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Gene

NPHS1

NPHS1 adhesion molecule, nephrin

Summary

Cytogenetic location
19q13.12
Coordinates
Chromosome 19: 35,825,372–35,852,504 (GRCh38)
Exons
29 exons across 27.1 kb
Protein
1,241 amino acids
Also known as
CNF, NPHN
MANE Select transcript
ENST00000378910.10NM_004646.4
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

  • Nephrotic Syndrome

    • Nephrosis

      Pathological processes of the KIDNEY without inflammatory or neoplastic components. Nephrosis may be a primary disorder or secondary complication of other diseases. It is characterized by the NEPHROTIC SYNDROME indicating the presence of PROTEINURIA and HYPOALBUMINEMIA with accompanying EDEMA.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong

How NPHS1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where NPHS1 sits. NPHS1 and 49 genes near it on chromosome 19, from 35,338,938 to 36,338,937.Chromosome 1919q13.12p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4335.4 Mb35.6 Mb35.8 Mb36 Mb36.2 MbCD22: 35,319,261–35,347,361, forward strandCD22FFAR1: 35,347,902–35,353,864, forward strandFFAR1FFAR3: 35,358,348–35,360,489, forward strandFFAR3GPR42: 35,371,068–35,372,962, forward strandGPR42FFAR2: 35,443,907–35,451,767, forward strandFFAR2KRTDAP: 35,487,324–35,495,558, reverse strandDMKN: 35,497,220–35,513,704, reverse strandDMKNSBSN: 35,523,367–35,528,351, reverse strandSBSNGAPDHS: 35,533,455–35,545,319, forward strandGAPDHSTMEM147: 35,545,600–35,547,527, forward strandTMEM147ATP4A: 35,549,339–35,563,658, reverse strandATP4APMIS2: 35,586,161–35,587,296, forward strandPMIS2HAUS5: 35,612,735–35,625,355, forward strandHAUS5RBM42: 35,628,989–35,638,927, forward strandRBM42ETV2: 35,641,730–35,644,871, forward strandETV2COX6B1: 35,648,230–35,662,890, forward strandCOX6B1UPK1A: 35,666,516–35,678,481, forward strandUPK1AZBTB32: 35,704,558–35,717,048, forward strandKMT2B: 35,717,973–35,738,880, forward strandIGFLR1: 35,738,798–35,742,459, reverse strand: 35,739,252–35,745,432, reverse strandU2AF1L4: 35,742,464–35,745,460, reverse strandPSENEN: 35,745,070–35,747,519, forward strand: 35,745,678–35,754,519, forward strandLIN37: 35,748,361–35,754,519, forward strandHSPB6: 35,754,566–35,758,079, reverse strandHSPB6PROSER3: 35,758,143–35,771,398, forward strandPROSER3ARHGAP33: 35,774,532–35,788,822, forward strandARHGAP33PRODH2: 35,799,975–35,813,299, reverse strandPRODH2NPHS1: 35,825,372–35,852,504, reverse strandNPHS1KIRREL2: 35,851,369–35,867,145, forward strandKIRREL2APLP1: 35,867,899–35,879,803, forward strandAPLP1NFKBID: 35,887,129–35,902,303, reverse strandNFKBIDHCST: 35,899,017–35,904,377, forward strandHCSTTYROBP: 35,904,398–35,908,318, reverse strandLRFN3: 35,935,358–35,946,624, forward strandLRFN3SDHAF1: 35,995,188–35,996,312, forward strandSDHAF1SYNE4: 36,000,545–36,008,831, reverse strandSYNE4ALKBH6: 36,009,113–36,014,297, reverse strandALKBH6CLIP3: 36,014,660–36,033,343, reverse strandCLIP3THAP8: 36,033,393–36,054,739, reverse strandWDR62: 36,054,649–36,105,112, forward strandWDR62OVOL3: 36,111,116–36,113,711, forward strandOVOL3POLR2I: 36,111,817–36,115,213, reverse strandPOLR2ITBCB: 36,114,289–36,125,948, forward