NPHP3 nephrocystin 3

Gene info


NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31

Previous symbol


External ID

HGNC: 7907
Entrez Gene: 27031
Ensembl: ENSG00000113971
UCSC: uc003epe.3
OMIM: 608002
UniProtKB: Q7Z494

Disease info

CHD Phenotype

  • Atrial septal defect
  • Patent ductus arteriosus
  • Aortic stenosis
  • Dysplastic mitral valve

Extra Cardiac Phenotype


Incomplete penetrance


Variable expressivity


Animal model

Mouse study

MGI: Homozygous knockout mouse has CHD


Variant info


Selected variant

The Clinvar variants presented in the below IGV track were selected based on the following criteria.

  1. Variant types are single nucleotide variant or Indel
  2. Clinical significance for the variant was assessed to be Pathogenic or Likely Pathogenic
  3. ClinVar review status for the variant is criteria provided

Download annotation file for NPHP3: BED file

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Selected References

  1. Bergmann, C., Fliegauf, M., Brüchle, N. O., Frank, V., Olbrich, H., Kirschner, J., Schermer, B., Schmedding, I., Kispert, A., Kränzlin, B., Nürnberg, G., Becker, C., Grimm, T., Girschick, G., Lynch, S. A., Kelehan, P., Senderek, J., Neuhaus, T. J., Stallmach, T., … Omran, H. (2008). Loss of Nephrocystin-3 Function Can Cause Embryonic Lethality, Meckel-Gruber-like Syndrome, Situs Inversus, and Renal-Hepatic-Pancreatic Dysplasia. The American Journal of Human Genetics, 82(4), 959–970. DOI:10.1016/j.ajhg.2008.02.017 PMID:18371931
  2. Simpson, M. A., Cross, H. E., Cross, L., Helmuth, M., & Crosby, A. H. (2009). Lethal Cystic Kidney Disease in Amish Neonates Associated With Homozygous Nonsense Mutation of NPHP3. American Journal of Kidney Diseases, 53(5), 790–795. DOI:10.1053/j.ajkd.2008.12.026 PMID:19303681
  3. Tory, K., Rousset-Rouvière, C., Gubler, M.-C., Morinière, V., Pawtowski, A., Becker, C., Guyot, C., Gié, S., Frishberg, Y., Nivet, H., Deschênes, G., Cochat, P., Gagnadoux, M.-F., Saunier, S., Antignac, C., & Salomon, R. (2009). Mutations of NPHP2 and NPHP3 in infantile nephronophthisis. Kidney International, 75(8), 839–847. DOI:10.1038/ki.2008.662 PMID:19177160