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    PDZK1 PDZ domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 5174, updated on 10-Dec-2024

    Summary

    Official Symbol
    PDZK1provided by HGNC
    Official Full Name
    PDZ domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:8821
    See related
    Ensembl:ENSG00000174827 MIM:603831; AllianceGenome:HGNC:8821
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CAP70; CLAMP; PDZD1; NHERF3; NHERF-3
    Summary
    This gene encodes a PDZ domain-containing scaffolding protein. PDZ domain-containing molecules bind to and mediate the subcellular localization of target proteins. The encoded protein mediates the localization of cell surface proteins and plays a critical role in cholesterol metabolism by regulating the HDL receptor, scavenger receptor class B type 1. Single nucleotide polymorphisms in this gene may be associated with metabolic syndrome, and overexpression of this gene may play a role in drug resistance of multiple myeloma. Pseudogenes of this gene are located on the long arm of chromosome 1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
    Expression
    Biased expression in kidney (RPKM 203.4), small intestine (RPKM 48.1) and 3 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PDZK1 in Genome Data Viewer
    Location:
    1q21.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (145670852..145707400, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (144787642..144824930, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (145727666..145764207)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NBPF member 25, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:145809563-145810063 Neighboring gene G protein-coupled receptor 89A Neighboring gene ReSE screen-validated silencer GRCh37_chr1:145788927-145789139 Neighboring gene NANOG hESC enhancer GRCh37_chr1:145744111-145744612 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:145727451-145728650 Neighboring gene CD160 molecule Neighboring gene ring finger protein 115 Neighboring gene MPRA-validated peak399 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:145629590-145630098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1611 Neighboring gene RNA polymerase III subunit C

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (41 hits/1256 screens)

    EBI GWAS Catalog

    Description
    Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
    EBI GWAS Catalog
    Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations.
    EBI GWAS Catalog
    Multiple genetic loci influence serum urate levels and their relationship with gout and cardiovascular disease risk factors.
    EBI GWAS Catalog
    Variants in the 1q21 risk region are associated with a visual endophenotype of autism and schizophrenia.
    EBI GWAS Catalog

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables PDZ domain binding PubMed 
    enables protein binding PubMed 
    enables protein-containing complex binding  
    enables protein-membrane adaptor activity  
    enables scavenger receptor binding  
    enables signaling receptor binding  
    Component Evidence Code Pubs
    is_active_in apical plasma membrane  
    located_in brush border PubMed 
    located_in brush border membrane PubMed 
    located_in extracellular exosome PubMed 
    located_in microvillus membrane  
    located_in plasma membrane PubMed 
    located_in plasma membrane  

    General protein information

    Preferred Names
    Na(+)/H(+) exchange regulatory cofactor NHE-RF3
    Names
    CFTR-associated protein of 70 kDa
    Na(+)/H(+) exchange regulatory cofactor 3
    PDZ-containing kidney protein 1
    na/Pi cotransporter C-terminal-associated protein 1
    naPi-Cap1
    sodium-hydrogen exchanger regulatory factor 3

    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.

    Genomic

    1. NG_050630.2 RefSeqGene

      Range
      5834..42217
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001201325.2 → NP_001188254.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 1

      See identical proteins and their annotated locations for NP_001188254.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC242845, AF012281, BX477678
      Consensus CDS
      CCDS72860.1
      UniProtKB/Swiss-Prot
      B4DPB9, E7EU02, O60450, Q5T2W1, Q5T5P6, Q9BQ41
      Related
      ENSP00000394485.1, ENST00000417171.6
      Conserved Domains (3) summary
      smart00228
      Location:375 → 455
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:241 → 320
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:437 → 481
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
    2. NM_001201326.1 → NP_001188255.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks two exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC242845, AK298269, BX477678
      Consensus CDS
      CCDS72859.1
      UniProtKB/Swiss-Prot
      Q5T2W1
      Related
      ENSP00000403422.2, ENST00000451928.6
      Conserved Domains (3) summary
      smart00228
      Location:264 → 344
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:133 → 209
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:326 → 370
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
    3. NM_001371359.1 → NP_001358288.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC242845
      Conserved Domains (3) summary
      smart00228
      Location:375 → 455
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:241 → 320
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:437 → 481
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
    4. NM_001371361.1 → NP_001358290.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC242845
      Conserved Domains (3) summary
      smart00228
      Location:168 → 248
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:34 → 113
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:230 → 274
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
    5. NM_002614.4 → NP_002605.2  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 1

      See identical proteins and their annotated locations for NP_002605.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC242845, BC006518, BX477678
      Consensus CDS
      CCDS72860.1
      UniProtKB/Swiss-Prot
      B4DPB9, E7EU02, O60450, Q5T2W1, Q5T5P6, Q9BQ41
      Related
      ENSP00000342143.2, ENST00000344770.6
      Conserved Domains (3) summary
      smart00228
      Location:375 → 455
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:241 → 320
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:437 → 481
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      145670852..145707400 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422527.1 → XP_047278483.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1

    2. XM_047422529.1 → XP_047278485.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X4

      UniProtKB/Swiss-Prot
      B4DPB9, E7EU02, O60450, Q5T2W1, Q5T5P6, Q9BQ41
    3. XM_047422528.1 → XP_047278484.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X2

    4. XM_024447620.2 → XP_024303388.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3

      Conserved Domains (3) summary
      smart00228
      Location:395 → 475
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:261 → 340
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:457 → 501
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
    5. XM_024447619.2 → XP_024303387.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3

      Conserved Domains (3) summary
      smart00228
      Location:395 → 475
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:261 → 340
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cl00365
      Location:457 → 501
      F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
    6. XM_047422530.1 → XP_047278486.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X5

    RNA

    1. XR_007061050.1 RNA Sequence

    2. XR_002956798.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      144787642..144824930 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336994.1 → XP_054192969.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1

    2. XM_054336993.1 → XP_054192968.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1

    3. XM_054336998.1 → XP_054192973.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X4

      UniProtKB/TrEMBL
      B2R7S7
    4. XM_054336995.1 → XP_054192970.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X2

    5. XM_054336997.1 → XP_054192972.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3

    6. XM_054336996.1 → XP_054192971.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3

    7. XM_054336999.1 → XP_054192974.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X5

    RNA

    1. XR_008486068.1 RNA Sequence

    2. XR_008486067.1 RNA Sequence

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