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 4
  • KIAA0251 2 4
  • EC 51
  • EC 4.1.1.- 4
  • EC 4.1.1 51
  • LP8165 3
  • PDXDC1 5

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. Diseases associated with PDXDC1 include Autosomal Recessive Nonsyndromic Deafness 32 and Fetal Akinesia Deformation Sequence 1. Gene Ontology (GO) annotations related to this gene include pyridoxal phosphate binding and carboxy-lyase activity. An important paralog of this gene is HDC.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDXDC1 Gene

Genomics for PDXDC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PDXDC1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDXDC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDXDC1

Top Transcription factor binding sites by QIAGEN in the PDXDC1 gene promoter:
  • AML1a
  • HEN1
  • ITF-2
  • Meis-1
  • Meis-1a
  • Meis-1b
  • POU2F1
  • POU2F1a
  • RP58
  • Tal-1beta

Genomic Locations for PDXDC1 Gene

Latest Assembly
178,753 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
164,676 bases
Plus strand

(GRCh37/hg19 by Ensembl)
164,749 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; Evidence={ECO:0000305}; Sequence=AAZ14099.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAA19780.1; Type=Erroneous initiation; Note=Extended N-terminus.; 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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for PDXDC1 Gene

Gene Families for PDXDC1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PDXDC1 Gene

Suggested Antigen Peptide Sequences for PDXDC1 Gene

GenScript: Design optimal peptide antigens:
  • Pyridoxal-dependent decarboxylase domain-containing protein 1 (PDXD1_HUMAN)

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:0003824 catalytic activity IEA --
GO:0008117 sphinganine-1-phosphate aldolase activity IBA 21873635
GO:0016829 lyase activity IEA --
GO:0016831 carboxy-lyase activity IEA --
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with PDXDC1: view
genes like me logo Genes that share phenotypes with PDXDC1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDXDC1

Clone products for research

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
endoplasmic reticulum 3
nucleus 2
cytosol 2
plasma membrane 1
extracellular 1

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:0005783 endoplasmic reticulum IBA 21873635
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

PathCards logo

SuperPathways for PDXDC1 Gene

No Data Available

SIGNOR curated interactions for PDXDC1 Gene

Other effect:

Gene Ontology (GO) - Biological Process for PDXDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001667 ameboidal-type cell migration IBA 21873635
GO:0019752 carboxylic acid metabolic process IEA --
GO:0030149 sphingolipid catabolic process IBA 21873635
genes like me logo Genes that share ontologies with PDXDC1: view

No data available for Pathways by source for PDXDC1 Gene

Drugs & Compounds for PDXDC1 Gene

(1) Drugs for PDXDC1 Gene - From: HMDB

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

Transcripts for PDXDC1 Gene

mRNA/cDNA for PDXDC1 Gene

25 NCBI additional mRNA sequence :
18 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDXDC1

Clone products for research

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

Expression for PDXDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for PDXDC1 Gene

Protein tissue co-expression partners for PDXDC1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDXDC1

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(3)
genes like me logo Genes that share expression patterns with PDXDC1: view

Primer products for research

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 30 31
  • 98.97 (n)
(Canis familiaris)
Mammalia PDXDC1 30 31
  • 87.35 (n)
(Bos Taurus)
Mammalia PDXDC1 30 31
  • 86.3 (n)
(Mus musculus)
Mammalia Pdxdc1 30 17 31
  • 85.56 (n)
(Rattus norvegicus)
Mammalia Pdxdc1 30
  • 84.84 (n)
(Ornithorhynchus anatinus)
Mammalia PDXDC1 31
  • 70 (a)
(Monodelphis domestica)
Mammalia PDXDC1 31
  • 68 (a)
(Gallus gallus)
Aves PDXDC1 30 31
  • 71.1 (n)
(Anolis carolinensis)
Reptilia PDXDC1 31
  • 68 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pdxdc1 30
  • 67.5 (n)
(Danio rerio)
Actinopterygii pdxdc1 30 31
  • 64.68 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000861 30
  • 43.98 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG1486 30 31
  • 43.96 (n)
(Caenorhabditis elegans)
Secernentea C14H10.3 30 31
  • 44.01 (n)
Species where no ortholog for PDXDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Evolutionary constrained regions (ECRs) for PDXDC1: view image

Paralogs for PDXDC1 Gene

Paralogs for PDXDC1 Gene

(1) SIMAP similar genes for PDXDC1 Gene using alignment to 13 proteins:

  • H3BM88_HUMAN
  • H3BQ54_HUMAN
  • H3BU11_HUMAN
  • Q86XE2_HUMAN Pseudogenes for PDXDC1 Gene

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

Variants for PDXDC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDXDC1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs11549900 Benign: not provided 15,004,190(+) C/G
NM_015027.4(PDXDC1):c.246C>G (p.Ile82Met)
rs140715398 Benign: not provided 15,032,887(+) G/A
NM_015027.4(PDXDC1):c.1598G>A (p.Ser533Asn)
rs150502355 Benign: not provided 15,008,813(+) C/A
NM_015027.4(PDXDC1):c.614C>A (p.Pro205His)
rs151006368 Benign: not provided 15,091,329(+) C/T
NM_018427.5(RRN3):c.238G>A (p.Asp80Asn)
rs3204898 Likely Benign: not provided 15,094,171(+) A/G
NM_018427.5(RRN3):c.63T>C (p.Val21=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PDXDC1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDXDC1 Gene

Disorders for PDXDC1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PDXDC1 Gene - From: COP

Disorder Aliases PubMed IDs
autosomal recessive nonsyndromic deafness 32
  • autosomal recessive deafness 105
fetal akinesia deformation sequence 1
  • fads1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PDXDC1

Genetic Association Database
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PDXDC1: view

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

Publications for PDXDC1 Gene

  1. 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 41
  2. Human metabolic individuality in biomedical and pharmaceutical research. (PMID: 21886157) Suhre K … Gieger C (Nature 2011) 3 41
  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 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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

Products for PDXDC1 Gene

Sources for PDXDC1 Gene