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Short report
Biallelic disruption of PKDCC is associated with a skeletal disorder characterised by rhizomelic shortening of extremities and dysmorphic features
  1. Samin A Sajan1,
  2. Jaya Ganesh2,
  3. Deepali N Shinde1,
  4. Zöe Powis1,
  5. Maria I Scarano2,
  6. Jennifer Stone2,
  7. Susan Winter3,
  8. Sha Tang1
  1. 1 Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
  2. 2 Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
  3. 3 Valley Children’s Hospital, Madera, California, USA
  1. Correspondence to Dr Samin A Sajan, Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA; asajan{at}ambrygen.com

Abstract

Background During mouse embryonic development the protein kinase domain containing, cytoplasmic (Pkdcc) gene, also known as Vlk, is expressed in several tissues including the ventral midbrain, with particularly strong expression in branchial arches and limb buds. Homozygous Pkdcc knockout mice have dysmorphic features and shortened long bones as the most obvious morphological abnormalities. The human PKDCC gene has currently not been associated with any disorders.

Objective To use clinical diagnostic exome sequencing (DES) for providing genetic diagnoses to two apparently unrelated patients with similar skeletal abnormalities comprising rhizomelic shortening of limbs and dysmorphic features.

Methods Patient–parents trio DES was carried out and the identified candidate variants were confirmed by Sanger sequencing.

Results Each patient had a homozygous gene disrupting variant in PKDCC considered to explain the skeletal phenotypes shared by both. The first patient was homozygous for the nonsense variant p.(Tyr217*) (NM_1 38 370 c.651C>A) expected to result in nonsense-mediated decay of the mutant transcripts, whereas the second patient was homozygous for the splice donor variant c.639+1G>T predicted to abolish the donor splice site by three in silico splice prediction algorithms.

Conclusions Biallelic gene disrupting variants in PKDCC in humans, just like in mice, cause dysmorphic features and rhizomelic shortening of limbs.

  • skeletal dysplasia
  • PKDCC
  • diagnostic exome
  • clinical exome

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Footnotes

  • SAS and JG contributed equally.

  • Contributors SAS analysed exome data, prepared and revised the manuscript. JG provided patient clinical data and helped to prepare and revise the manuscript. Both SAS and JG are considered to have contributed equally to the manuscript. DNS did background research and revised the manuscript. ZP and ST reviewed exome results and revised the manuscript. MIS, JS and SW provided patient clinical data and revised the manuscript.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests SAS, DNS, ZP and ST are employed by and receive a salary from Ambry Genetics, one of whose commercially available tests is exome sequencing.

  • Patient consent Not required.

  • Ethics approval All research described in this case report was conducted in accordance with the World Medical Association Declaration of Helsinki.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement The VCF files of exome data are available to researchers and clinicians upon request.

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