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    PDXDC1 pyridoxal dependent decarboxylase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23042, updated on 4-Jul-2021

    Summary

    Official Symbol
    PDXDC1provided by HGNC
    Official Full Name
    pyridoxal dependent decarboxylase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28995
    See related
    Ensembl:ENSG00000179889 MIM:614244
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LP8165
    Expression
    Ubiquitous expression in testis (RPKM 42.5), duodenum (RPKM 33.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDXDC1 in Genome Data Viewer
    Location:
    16p13.11
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (14974591..15153343)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15068592..15233267)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene PKD1P3-NPIPA1 readthrough Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 3 Neighboring gene microRNA 6770-1 Neighboring gene nuclear pore complex interacting protein family member A1 Neighboring gene KIAA2013 pseudogene Neighboring gene microRNA 1972-1 Neighboring gene Sharpr-MPRA regulatory region 1947 Neighboring gene N-terminal asparagine amidase Neighboring gene RRN3 homolog, RNA polymerase I transcription factor Neighboring gene Sharpr-MPRA regulatory region 13846 Neighboring gene uncharacterized LOC100505915 Neighboring gene PKD1P6-NPIPP1 readthrough Neighboring gene nuclear pore complex interacting protein pseudogene 1 Neighboring gene microRNA 6511b-2 Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 6 Neighboring gene microRNA 3180-4 Neighboring gene uncharacterized LOC105371096

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Phenotypes

    Associated conditions

    Description Tests
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    GeneReviews: Not available
    An atlas of genetic influences on human blood metabolites.
    GeneReviews: Not available
    Discovery and refinement of loci associated with lipid levels.
    GeneReviews: Not available
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    GeneReviews: Not available
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    GeneReviews: Not available
    Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
    GeneReviews: Not available
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    GeneReviews: Not available
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    GeneReviews: Not available
    Human metabolic individuality in biomedical and pharmaceutical research.
    GeneReviews: Not available

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0251

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding HDA PubMed 
    enables carboxy-lyase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in carboxylic acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    pyridoxal-dependent decarboxylase domain-containing protein 1
    NP_001272373.1
    NP_001272374.1
    NP_001272376.1
    NP_001272377.1
    NP_001272378.1
    NP_001272379.1
    NP_001310948.1
    NP_001310949.1
    NP_001310950.1
    NP_055842.2
    XP_005255233.1
    XP_006720928.2
    XP_016878548.1
    XP_016878549.1
    XP_016878550.1
    XP_016878551.1
    XP_016878552.1
    XP_016878553.1
    XP_016878554.1
    XP_024305962.1
    XP_024305963.1
    XP_024305964.1
    XP_024305965.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001285444.2NP_001272373.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001272373.1

      Status: VALIDATED

      Source sequence(s)
      AC138932, BC042104, BC053946, BC060871, BM997114, BX647809, HY036748
      Consensus CDS
      CCDS66954.1
      UniProtKB/Swiss-Prot
      Q6P996
      Related
      ENSP00000455070.1, ENST00000569715.5
      Conserved Domains (1) summary
      cl18945
      Location:145367
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    2. NM_001285445.2NP_001272374.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC138932, AK299111, BC042104, BC053946, BC060871, BM997114, D87438, HY036748
      Consensus CDS
      CCDS66955.1
      UniProtKB/Swiss-Prot
      Q6P996
      Related
      ENSP00000486662.1, ENST00000627450.2
      Conserved Domains (1) summary
      cl18945
      Location:144366
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    3. NM_001285447.1NP_001272376.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001272376.1

      Status: VALIDATED

      Source sequence(s)
      AK295168, BC033748, BC042104, BC060871, BM997114, DA775396
      UniProtKB/Swiss-Prot
      Q6P996
      UniProtKB/TrEMBL
      B4DHL7
      Related
      ENSP00000454791.1, ENST00000563679.5
      Conserved Domains (1) summary
      cl18945
      Location:157379
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    4. NM_001285448.1NP_001272377.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AK299799, BC042104, BC060871, BM997114, DA321929
      Consensus CDS
      CCDS66957.1
      UniProtKB/Swiss-Prot
      Q6P996
      Related
      ENSP00000391147.3, ENST00000450288.3
      Conserved Domains (1) summary
      cl18945
      Location:81303
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    5. NM_001285449.2NP_001272378.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 6

      See identical proteins and their annotated locations for NP_001272378.1

      Status: VALIDATED

      Source sequence(s)
      AC139256, BC045554, CD370048
      Consensus CDS
      CCDS73830.1
      UniProtKB/TrEMBL
      Q86XE2
      Related
      ENSP00000437835.2, ENST00000535621.6
      Conserved Domains (1) summary
      cl18945
      Location:172394
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    6. NM_001285450.2NP_001272379.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC138932, BC033748, BC053946, CA423507, HY036748
      Consensus CDS
      CCDS73831.1
      UniProtKB/Swiss-Prot
      Q6P996
      Related
      ENSP00000406703.2, ENST00000455313.6
      Conserved Domains (1) summary
      cl18945
      Location:172371
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    7. NM_001324019.2NP_001310948.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC138932
    8. NM_001324020.2NP_001310949.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC138932, AC139256
    9. NM_001324021.2NP_001310950.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC138932, AC139256
    10. NM_015027.4NP_055842.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_055842.2

      Status: VALIDATED

      Source sequence(s)
      AC138932, AY203955, BC042104, BC060871, BM997114, DB019664
      Consensus CDS
      CCDS32393.1
      UniProtKB/Swiss-Prot
      Q6P996
      UniProtKB/TrEMBL
      Q6XYB5
      Related
      ENSP00000379691.4, ENST00000396410.9
      Conserved Domains (1) summary
      cl18945
      Location:172394
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

      Range
      14974591..15153343
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450195.1XP_024305963.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8

      Conserved Domains (1) summary
      cl18945
      Location:190412
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    2. XM_024450194.1XP_024305962.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X7

      Conserved Domains (1) summary
      cl18945
      Location:157379
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    3. XM_017023065.1XP_016878554.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

    4. XM_017023063.1XP_016878552.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

    5. XM_017023059.1XP_016878548.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      cl18945
      Location:157379
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    6. XM_006720865.2XP_006720928.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

      Conserved Domains (1) summary
      cl18945
      Location:130352
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    7. XM_017023062.1XP_016878551.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      cl18945
      Location:157379
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    8. XM_017023064.1XP_016878553.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

      Conserved Domains (1) summary
      cl18945
      Location:130352
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    9. XM_005255176.3XP_005255233.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005255233.1

      Conserved Domains (1) summary
      cl18945
      Location:157379
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    10. XM_024450196.1XP_024305964.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X9

      Conserved Domains (1) summary
      cl18945
      Location:181403
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    11. XM_017023060.1XP_016878549.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

      Conserved Domains (1) summary
      cl18945
      Location:181403
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    12. XM_017023061.2XP_016878550.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      cl18945
      Location:157379
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
    13. XM_024450197.1XP_024305965.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X10

      Conserved Domains (1) summary
      cl18945
      Location:130352
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

    Reference GRCh38.p13 ALT_REF_LOCI_1

    Genomic

    1. NT_187607.1 Reference GRCh38.p13 ALT_REF_LOCI_1

      Range
      523098..694938 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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