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Gene

NPHP3

nephrocystin 3

Summary

Cytogenetic location
3q22.1
Coordinates
Chromosome 3: 132,680,609–132,722,409 (GRCh38)
Exons
27 exons across 41.8 kb
Protein
1,330 amino acids
Inheritance
Autosomal recessive
Also known as
NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31
MANE Select transcript
ENST00000337331.10NM_153240.5
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 report relevant to this gene

  • Nephronophthisis and Senior-Løken Syndrome

    • Senior-Løken SyndromeAutosomal recessive

      A form of nephronophthisis combined with retinal degeneration that can cause early vision loss.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing prompts referral for an eye examination alongside kidney monitoring.

    • 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 NPHP3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where NPHP3 sits. NPHP3 and 8 genes near it on chromosome 3, from 132,201,509 to 133,201,508.Chromosome 33q22.1p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29132.4 Mb132.6 Mb132.8 Mb133 Mb133.2 MbCPNE4: 131,533,555–132,285,410, reverse strandCPNE4ACP3: 132,317,364–132,369,035, forward strandACP3DNAJC13: 132,417,488–132,539,032, forward strandDNAJC13ACAD11: 132,558,138–132,660,727, reverse strandACAD11NPHP3-ACAD11: 132,558,142–132,722,459, reverse strandNPHP3-ACAD11ACKR4: 132,597,250–132,618,967, forward strandACKR4UBA5: 132,654,446–132,679,794, forward strandUBA5NPHP3: 132,680,609–132,722,409, reverse strandNPHP3TMEM108: 133,038,276–133,397,775, forward strandTMEM108Diagram of NPHP3: 27 exons on the reverse strand of chromosome 3Exon 27: 3 known disease-causing sitesExon 26: 5 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 24: 8 known disease-causing sitesExon 23: 3 known disease-causing sitesExon 22: 3 known disease-causing sitesExon 21: 9 known disease-causing sitesExon 20: 8 known disease-causing sitesExon 19: 1 known disease-causing siteExon 18: 1 known disease-causing siteExon 17: 3 known disease-causing sitesExon 16: 5 known disease-causing sitesExon 15: 4 known disease-causing sitesExon 14: 1 known disease-causing siteExon 13: 7 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 11: 3 known disease-causing sitesExon 10: 1 known disease-causing siteExon 9: 2 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 7: 6 known disease-causing sitesExon 6: 6 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 2: 8 known disease-causing sitesExon 1: 11 known disease-causing sitesExon 27: 132,680,609–132,682,090, 1,482 basesExon 26: 132,682,703–132,682,818, 116 basesExon 25: 132,683,399–132,683,524, 126 basesExon 24: 132,684,554–132,684,794, 241 basesExon 23: 132,686,260–132,686,387, 128 basesExon 22: 132,687,151–132,687,226, 76 basesExon 21: 132,688,650–132,688,891, 242 basesExon 20: 132,689,074–132,689,263, 190 basesExon 19: 132,690,528–132,690,650, 123 basesExon 18: 132,691,192–132,691,286, 95 basesExon 17: 132,692,654–132,692,818, 165 basesExon 16: 132,694,827–132,694,965, 139 basesExon 15: 132,696,731–132,696,813, 83 basesExon 14: 132,697,260–132,697,362, 103 basesExon 13: 132,699,353–132,699,450, 98 basesExon 12: 132,699,918–132,700,061, 144 basesExon 11: 132,700,334–132,700,448, 115 basesExon 10: 132,701,430–132,701,533, 104 basesExon 9: 132,704,198–132,704,371, 174 basesExon 8: 132,705,740–132,705,814, 75 basesExon 7: 132,708,101–132,708,257, 157 basesExon 6: 132,713,126–132,713,286, 161 basesExon 5: 132,715,085–132,715,218, 134 basesExon 4: 132,716,757–132,716,909, 153 basesExon 3: 132,718,994–132,719,144, 151 basesExon 2: 132,719,705–132,719,830, 126 basesExon 1: 132,721,963–132,722,409, 447 bases27262422201816141210864215′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 5.3 kb of the gene's 41.8 kb; 3,993 of those bases code for the protein.

How a genome test reads NPHP3

139

positions in NPHP3 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 41.8 kb of NPHP3, introns included, not only the 5.3 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.). NPHP3 gene: nephrocystin 3. Retrieved 16 October 2026, from https://dantelabs.com/genes/nphp3

Vancouver

Dante Labs. NPHP3 gene: nephrocystin 3 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/nphp3

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