Seroatlas · Human Serome Atlas

PDZRN3

E3 ubiquitin-protein ligase PDZRN3

Also known as: KIAA1095, LNX3, PZRN3_HUMAN, SEMACAP3, SEMCAP3

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

Protein identityUniProt · HPA

UniProt accession: Q9UPQ7
Gene: PDZRN3
Ensembl: ENSG00000121440
Chromosome: 3
Canonical length: 1066 aa
Protein class: Enzymes, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Cytosol

OverviewNCBI Gene

This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted for degradation by the human papilloma virus E6 protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

Canonical amino-acid sequenceUniProt

1066 residues, UniProt reviewed canonical sequence.

>Q9UPQ7|PDZRN3
     1  MGFELDRFDG DVDPDLKCAL CHKVLEDPLT TPCGHVFCAG CVLPWVVQEG SCPARCRGRL
    61  SAKELNHVLP LKRLILKLDI KCAYATRGCG RVVKLQQLPE HLERCDFAPA RCRHAGCGQV
   121  LLRRDVEAHM RDACDARPVG RCQEGCGLPL THGEQRAGGH CCARALRAHN GALQARLGAL
   181  HKALKKEALR AGKREKSLVA QLAAAQLELQ MTALRYQKKF TEYSARLDSL SRCVAAPPGG
   241  KGEETKSLTL VLHRDSGSLG FNIIGGRPSV DNHDGSSSEG IFVSKIVDSG PAAKEGGLQI
   301  HDRIIEVNGR DLSRATHDQA VEAFKTAKEP IVVQVLRRTP RTKMFTPPSE SQLVDTGTQT
   361  DITFEHIMAL TKMSSPSPPV LDPYLLPEEH PSAHEYYDPN DYIGDIHQEM DREELELEEV
   421  DLYRMNSQDK LGLTVCYRTD DEDDIGIYIS EIDPNSIAAK DGRIREGDRI IQINGIEVQN
   481  REEAVALLTS EENKNFSLLI ARPELQLDEG WMDDDRNDFL DDLHMDMLEE QHHQAMQFTA
   541  SVLQQKKHDE DGGTTDTATI LSNQHEKDSG VGRTDESTRN DESSEQENNG DDATASSNPL
   601  AGQRKLTCSQ DTLGSGDLPF SNESFISADC TDADYLGIPV DECERFRELL ELKCQVKSAT
   661  PYGLYYPSGP LDAGKSDPES VDKELELLNE ELRSIELECL SIVRAHKMQQ LKEQYRESWM
   721  LHNSGFRNYN TSIDVRRHEL SDITELPEKS DKDSSSAYNT GESCRSTPLT LEISPDNSLR
   781  RAAEGISCPS SEGAVGTTEA YGPASKNLLS ITEDPEVGTP TYSPSLKELD PNQPLESKER
   841  RASDGSRSPT PSQKLGSAYL PSYHHSPYKH AHIPAHAQHY QSYMQLIQQK SAVEYAQSQM
   901  SLVSMCKDLS SPTPSEPRME WKVKIRSDGT RYITKRPVRD RLLRERALKI REERSGMTTD
   961  DDAVSEMKMG RYWSKEERKQ HLVKAKEQRR RREFMMQSRL DCLKEQQAAD DRKEMNILEL
  1021  SHKKMMKKRN KKIFDNWMTI QELLTHGTKS PDGTRVYNSF LSVTTV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDZRN3 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: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.53
Highest tissue expression: 86 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 86 nTPM
colon: 79 nTPM
blood vessel: 62 nTPM
ovary: 58 nTPM
endometrium: 58 nTPM
urinary bladder: 51 nTPM

Single-cell type

choroid plexus epithelial cells: 3,032 nCPM
cardiomyocytes: 1,323 nCPM
adipocytes: 1,163 nCPM
adrenal cortex cells: 883 nCPM
endometrial stromal cells: 837 nCPM
myonuclei: 625 nCPM

Immune cell

plasmacytoid DC: 1.9 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

choroid plexus: 117 nTPM
cerebral cortex: 38 nTPM
thalamus: 30 nTPM
amygdala: 25 nTPM
basal ganglia: 23 nTPM
spinal cord: 22 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PDZRN3.

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 216 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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): 0.3
gnomAD pLI: 0.98
gnomAD missense Z: -0.01
DepMap mean gene effect: -0.06
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 PDZRN3 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 PDZRN3 as an antibody target. Whether an autoantibody or antibody against PDZRN3 could matter depends on whether native PDZRN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDZRN3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PDZRN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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