Seroatlas · Human Serome Atlas

NPHP4

Nephrocystin-4

Also known as: KIAA0673, NPHP4_HUMAN, POC10, SLSN4

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

Protein identityUniProt · HPA

UniProt accession
O75161
Gene
NPHP4
Ensembl
ENSG00000131697
Chromosome
1
Canonical length
1426 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location
Nucleoplasm,Nuclear bodies,Vesicles,Cytosol

OverviewNCBI Gene

This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

Canonical amino-acid sequenceUniProt

1426 residues, UniProt reviewed canonical sequence.

>O75161|NPHP4
     1  MNDWHRIFTQ NVLVPPHPQR ARQPWKESTA FQCVLKWLDG PVIRQGVLEV LSEVECHLRV
    61  SFFDVTYRHF FGRTWKTTVK PTKRPPSRIV FNEPLYFHTS LNHPHIVAVV EVVAEGKKRD
   121  GSLQTLSCGF GILRIFSNQP DSPISASQDK RLRLYHGTPR ALLHPLLQDP AEQNRHMTLI
   181  ENCSLQYTLK PHPALEPAFH LLPENLLVSG LQQIPGLLPA HGESGDALRK PRLQKPITGH
   241  LDDLFFTLYP SLEKFEEELL ELHVQDHFQE GCGPLDGGAL EILERRLRVG VHNGLGFVQR
   301  PQVVVLVPEM DVALTRSASF SRKVVSSSKT SSGSQALVLR SRLRLPEMVG HPAFAVIFQL
   361  EYVFSSPAGV DGNAASVTSL SNLACMHMVR WAVWNPLLEA DSGRVTLPLQ GGIQPNPSHC
   421  LVYKVPSASM SSEEVKQVES GTLRFQFSLG SEEHLDAPTE PVSGPKVERR PSRKPPTSPS
   481  SPPAPVPRVL AAPQNSPVGP GLSISQLAAS PRSPTQHCLA RPTSQLPHGS QASPAQAQEF
   541  PLEAGISHLE ADLSQTSLVL ETSIAEQLQE LPFTPLHAPI VVGTQTRSSA GQPSRASMVL
   601  LQSSGFPEIL DANKQPAEAV SATEPVTFNP QKEESDCLQS NEMVLQFLAF SRVAQDCRGT
   661  SWPKTVYFTF QFYRFPPATT PRLQLVQLDE AGQPSSGALT HILVPVSRDG TFDAGSPGFQ
   721  LRYMVGPGFL KPGERRCFAR YLAVQTLQID VWDGDSLLLI GSAAVQMKHL LRQGRPAVQA
   781  SHELEVVATE YEQDNMVVSG DMLGFGRVKP IGVHSVVKGR LHLTLANVGH PCEQKVRGCS
   841  TLPPSRSRVI SNDGASRFSG GSLLTTGSSR RKHVVQAQKL ADVDSELAAM LLTHARQGKG
   901  PQDVSRESDA TRRRKLERMR SVRLQEAGGD LGRRGTSVLA QQSVRTQHLR DLQVIAAYRE
   961  RTKAESIASL LSLAITTEHT LHATLGVAEF FEFVLKNPHN TQHTVTVEID NPELSVIVDS
  1021  QEWRDFKGAA GLHTPVEEDM FHLRGSLAPQ LYLRPHETAH VPFKFQSFSA GQLAMVQASP
  1081  GLSNEKGMDA VSPWKSSAVP TKHAKVLFRA SGGKPIAVLC LTVELQPHVV DQVFRFYHPE
  1141  LSFLKKAIRL PPWHTFPGAP VGMLGEDPPV HVRCSDPNVI CETQNVGPGE PRDIFLKVAS
  1201  GPSPEIKDFF VIIYSDRWLA TPTQTWQVYL HSLQRVDVSC VAGQLTRLSL VLRGTQTVRK
  1261  VRAFTSHPQE LKTDPKGVFV LPPRGVQDLH VGVRPLRAGS RFVHLNLVDV DCHQLVASWL
  1321  VCLCCRQPLI SKAFEIMLAA GEGKGVNKRI TYTNPYPSRR TFHLHSDHPE LLRFREDSFQ
  1381  VGGGETYTIG LQFAPSQRVG EEEILIYIND HEDKNEEAFC VKVIYQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against NPHP4 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)
0.36
Highest tissue expression
7.6 nTPM

Expression across tissuesHPA

Tissue

  • pituitary gland: 7.6 nTPM
  • fallopian tube: 7.4 nTPM
  • thyroid gland: 6.6 nTPM
  • testis: 5.2 nTPM
  • skin: 4.7 nTPM
  • bone marrow: 3.5 nTPM

Single-cell type

  • gonadotrophs: 100 nCPM
  • lactotrophs: 91 nCPM
  • ependymal cells: 85 nCPM
  • corticotrophs: 84 nCPM
  • somatotrophs: 79 nCPM
  • choroid plexus epithelial cells: 74 nCPM

Immune cell

  • basophil: 0.7 nTPM
  • neutrophil: 0.2 nTPM
  • classical monocyte: 0.1 nTPM
  • MAIT T-cell: 0.1 nTPM
  • NK-cell: 0.1 nTPM
  • non-classical monocyte: 0.1 nTPM

Brain region

  • hippocampal formation: 19 nTPM
  • cerebral cortex: 18 nTPM
  • choroid plexus: 18 nTPM
  • amygdala: 14 nTPM
  • basal ganglia: 14 nTPM
  • white matter: 12 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about NPHP4.

Disease | AllUniProt

Conditions NPHP4 is implicated in, by any mechanism.

Disease | GeneticClinVar

159 pathogenic / likely-pathogenic of 1,955 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)
0.98
gnomAD pLI
0
gnomAD missense Z
-0.24
DepMap mean gene effect
-0.13
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

  • NPH4
  • NPHP4, Ig-like domain 4
  • NPHP4, Ig-like domain 3
  • NPHP4, Ig-like domain 1
  • NPHP4, Ig-like domain 2
  • NPHP4, SK-like domain
  • NPHP4, C2-like domain
  • NPH4 Ig-like domain 3
  • Nephrocystin-4 SK-like domain
  • Nephrocystin-4 C2 third domain
  • NPH4 Ig-like domain 4
  • NPH4 Ig-like domain 2
  • NPH4 Ig-like domain 1

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of NPHP4 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 NPHP4 as an antibody target. Whether an autoantibody or antibody against NPHP4 could matter depends on whether native NPHP4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

NPHP4 is annotated at the cell surface, where native NPHP4 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 NPHP4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/NPHP4. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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