Skip navigation

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

URL of this page:

NPHP1 gene

nephrocystin 1

Normal Function

The NPHP1 gene provides instructions for making the nephrocystin-1 protein. This protein is thought to play a role in cell structures called cilia, which are microscopic, finger-like projections that stick out from the surface of cells. Cilia participate in signaling pathways that transmit information within and between cells and are important for the development and function of many types of cells and tissues. Nephrocystin-1 is found at the base of cilia in cells of the kidneys, respiratory tract, and the light-sensitive tissue at the back of the eye (the retina). Although the specific function of nephrocystin-1 is not well understood, it is thought to interact with a number of other proteins as part of a large protein complex that may be important for normal cilia function.

Health Conditions Related to Genetic Changes


At least 23 mutations in the NPHP1 gene have been found to cause a kidney disorder called nephronophthisis type 1. Type 1 is the most common type of nephronophthisis, accounting for approximately 20 percent of cases of the disorder. Nephronophthisis is characterized by inflammation and scarring of the kidneys and ultimately leads to a life-threatening failure of kidney function (end-stage renal disease or ESRD). In nephronophthisis type 1, ESRD usually occurs around age 13.

The most common genetic change in nephronophthisis type 1 is a large deletion on chromosome 2 that removes the whole NPHP1 gene. Other deletions that remove all or most of the gene or a small portion of the gene can also be involved in this condition. Some mutations change single protein building blocks (amino acids) or lead to an abnormally short nephrocystin-1 protein. It is thought that people with nephronophthisis type 1 have little or no functional nephrocystin-1. The lack of this protein probably impairs the function of cilia in some way, which likely disrupts important chemical signaling pathways during development. Although researchers believe that defective cilia are responsible for the features of nephronophthisis, the mechanism remains unclear.

More About This Health Condition

Joubert syndrome

MedlinePlus Genetics provides information about Joubert syndrome

More About This Health Condition

Senior-Løken syndrome

MedlinePlus Genetics provides information about Senior-Løken syndrome

More About This Health Condition

Other disorders

Mutations in the NPHP1 gene can cause syndromes that include nephronophthisis among their features; such conditions are known as nephronophthisis-associated ciliopathies. Senior-Løken syndrome is characterized by the combination of nephronophthisis and breakdown of the retina (retinal degeneration). Joubert syndrome is a multisystem disorder that typically involves neurological problems and can include nephronophthisis, eye abnormalities, liver disease, and other abnormalities. As in nephronophthisis type1 (described above), NPHP1 gene mutations probably impair cilia function. Defective cilia likely cause the features of these nephronophthisis-associated ciliopathies, although it remains unclear how these defects lead to the specific abnormalities of each condition. It is unknown why some individuals with NPHP1 gene mutations develop the additional signs and symptoms of Senior-Løken syndrome or Joubert syndrome.

Other Names for This Gene

  • JBTS4
  • juvenile nephronophthisis 1 protein
  • nephrocystin-1
  • nephronophthisis 1 (juvenile)
  • NPH1
  • SLSN1

Additional Information & Resources

Tests Listed in the Genetic Testing Registry

Scientific Articles on PubMed

Catalog of Genes and Diseases from OMIM

Gene and Variant Databases


  • Fliegauf M, Horvath J, von Schnakenburg C, Olbrich H, Muller D, Thumfart J, Schermer B, Pazour GJ, Neumann HP, Zentgraf H, Benzing T, Omran H. Nephrocystin specifically localizes to the transition zone of renal and respiratory cilia and photoreceptor connecting cilia. J Am Soc Nephrol. 2006 Sep;17(9):2424-33. doi: 10.1681/ASN.2005121351. Epub 2006 Aug 2. Citation on PubMed
  • Hildebrandt F, Otto E, Rensing C, Nothwang HG, Vollmer M, Adolphs J, Hanusch H, Brandis M. A novel gene encoding an SH3 domain protein is mutated in nephronophthisis type 1. Nat Genet. 1997 Oct;17(2):149-53. doi: 10.1038/ng1097-149. Citation on PubMed
  • Hildebrandt F, Zhou W. Nephronophthisis-associated ciliopathies. J Am Soc Nephrol. 2007 Jun;18(6):1855-71. doi: 10.1681/ASN.2006121344. Epub 2007 May 18. Citation on PubMed
  • Hurd TW, Hildebrandt F. Mechanisms of nephronophthisis and related ciliopathies. Nephron Exp Nephrol. 2011;118(1):e9-14. doi: 10.1159/000320888. Epub 2010 Nov 11. Citation on PubMed or Free article on PubMed Central
  • Lindstrand A, Davis EE, Carvalho CM, Pehlivan D, Willer JR, Tsai IC, Ramanathan S, Zuppan C, Sabo A, Muzny D, Gibbs R, Liu P, Lewis RA, Banin E, Lupski JR, Clark R, Katsanis N. Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. Am J Hum Genet. 2014 May 1;94(5):745-54. doi: 10.1016/j.ajhg.2014.03.017. Epub 2014 Apr 17. Citation on PubMed or Free article on PubMed Central
  • Parisi MA, Bennett CL, Eckert ML, Dobyns WB, Gleeson JG, Shaw DW, McDonald R, Eddy A, Chance PF, Glass IA. The NPHP1 gene deletion associated with juvenile nephronophthisis is present in a subset of individuals with Joubert syndrome. Am J Hum Genet. 2004 Jul;75(1):82-91. doi: 10.1086/421846. Epub 2004 May 11. Citation on PubMed or Free article on PubMed Central
  • Ronquillo CC, Bernstein PS, Baehr W. Senior-Loken syndrome: a syndromic form of retinal dystrophy associated with nephronophthisis. Vision Res. 2012 Dec 15;75:88-97. doi: 10.1016/j.visres.2012.07.003. Epub 2012 Jul 20. Citation on PubMed or Free article on PubMed Central
  • Saunier S, Calado J, Benessy F, Silbermann F, Heilig R, Weissenbach J, Antignac C. Characterization of the NPHP1 locus: mutational mechanism involved in deletions in familial juvenile nephronophthisis. Am J Hum Genet. 2000 Mar;66(3):778-89. doi: 10.1086/302819. Citation on PubMed or Free article on PubMed Central

The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.