strandTBCBCAPNS1: 36,139,953–36,150,356, forward strandCAPNS1COX7A1: 36,150,287–36,152,699, reverse strandZNF565: 36,181,542–36,246,257, reverse strandZNF565ZNF146: 36,214,602–36,239,969, forward strandZNF146ZFP14: 36,334,453–36,379,208, reverse strandZFP14Diagram of NPHS1: 29 exons on the reverse strand of chromosome 19Exon 29: 4 known disease-causing sitesExon 28: 5 known disease-causing sitesExon 27: 3 known disease-causing sitesExon 26: 8 known disease-causing sitesExon 24: 6 known disease-causing sitesExon 23: 2 known disease-causing sitesExon 22: 9 known disease-causing sitesExon 21: 8 known disease-causing sitesExon 20: 9 known disease-causing sitesExon 19: 19 known disease-causing sitesExon 18: 20 known disease-causing sitesExon 17: 5 known disease-causing sitesExon 16: 19 known disease-causing sitesExon 15: 10 known disease-causing sitesExon 14: 12 known disease-causing sitesExon 13: 6 known disease-causing sitesExon 12: 12 known disease-causing sitesExon 11: 9 known disease-causing sitesExon 10: 10 known disease-causing sitesExon 9: 10 known disease-causing sitesExon 8: 14 known disease-causing sitesExon 7: 13 known disease-causing sitesExon 6: 9 known disease-causing sitesExon 5: 11 known disease-causing sitesExon 4: 13 known disease-causing sitesExon 3: 8 known disease-causing sitesExon 2: 22 known disease-causing sitesExon 1: 6 known disease-causing sitesExon 29: 35,825,372–35,826,645, 1,274 basesExon 28: 35,830,844–35,830,956, 113 basesExon 27: 35,831,053–35,831,146, 94 basesExon 26: 35,831,296–35,831,371, 76 basesExon 25: 35,831,476–35,831,500, 25 basesExon 24: 35,831,643–35,831,762, 120 basesExon 23: 35,835,705–35,835,761, 57 basesExon 22: 35,839,237–35,839,418, 182 basesExon 21: 35,839,496–35,839,607, 112 basesExon 20: 35,841,715–35,841,866, 152 basesExon 19: 35,842,124–35,842,280, 157 basesExon 18: 35,842,379–35,842,550, 172 basesExon 17: 35,843,472–35,843,593, 122 basesExon 16: 35,844,103–35,844,243, 141 basesExon 15: 35,844,319–35,844,459, 141 basesExon 14: 35,845,368–35,845,540, 173 basesExon 13: 35,845,669–35,845,798, 130 basesExon 12: 35,846,008–35,846,194, 187 basesExon 11: 35,848,041–35,848,165, 125 basesExon 10: 35,848,253–35,848,397, 145 basesExon 9: 35,848,637–35,848,794, 158 basesExon 8: 35,848,976–35,849,147, 172 basesExon 7: 35,849,236–35,849,363, 128 basesExon 6: 35,849,550–35,849,653, 104 basesExon 5: 35,850,364–35,850,445, 82 basesExon 4: 35,850,961–35,851,089, 129 basesExon 3: 35,851,262–35,851,384, 123 basesExon 2: 35,851,457–35,851,672, 216 basesExon 1: 35,851,780–35,852,504, 725 bases2925201510515′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 5.5 kb of the gene's 27.1 kb; 3,726 of those bases code for the protein.

How a genome test reads NPHS1

340

positions in NPHS1 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 27.1 kb of NPHS1, introns included, not only the 5.5 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.). NPHS1 gene: NPHS1 adhesion molecule, nephrin. Retrieved 17 October 2026, from https://dantelabs.com/genes/nphs1

Vancouver

Dante Labs. NPHS1 gene: NPHS1 adhesion molecule, nephrin [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nphs1

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