Seroatlas · Human Serome Atlas

PDZK1

Na(+)/H(+) exchange regulatory cofactor NHE-RF3

Also known as: NHERF3, NHRF3_HUMAN, PDZD1

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q5T2W1
Gene: PDZK1
Ensembl: ENSG00000174827
Chromosome: 1
Canonical length: 519 aa
Protein class: Predicted intracellular proteins
Subcellular location: Nucleoplasm,Vesicles,Cytosol

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

519 residues, UniProt reviewed canonical sequence.

>Q5T2W1|PDZK1
     1  MTSTFNPREC KLSKQEGQNY GFFLRIEKDT EGHLVRVVEK CSPAEKAGLQ DGDRVLRING
    61  VFVDKEEHMQ VVDLVRKSGN SVTLLVLDGD SYEKAVKTRV DLKELGQSQK EQGLSDNILS
   121  PVMNGGVQTW TQPRLCYLVK EGGSYGFSLK TVQGKKGVYM TDITPQGVAM RAGVLADDHL
   181  IEVNGENVED ASHEEVVEKV KKSGSRVMFL LVDKETDKRH VEQKIQFKRE TASLKLLPHQ
   241  PRIVEMKKGS NGYGFYLRAG SEQKGQIIKD IDSGSPAEEA GLKNNDLVVA VNGESVETLD
   301  HDSVVEMIRK GGDQTSLLVV DKETDNMYRL AHFSPFLYYQ SQELPNGSVK EAPAPTPTSL
   361  EVSSPPDTTE EVDHKPKLCR LAKGENGYGF HLNAIRGLPG SFIKEVQKGG PADLAGLEDE
   421  DVIIEVNGVN VLDEPYEKVV DRIQSSGKNV TLLVCGKKAY DYFQAKKIPI VSSLADPLDT
   481  PPDSKEGIVV ESNHDSHMAK ERAHSTASHS SSNSEDTEM

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDZK1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.37
Highest tissue expression: 556 nTPM

Expression across tissuesHPA

Tissue

kidney: 556 nTPM
liver: 120 nTPM
small intestine: 118 nTPM
duodenum: 71 nTPM
cerebellum: 27 nTPM
gallbladder: 21 nTPM

Single-cell type

proximal tubule cells: 391 nCPM
enterocytes: 325 nCPM
epididymal efferent duct absorptive cells: 102 nCPM
cholangiocytes: 85 nCPM
hepatocytes: 63 nCPM
loop of henle epithelial cells: 50 nCPM

Immune cell

NK-cell: 4.2 nTPM
memory CD8 T-cell: 0.9 nTPM
gdT-cell: 0.7 nTPM
memory B-cell: 0.6 nTPM
plasmacytoid DC: 0.5 nTPM
naive B-cell: 0.4 nTPM

Brain region

cerebellum: 37 nTPM
cerebral cortex: 9.7 nTPM
pons: 8.6 nTPM
white matter: 8.4 nTPM
choroid plexus: 8.3 nTPM
medulla oblongata: 7.9 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.71
gnomAD pLI: 0
gnomAD missense Z: -0.05
DepMap mean gene effect: -0.26
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PDZK1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PDZK1 as an antibody target. Whether an autoantibody or antibody against PDZK1 could matter depends on whether native PDZK1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDZK1 is annotated at the cell surface, where native PDZK1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label PDZK1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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