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Gene

NPHP1

nephrocystin 1

Summary

Cytogenetic location
2q13
Coordinates
Chromosome 2: 110,123,348–110,205,013 (GRCh38)
Exons
20 exons across 81.7 kb
Protein
677 amino acids
Inheritance
Autosomal recessive
Also known as
JBTS4, SLSN1
Previous symbols
NPH1
MANE Select transcript
ENST00000445609.7NM_001128178.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Joubert Syndrome And Related Disorders

    • Joubert Syndrome

      A ciliopathy defined by a malformation of the cerebellum and brainstem (the molar tooth sign), with low muscle tone, developmental delay and abnormal eye movements, sometimes with kidney, liver or eye involvement.

      • 1 GenCC submitter rates it definitive or strong

  • Nephronophthisis and Senior-Løken Syndrome

    • NephronophthisisAutosomal recessive

      A recessively inherited kidney disease, caused by variants in NPHP1 and other cilia genes, in which progressive tubulointerstitial scarring leads to kidney failure, typically in the first three decades of life.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows regular kidney function monitoring, timely planning for dialysis or transplantation, and carrier testing for relatives.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How NPHP1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where NPHP1 sits. NPHP1 and 9 genes near it on chromosome 2, from 109,664,181 to 110,664,180.Chromosome 22q13p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3109.8 Mb110 Mb110.2 Mb110.4 Mb110.6 MbRGPD5: 109,792,758–109,857,705, forward strandRGPD5LIMS3: 109,898,428–109,925,625, forward strandLIMS3: 109,898,432–109,968,557, forward strandMALL: 110,083,870–110,116,075, reverse strandMALLNPHP1: 110,123,348–110,205,013, reverse strandNPHP1MTLN: 110,211,528–110,245,420, reverse strandMTLN: 110,402,934–110,473,075, reverse strandLIMS4: 110,445,883–110,473,075, reverse strandLIMS4RGPD6: 110,513,802–110,610,840, reverse strandRGPD6BUB1: 110,635,468–110,678,098, reverse strandBUB1Diagram of NPHP1: 20 exons on the reverse strand of chromosome 2Exon 20: 9 known disease-causing sitesExon 19: 4 known disease-causing sitesExon 17: 4 known disease-causing sitesExon 16: 3 known disease-causing sitesExon 15: 6 known disease-causing sitesExon 14: 5 known disease-causing sitesExon 13: 5 known disease-causing sitesExon 12: 4 known disease-causing sitesExon 11: 8 known disease-causing sitesExon 10: 6 known disease-causing sitesExon 9: 4 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 5: 8 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 2: 4 known disease-causing sitesExon 1: 7 known disease-causing sitesExon 20: 110,123,348–110,124,063, 716 basesExon 19: 110,125,637–110,125,681, 45 basesExon 18: 110,129,186–110,129,259, 74 basesExon 17: 110,131,679–110,131,791, 113 basesExon 16: 110,143,542–110,143,641, 100 basesExon 15: 110,144,493–110,144,569, 77 basesExon 14: 110,146,753–110,146,835, 83 basesExon 13: 110,147,916–110,148,026, 111 basesExon 12: 110,150,182–110,150,256, 75 basesExon 11: 110,160,127–110,160,255, 129 basesExon 10: 110,161,603–110,161,697, 95 basesExon 9: 110,163,048–110,163,135, 88 basesExon 8: 110,164,688–110,164,730, 43 basesExon 7: 110,165,052–110,165,155, 104 basesExon 6: 110,168,452–110,168,553, 102 basesExon 5: 110,169,806–110,169,998, 193 basesExon 4: 110,178,423–110,178,547, 125 basesExon 3: 110,179,624–110,179,684, 61 basesExon 2: 110,201,421–110,201,494, 74 basesExon 1: 110,204,900–110,205,013, 114 bases201816141210864215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.5 kb of the gene's 81.7 kb; 2,034 of those bases code for the protein.

How a genome test reads NPHP1

129

positions in NPHP1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 81.7 kb of NPHP1, introns included, not only the 2.5 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). NPHP1 gene: nephrocystin 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/nphp1

Vancouver

Dante Labs. NPHP1 gene: nephrocystin 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/nphp1

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