De novo PHIP-predicted deleterious variants are associated with developmental delay, intellectual disability, obesity, and dysmorphic features

Cold Spring Harb Mol Case Stud. 2016 Nov;2(6):a001172. doi: 10.1101/mcs.a001172.


Using whole-exome sequencing, we have identified novel de novo heterozygous pleckstrin homology domain-interacting protein (PHIP) variants that are predicted to be deleterious, including a frameshift deletion, in two unrelated patients with common clinical features of developmental delay, intellectual disability, anxiety, hypotonia, poor balance, obesity, and dysmorphic features. A nonsense mutation in PHIP has previously been associated with similar clinical features. Patients with microdeletions of 6q14.1, including PHIP, have a similar phenotype of developmental delay, intellectual disability, hypotonia, and obesity, suggesting that the phenotype of our patients is a result of loss-of-function mutations. PHIP produces multiple protein products, such as PHIP1 (also known as DCAF14), PHIP, and NDRP. PHIP1 is one of the multiple substrate receptors of the proteolytic CUL4-DDB1 ubiquitin ligase complex. CUL4B deficiency has been associated with intellectual disability, central obesity, muscle wasting, and dysmorphic features. The overlapping phenotype associated with CUL4B deficiency suggests that PHIP mutations cause disease through disruption of the ubiquitin ligase pathway.

Keywords: abdominal obesity; central hypotonia; intellectual disability, mild; mild global developmental delay.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Child, Preschool
  • Developmental Disabilities / genetics
  • Exome
  • Female
  • Frameshift Mutation
  • Heterozygote
  • Humans
  • Intellectual Disability / genetics
  • Intracellular Signaling Peptides and Proteins / genetics*
  • Muscle Hypotonia / genetics
  • Mutation
  • Obesity / genetics
  • Phenotype
  • Pleckstrin Homology Domains
  • Whole Exome Sequencing / methods


  • Intracellular Signaling Peptides and Proteins
  • PHIP protein, human