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Gene

PDE6D

phosphodiesterase 6D

Summary

Cytogenetic location
2q37.1
Coordinates
Chromosome 2: 231,732,433–231,781,282 (GRCh38)
Exons
5 exons across 48.9 kb
Protein
150 amino acids
Also known as
JBTS22
MANE Select transcript
ENST00000287600.9NM_002601.4
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

  • 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.

      • 2 GenCC submitters rate it definitive or strong

How PDE6D 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 PDE6D sits. PDE6D and 9 genes near it on chromosome 2, from 231,256,858 to 232,256,857.Chromosome 22q37.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3231.4 Mb231.6 Mb231.8 Mb232 Mb232.2 MbARMC9: 231,198,546–231,376,848, forward strandARMC9B3GNT7: 231,395,558–231,408,799, forward strandB3GNT7NUCLEOLIN: 231,453,531–231,483,641, reverse strandNUCLEOLINNMUR1: 231,523,187–231,530,471, reverse strandNMUR1TEX44: 231,592,864–231,594,276, forward strandTEX44PTMA: 231,706,895–231,713,552, forward strandPTMAPDE6D: 231,732,433–231,781,282, reverse strandPDE6DCOPS7B: 231,781,660–231,809,254, forward strandCOPS7BNPPC: 231,921,809–231,926,403, reverse strandNPPCDIS3L2: 231,961,245–232,344,350, forward strandDIS3L2Diagram of PDE6D: 5 exons on the reverse strand of chromosome 2Exon 4: 1 known disease-causing siteExon 3: 2 known disease-causing sitesExon 2: 2 known disease-causing sitesExon 5: 231,732,433–231,733,033, 601 basesExon 4: 231,737,187–231,737,292, 106 basesExon 3: 231,738,013–231,738,138, 126 basesExon 2: 231,739,100–231,739,188, 89 basesExon 1: 231,781,065–231,781,282, 218 bases543215′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 1.1 kb of the gene's 48.9 kb; 453 of those bases code for the protein.

How a genome test reads PDE6D

5

positions in PDE6D 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 48.9 kb of PDE6D, introns included, not only the 1.1 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.). PDE6D gene: phosphodiesterase 6D. Retrieved 17 October 2026, from https://dantelabs.com/genes/pde6d

Vancouver

Dante Labs. PDE6D gene: phosphodiesterase 6D [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pde6d

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