNV duplication 23825009
nsv977910 CNV duplication 23825009
nsv977908 CNV duplication 23825009
nsv977116 CNV duplication 23825009
nsv977115 CNV duplication 23825009
nsv977114 CNV duplication 23825009
nsv974860 CNV duplication 23825009
nsv952934 CNV deletion 24416366
nsv952933 CNV duplication 24416366
nsv952932 CNV duplication 24416366
nsv9359 CNV gain+loss 18304495
nsv9357 CNV loss 18304495
nsv821043 CNV duplication 20802225
nsv819280 CNV loss 19587683
nsv7277 OTHER inversion 18451855
nsv571527 CNV gain+loss 21841781
nsv571523 CNV gain+loss 21841781
nsv514794 CNV gain 21397061
nsv514793 CNV gain 21397061
nsv511045 OTHER complex 20534489
nsv509598 CNV insertion 20534489
nsv499138 OTHER inversion 21111241
nsv482191 CNV gain 20164927
nsv457426 CNV gain 19166990
nsv442710 CNV gain 18776908
nsv1160358 CNV duplication 26073780
nsv1160357 CNV duplication 26073780
nsv1160356 CNV duplication 26073780
nsv1160355 CNV duplication 26073780
nsv1153482 CNV duplication 26484159
nsv1146292 CNV duplication 26484159
nsv1144758 CNV deletion 24896259
nsv1141278 CNV duplication 24896259
nsv1132417 CNV duplication 24896259
nsv1115491 CNV duplication 24896259
nsv1110266 CNV duplication 24896259
nsv1076419 CNV duplication 25765185
nsv1070753 CNV deletion 25765185
nsv1053467 CNV loss 25217958
nsv1050325 CNV loss 25217958
nsv1042130 CNV gain 25217958
nsv1041074 CNV gain 25217958
nsv1038955 CNV loss 25217958
nsv1037396 CNV gain+loss 25217958
nsv1036298 CNV gain 25217958
esv3892797 CNV gain 25118596
esv3892796 CNV loss 25118596
esv3638025 CNV gain 21293372
esv3638024 CNV loss 21293372
esv3638023 CNV gain 21293372
esv3638022 CNV loss 21293372
esv3638021 CNV gain 21293372

Variation tolerance for PDXDC1 Gene

Residual Variation Intolerance Score: 81.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.02; 68.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDXDC1 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 PDXDC1 Gene

Disorders for PDXDC1 Gene

Additional Disease Information for PDXDC1

No disorders were found for PDXDC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDXDC1 Gene

Publications for PDXDC1 Gene

  1. Human metabolic individuality in biomedical and pharmaceutical research. (PMID: 21886157) Suhre K … Gieger C (Nature 2011) 3 44 58
  2. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. (PMID: 21829377) Lemaitre RN … Steffen LM (PLoS genetics 2011) 3 44 58
  3. A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. (PMID: 20189936) Okada Y … Kamatani N (Human molecular genetics 2010) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1996) 3 4 58

Products for PDXDC1 Gene

Sources for PDXDC1 Gene

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