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Gene

PKHD1

PKHD1 ciliary IPT domain containing fibrocystin/polyductin

Summary

Cytogenetic location
6p12.3-p12.2
Coordinates
Chromosome 6: 51,615,299–52,087,613 (GRCh38)
Exons
67 exons across 472.3 kb
Protein
4,074 amino acids
Also known as
ARPKD, FCYT, FPC
Previous symbols
TIGM1
MANE Select transcript
ENST00000371117.8NM_138694.4
Locus type
gene with protein product

Reference genomeGRCh38

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

Curated report relevant to this gene

  • Polycystic Kidney Disease

    • A usually autosomal dominant and less frequently autosomal recessive genetic disorder characterized by the presence of numerous cysts in the kidneys leading to end-stage renal failure. The autosomal dominant trait is associated with abnormalities on the short arm of chromosome 16. Symptoms in patients with the autosomal dominant trait usually appear at middle age and include abdominal pain, hematuria, and high blood pressure. Patients may develop brain aneurysms and liver cysts. Patients with the autosomal recessive trait present with progressive renal failure early in life and symptoms resulting from hepatic fibrosis. The autosomal recessive trait is associated with abnormalities of chromosome 6. Polycystic kidney disease may also result as a side effect in patients on renal dialysis.

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

      Tolvaptan (Jynarque, FDA 2018) for rapidly progressive ADPKD; blood pressure control (target <110/75); pain management; cyst infection treatment; brain MRA screening for intracranial aneurysms; kidney transplantation for ESRD

