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Guo, L. NPHP1 Gene. Encyclopedia. Available online: (accessed on 25 April 2024).
Guo L. NPHP1 Gene. Encyclopedia. Available at: Accessed April 25, 2024.
Guo, Lily. "NPHP1 Gene" Encyclopedia, (accessed April 25, 2024).
Guo, L. (2020, December 24). NPHP1 Gene. In Encyclopedia.
Guo, Lily. "NPHP1 Gene." Encyclopedia. Web. 24 December, 2020.
NPHP1 Gene

nephrocystin 1


1. Introduction

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.

2. Health Conditions Related to Genetic Changes

2.1. Nephronophthisis

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.

2.2. 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.

3. Other Names for This Gene

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


  1. Fliegauf M, Horvath J, von Schnakenburg C, Olbrich H, Müller D, Thumfart J,Schermer B, Pazour GJ, Neumann HP, Zentgraf H, Benzing T, Omran H. Nephrocystinspecifically localizes to the transition zone of renal and respiratory cilia and photoreceptor connecting cilia. J Am Soc Nephrol. 2006 Sep;17(9):2424-33.
  2. Hildebrandt F, Otto E, Rensing C, Nothwang HG, Vollmer M, Adolphs J, HanuschH, Brandis M. A novel gene encoding an SH3 domain protein is mutated innephronophthisis type 1. Nat Genet. 1997 Oct;17(2):149-53.
  3. Hildebrandt F, Zhou W. Nephronophthisis-associated ciliopathies. J Am SocNephrol. 2007 Jun;18(6):1855-71.
  4. Hurd TW, Hildebrandt F. Mechanisms of nephronophthisis and relatedciliopathies. Nephron Exp Nephrol. 2011;118(1):e9-14. doi: 10.1159/000320888.
  5. 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 locuscontribute 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.
  6. 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 juvenilenephronophthisis is present in a subset of individuals with Joubert syndrome. Am J Hum Genet. 2004 Jul;75(1):82-91.
  7. Ronquillo CC, Bernstein PS, Baehr W. Senior-Løken syndrome: a syndromic formof retinal dystrophy associated with nephronophthisis. Vision Res. 2012 Dec15;75:88-97. doi: 10.1016/j.visres.2012.07.003.
  8. Saunier S, Calado J, Benessy F, Silbermann F, Heilig R, Weissenbach J,Antignac C. Characterization of the NPHP1 locus: mutational mechanism involved indeletions in familial juvenile nephronophthisis. Am J Hum Genet. 2000Mar;66(3):778-89.
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Update Date: 24 Dec 2020