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

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PDZK1 protects against mechanical overload-induced chondrocyte senescence and osteoarthritis by targeting mitochondrial function.
Title: PDZK1 protects against mechanical overload-induced chondrocyte senescence and osteoarthritis by targeting mitochondrial function.
Promoter hypomethylated PDZK1 acts as a tumorigenic gene in glioma by interacting with AKT1.
Title: Promoter hypomethylated PDZK1 acts as a tumorigenic gene in glioma by interacting with AKT1.
CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
Title: CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
PDZK1 is correlated with DCE-MRI perfusion parameters in high-grade glioma.
Title: PDZK1 is correlated with DCE-MRI perfusion parameters in high-grade glioma.
PDZK1 suppresses TNBC development and sensitizes TNBC cells to erlotinib via the EGFR pathway.
Title: PDZK1 suppresses TNBC development and sensitizes TNBC cells to erlotinib via the EGFR pathway.
Interaction of Human OATP1B1 with PDZK1 Is Required for Its Trafficking to the Hepatocyte Plasma Membrane.
Title: Interaction of Human OATP1B1 with PDZK1 Is Required for Its Trafficking to the Hepatocyte Plasma Membrane.
HBV Infection-Related PDZK1 Plays an Oncogenic Role by Regulating the PI3K-Akt Pathway and Fatty Acid Metabolism and Enhances Immunosuppression.
Title: HBV Infection-Related PDZK1 Plays an Oncogenic Role by Regulating the PI3K-Akt Pathway and Fatty Acid Metabolism and Enhances Immunosuppression.
PDZK1 induces resistance to apoptosis in esophageal adenocarcinoma cells.
Title: PDZK1 induces resistance to apoptosis in esophageal adenocarcinoma cells.
Interleukin-37 contributes to the pathogenesis of gout by affecting PDZ domain-containing 1 protein through the nuclear factor-kappa B pathway.
Title: Interleukin-37 contributes to the pathogenesis of gout by affecting PDZ domain-containing 1 protein through the nuclear factor-kappa B pathway.
Long noncoding RNA PENG upregulates PDZK1 expression by sponging miR-15b to suppress clear cell renal cell carcinoma cell proliferation.
Title: Long noncoding RNA PENG upregulates PDZK1 expression by sponging miR-15b to suppress clear cell renal cell carcinoma cell proliferation.

Submit: New GeneRIF Correction See all GeneRIFs (64)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH35978 (e-PCR)
- UniSTS:64586

WI-11369 (e-PCR)
- UniSTS:67681

PDZK1_8530 (e-PCR)
- UniSTS:467822

RH79649 (e-PCR)
- UniSTS:85753

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables PDZ domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables protein-membrane adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables scavenger receptor binding	IEA Inferred from Electronic Annotation more info
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in carnitine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cation transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein localization to membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein targeting to membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of monoatomic anion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in xenobiotic detoxification by transmembrane export across the plasma membrane	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in apical plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in brush border	IDA Inferred from Direct Assay more info	PubMed
located_in brush border membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in microvillus membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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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)

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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

NG_050630.2 RefSeqGene

Range

5834..42217

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

145670852..145707400 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422527.1 → XP_047278483.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1
XM_047422529.1 → XP_047278485.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X4

UniProtKB/Swiss-Prot

B4DPB9, E7EU02, O60450, Q5T2W1, Q5T5P6, Q9BQ41
XM_047422528.1 → XP_047278484.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X2
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
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
XM_047422530.1 → XP_047278486.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X5

RNA

XR_007061050.1 RNA Sequence
XR_002956798.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

144787642..144824930 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054336994.1 → XP_054192969.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1
XM_054336993.1 → XP_054192968.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X1
XM_054336998.1 → XP_054192973.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X4

UniProtKB/TrEMBL

B2R7S7
XM_054336995.1 → XP_054192970.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X2
XM_054336997.1 → XP_054192972.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3
XM_054336996.1 → XP_054192971.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X3
XM_054336999.1 → XP_054192974.1 Na(+)/H(+) exchange regulatory cofactor NHE-RF3 isoform X5