How PKHD1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where PKHD1 sits. PKHD1 and 6 genes near it on chromosome 6, from 51,142,984 to 52,559,928.Chromosome 66p12.3-p12.2p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2751.2 Mb51.4 Mb51.6 Mb51.8 Mb52 Mb52.2 Mb52.4 MbPKHD1: 51,615,299–52,087,613, reverse strandPKHD1IL17A: 52,186,375–52,190,638, forward strandIL17AIL17F: 52,236,681–52,245,689, reverse strandIL17FMCM3: 52,264,009–52,284,881, reverse strandMCM3PAQR8: 52,361,421–52,407,777, forward strandPAQR8EFHC1: 52,362,123–52,529,886, forward strandEFHC1TRAM2: 52,497,408–52,577,316, reverse strandTRAM2Diagram of PKHD1: 67 exons on the reverse strand of chromosome 6Exon 67: 15 known disease-causing sitesExon 66: 15 known disease-causing sitesExon 65: 7 known disease-causing sitesExon 64: 11 known disease-causing sitesExon 63: 8 known disease-causing sitesExon 62: 14 known disease-causing sitesExon 61: 85 known disease-causing sitesExon 60: 14 known disease-causing sitesExon 59: 20 known disease-causing sitesExon 58: 101 known disease-causing sitesExon 57: 21 known disease-causing sitesExon 56: 16 known disease-causing sitesExon 55: 8 known disease-causing sitesExon 54: 15 known disease-causing sitesExon 53: 13 known disease-causing sitesExon 52: 15 known disease-causing sitesExon 51: 9 known disease-causing sitesExon 50: 24 known disease-causing sitesExon 49: 15 known disease-causing sitesExon 48: 25 known disease-causing sitesExon 47: 11 known disease-causing sitesExon 46: 16 known disease-causing sitesExon 45: 11 known disease-causing sitesExon 44: 12 known disease-causing sitesExon 43: 14 known disease-causing sitesExon 42: 4 known disease-causing sitesExon 41: 11 known disease-causing sitesExon 40: 17 known disease-causing sitesExon 39: 17 known disease-causing sitesExon 38: 18 known disease-causing sitesExon 37: 29 known disease-causing sitesExon 36: 22 known disease-causing sitesExon 35: 20 known disease-causing sitesExon 34: 23 known disease-causing sitesExon 33: 20 known disease-causing sitesExon 32: 173 known disease-causing sitesExon 31: 8 known disease-causing sitesExon 30: 26 known disease-causing sitesExon 29: 8 known disease-causing sitesExon 28: 12 known disease-causing sitesExon 27: 34 known disease-causing sitesExon 26: 12 known disease-causing sitesExon 25: 14 known disease-causing sitesExon 24: 17 known disease-causing sitesExon 23: 13 known disease-causing sitesExon 22: 19 known disease-causing sitesExon 21: 21 known disease-causing sitesExon 20: 16 known disease-causing sitesExon 19: 14 known disease-causing sitesExon 18: 12 known disease-causing sitesExon 17: 8 known disease-causing sitesExon 16: 29 known disease-causing sitesExon 15: 15 known disease-causing sitesExon 14: 13 known disease-causing sitesExon 13: 10 known disease-causing sitesExon 12: 15 known disease-causing sitesExon 11: 8 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 9: 13 known disease-causing sitesExon 8: 8 known disease-causing sitesExon 7: 14 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 5: 12 known disease-causing sitesExon 4: 9 known disease-causing sitesExon 3: 7 known disease-causing sitesExon 2: 9 known disease-causing sitesExon 67: 51,615,299–51,619,520, 4,222 basesExon 66: 51,626,997–51,627,116, 120 basesExon 65: 51,632,565–51,632,723, 159 basesExon 64: 51,638,849–51,638,956, 108 basesExon 63: 51,648,031–51,648,118, 88 basesExon 62: 51,649,085–51,649,220, 136 basesExon 61: 51,658,952–51,659,969, 1,018 basesExon 60: 51,744,385–51,744,542, 158 basesExon 59: 51,746,721–51,746,889, 169 basesExon 58: 51,747,787–51,748,665, 879 basesExon 57: 51,753,201–51,753,353, 153 basesExon 56: 51,754,784–51,754,938, 155 basesExon 55: 51,772,702–51,772,789, 88 basesExon 54: 51,775,808–51,775,921, 114 basesExon 53: 51,791,236–51,791,373, 138 basesExon 52: 51,830,861–51,830,989, 129 basesExon 51: 51,836,404–51,836,469, 66 basesExon 50: 51,847,775–51,847,970, 196 basesExon 49: 51,855,893–51,856,070, 178 basesExon 48: 51,867,863–51,868,109, 247 basesExon 47: 51,870,504–51,870,639, 136 basesExon 46: 51,883,093–51,883,227, 135 basesExon 45: 51,885,867–51,885,972, 106 basesExon 44: 51,887,133–51,887,245, 113 basesExon 43: 51,903,597–51,903,727, 131 basesExon 42: 51,903,986–51,904,042, 57 basesExon 41: 51,906,215–51,906,340, 126 basesExon 40: 51,909,283–51,909,474, 192 basesExon 39: 51,911,799–51,911,956, 158 basesExon 38: 51,912,366–51,912,576, 211 basesExon 37: 51,934,110–51,934,322, 213 basesExon 36: 51,959,870–51,960,026, 157 basesExon 35: 52,010,309–52,010,459, 151 basesExon 34: 52,017,410–52,017,629, 220 basesExon 33: 52,022,801–52,022,944, 144 basesExon 32: 52,024,574–52,026,181, 1,608 basesExon 31: 52,027,829–52,027,896, 68 basesExon 30: 52,028,156–52,028,351, 196 basesExon 29: 52,033,030–52,033,165, 136 basesExon 28: 52,035,591–52,035,721, 131 basesExon 27: 52,042,859–52,043,134, 276 basesExon 26: 52,043,625–52,043,730, 106 basesExon 25: 52,044,966–52,045,088, 123 basesExon 24: 52,046,004–52,046,188, 185 basesExon 23: 52,048,492–52,048,619, 128 basesExon 22: 52,050,157–52,050,295, 139 basesExon 21: 52,053,076–52,053,251, 176 basesExon 20: 52,054,038–52,054,165, 128 basesExon 19: 52,055,587–52,055,729, 143 basesExon 18: 52,056,698–52,056,788, 91 basesExon 17: 52,056,890–52,056,979, 90 basesExon 16: 52,058,323–52,058,601, 279 basesExon 15: 52,059,928–52,060,042, 115 basesExon 14: 52,062,519–52,062,660, 142 basesExon 13: 52,064,955–52,065,050, 96 basesExon 12: 52,065,976–52,066,077, 102 basesExon 11: 52,069,457–52,069,527, 71 basesExon 10: 52,070,406–52,070,445, 40 basesExon 9: 52,071,006–52,071,070, 65 basesExon 8: 52,072,115–52,072,189, 75 basesExon 7: 52,073,463–52,073,541, 79 basesExon 6: 52,076,276–52,076,333, 58 basesExon 5: 52,079,900–52,080,008, 109 basesExon 4: 52,082,392–52,082,542, 151 basesExon 3: 52,083,178–52,083,255, 78 basesExon 2: 52,084,882–52,085,017, 136 basesExon 1: 52,087,434–52,087,613, 180 bases6760504030201015′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 16.3 kb of the gene's 472.3 kb; 12,225 of those bases code for the protein.

How a genome test reads PKHD1

1,481

positions in PKHD1 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 472.3 kb of PKHD1, introns included, not only the 16.3 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.). PKHD1 gene: PKHD1 ciliary IPT domain containing fibrocystin/polyductin. Retrieved 17 October 2026, from https://dantelabs.com/genes/pkhd1

Vancouver

Dante Labs. PKHD1 gene: PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pkhd1

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