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

Gene ID: 5174, updated on 4-Oct-2020

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
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

Genomic context

See PDZK1 in Genome Data Viewer
Location:
1q21.1
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (145670852..145708201, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (145727662..145764207)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene PDE4DIP pseudogene 5 Neighboring gene NBPF member 25, pseudogene Neighboring gene G protein-coupled receptor 89A Neighboring gene CD160 molecule Neighboring gene ring finger protein 115 Neighboring gene RNA polymerase III subunit C

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
GeneReviews: Not available
Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations.
GeneReviews: Not available
Multiple genetic loci influence serum urate levels and their relationship with gout and cardiovascular disease risk factors.
GeneReviews: Not available
Variants in the 1q21 risk region are associated with a visual endophenotype of autism and schizophrenia.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
PDZ domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein membrane anchor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
scavenger receptor binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
carnitine transport IDA
Inferred from Direct Assay
more info
PubMed 
drug transmembrane export NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of cation transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein localization to membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein targeting to membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of anion transport ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
apical plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
brush border IDA
Inferred from Direct Assay
more info
PubMed 
brush border membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
extracellular exosome HDA PubMed 
membrane raft IEA
Inferred from Electronic Annotation
more info
 
microvillus membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Names
CFTR-associated protein of 70 kDa
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)

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_001201325.2NP_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
    Q5T2W1
    Related
    ENSP00000394485.1, ENST00000417171.6
    Conserved Domains (3) summary
    smart00228
    Location:375455
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:241320
    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:437481
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  2. NM_001201326.1NP_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:264344
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:133209
    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:326370
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  3. NM_001371359.1NP_001358288.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC242845
  4. NM_001371361.1NP_001358290.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC242845
    Conserved Domains (3) summary
    smart00228
    Location:168248
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:34113
    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:230274
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  5. NM_002614.4NP_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
    Q5T2W1
    Related
    ENSP00000342143.2, ENST00000344770.6
    Conserved Domains (3) summary
    smart00228
    Location:375455
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:241320
    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:437481
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    145670852..145708201 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001467.2XP_016856956.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X5

    Conserved Domains (3) summary
    smart00228
    Location:168248
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:34113
    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:230274
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  2. XM_024447619.1XP_024303387.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3

    Conserved Domains (3) summary
    smart00228
    Location:395475
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:261340
    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:457501
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  3. XM_024447616.1XP_024303384.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1

    Conserved Domains (3) summary
    smart00228
    Location:395475
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:261340
    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:457501
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  4. XM_024447620.1XP_024303388.1  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3

    Conserved Domains (3) summary
    smart00228
    Location:395475
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:261340
    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:457501
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit
  5. XM_011509616.3XP_011507918.2  Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X2

    Conserved Domains (3) summary
    smart00228
    Location:395475
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:261340
    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:457501
    F1-ATPase_gamma; mitochondrial ATP synthase gamma subunit

RNA

  1. XR_002956799.1 RNA Sequence

  2. XR_002956801.1 RNA Sequence

  3. XR_002956800.1 RNA Sequence

  4. XR_002956798.1 RNA Sequence

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