Seroatlas · Human Serome Atlas

NPHP3

Nephrocystin-3

Also known as: CFAP31, FLJ30691, FLJ36696, KIAA2000, MKS7, NPH3, NPHP3_HUMAN, SLSN3

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

Protein identityUniProt · HPA

UniProt accession: Q7Z494
Gene: NPHP3
Ensembl: ENSG00000113971
Chromosome: 3
Canonical length: 1330 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Nucleoli,Vesicles,Primary cilium,Cytosol

OverviewNCBI Gene

This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]

Canonical amino-acid sequenceUniProt

1330 residues, UniProt reviewed canonical sequence.

>Q7Z494|NPHP3
     1  MGTASSLVSP AGGEVIEDTY GAGGGEACEI PVEVKPKARL LRNSFRRGAG AAAGAGPGSL
    61  PRGVGAGGLL GASFKSTGSS VPELEYAAAE YERLRKEYEI FRVSKNQELL SMGRREAKLD
   121  TENKRLRAEL QALQKTYQKI LREKESALEA KYQAMERAAT FEHDRDKVKR QFKIFRETKE
   181  NEIQDLLRAK RELESKLQRL QAQGIQVFDP GESDSDDNCT DVTAAGTQCE YWTGGALGSE
   241  PSIGSMIQLQ QSFRGPEFAH SSIDVEGPFA NVNRDDWDIA VASLLQVTPL FSHSLWSNTV
   301  RCYLIYTDET QPEMDLFLKD YSPKLKRMCE TMGYFFHAVY FPIDVENQYL TVRKWEIEKS
   361  SLVILFIHLT LPSLLLEDCE EAFLKNPEGK PRLIFHRLED GKVSSDSVQQ LIDQVSNLNK
   421  TSKAKIIDHS GDPAEGVYKT YICVEKIIKQ DILGFENTDL ETKDLGSEDS IPEEDDFGDV
   481  LWDIHDEQEQ METFQQASNS AHELGFEKYY QRLNDLVAAP APIPPLLVSG GPGSGKSLLL
   541  SKWIQLQQKN SPNTLILSHF VGRPMSTSSE SSLIIKRLTL KLMQHSWSVS ALTLDPAKLL
   601  EEFPRWLEKL SARHQGSIII VIDSIDQVQQ VEKHMKWLID PLPVNVRVIV SVNVETCPPA
   661  WRLWPTLHLD PLSPKDAKSI IIAECHSVDI KLSKEQEKKL ERHCRSATTC NALYVTLFGK
   721  MIARAGRAGN LDKILHQCFQ CQDTLSLYRL VLHSIRESMA NDVDKELMKQ ILCLVNVSHN
   781  GVSESELMEL YPEMSWTFLT SLIHSLYKMC LLTYGCGLLR FQHLQAWETV RLEYLEGPTV
   841  TSSYRQKLIN YFTLQLSQDR VTWRSADELP WLFQQQGSKQ KLHDCLLNLF VSQNLYKRGH
   901  FAELLSYWQF VGKDKSAMAT EYFDSLKQYE KNCEGEDNMS CLADLYETLG RFLKDLGLLS
   961  QAIVPLQRSL EIRETALDPD HPRVAQSLHQ LASVYVQWKK FGNAEQLYKQ ALEISENAYG
  1021  ADHPYTAREL EALATLYQKQ NKYEQAEHFR KKSFKIHQKA IKKKGNLYGF ALLRRRALQL
  1081  EELTLGKDTP DNARTLNELG VLYYLQNNLE TADQFLKRSL EMRERVLGPD HPDCAQSLNN
  1141  LAALCNEKKQ YDKAEELYER ALDIRRRALA PDHPSLAYTV KHLAILYKKM GKLDKAVPLY
  1201  ELAVEIRQKS FGPKHPSVAT ALVNLAVLYS QMKKHVEALP LYERALKIYE DSLGRMHPRV
  1261  GETLKNLAVL SYEGGDFEKA AELYKRAMEI KEAETSLLGG KAPSRHSSSG DTFSLKTAHS
  1321  PNVFLQQGQR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against NPHP3 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): 0.33
Highest tissue expression: 20 nTPM

Expression across tissuesHPA

Tissue

ovary: 20 nTPM
cervix: 16 nTPM
fallopian tube: 13 nTPM
blood vessel: 13 nTPM
endometrium: 13 nTPM
thyroid gland: 11 nTPM

Single-cell type

oligodendrocytes: 140 nCPM
astrocytes: 101 nCPM
bergmann glia: 98 nCPM
choroid plexus epithelial cells: 84 nCPM
oligodendrocyte progenitor cells: 79 nCPM
ependymal cells: 73 nCPM

Immune cell

neutrophil: 1.3 nTPM
basophil: 0.7 nTPM
non-classical monocyte: 0.6 nTPM
memory B-cell: 0.5 nTPM
naive B-cell: 0.5 nTPM
memory CD4 T-cell: 0.3 nTPM

Brain region

white matter: 19 nTPM
medulla oblongata: 15 nTPM
cerebral cortex: 14 nTPM
basal ganglia: 14 nTPM
thalamus: 14 nTPM
pons: 14 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about NPHP3.

Disease | AllUniProt

Conditions NPHP3 is implicated in, by any mechanism.

Nephronophthisis 3 (NPHP3) MIM:604387
Renal-hepatic-pancreatic dysplasia 1 (RHPD1) MIM:208540
Meckel syndrome 7 (MKS7) MIM:267010

Disease | GeneticClinVar

159 pathogenic / likely-pathogenic of 1,428 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Nephronophthisis
Nephronophthisis 3
NPHP3-related Meckel-like syndrome
Renal-hepatic-pancreatic dysplasia 1
NPHP3-related disorder

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): 0.65
gnomAD pLI: 0
gnomAD missense Z: 0.86
DepMap mean gene effect: -0.04
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Cellular components

Protein domainsUniProt · Pfam · InterPro

Tetratricopeptide-like helical domain superfamily
Tetratricopeptide repeat
P-loop containing nucleoside triphosphate hydrolase
Nephrocystin 3-like, N-terminal
Tetratricopeptide repeat
Tetratricopeptide repeat
Nephrocystin 3, N-terminal
Nephrocystin 3, helical domain
Nephrocystin-3, TPR-repeats region
Nephrocystin-3, alpha-beta domain
Nephrocystin 3, helical domain
Nephrocystin-3 TPR domain
Nephrocystin-3 domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of NPHP3 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 NPHP3 as an antibody target. Whether an autoantibody or antibody against NPHP3 could matter depends on whether native NPHP3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

NPHP3 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 NPHP3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...