Chromosome 22q13.3 deletion syndrome with a de novo interstitial 22q13.3 cryptic deletion disrupting SHANK3

Eur J Med Genet. Sep-Oct 2009;52(5):328-32. doi: 10.1016/j.ejmg.2009.05.004. Epub 2009 May 18.


Background: The 22q13.3 deletion syndrome (or Phelan-McDermid syndrome, MIM 606232) is characterized by developmental delay, absent or severely delayed speech, neonatal hypotonia, autistic behavior, normal to accelerated growth, and minor dysmorphic facial features. Among the three genes in the minimal critical region (from the centromere to the telomere: SHANK3, ACR and RABL2B), the defect in the SHANK3 gene is considered to be the cause of the neurobehavioral symptoms.

Objective: We describe the molecular characterization of a de novo interstitial del(22)(q13.3q13.3) disrupting the SHANK3 gene in a child with a phenotype compatible with the 22q13.3 deletion syndrome.

Methods: Clinical work-up included clinical histories, physical, neurological, and ophthalmological examinations, and imaging of the brain. Commercially available MLPA for subtelomeric analysis, FISH specific probes and quantitative real-time PCR were used to characterize the rearrangement.

Results: Subtelomere analysis by MLPA showed a discrepancy between P036B and P070 kits (MCR Holland): the P070 MLPA 22q probe (targeting the ARSA gene) showed a deletion but the P036B one (targeting the RABL2B gene) showed a normal result. FISH analysis using LSI TUPLE1/LSI ARSA (Vysis) probes confirmed deletion of ARSA, whereas FISH with N25/N85A3 (Cytocell) probes, targeting the SHANK3 locus was normal. Supplemented FISH analysis using BAC clones allowed us to specify the centromeric breakpoint region of the interstitial deletion between clones RP11-354I12 and RP11-232E17, at less than 2 Mb from the telomere. Quantitative real-time PCR of exon 5, 22 and 24 and intron 9 of SHANK3 showed that the telomeric breakpoint occurred between intron 9 and exon 22.

Conclusions: These data highlight the difficulty of performing an appropriate test aimed at looking for cryptic 22q13.3 deletion. Furthermore, the molecular characterization of this interstitial 22q13.3 deletion contributes to the clinical and genetic delineation of the 22q13.3 deletion syndrome.

Publication types

  • Case Reports

MeSH terms

  • Carrier Proteins / genetics*
  • Child
  • Chromosome Banding
  • Chromosome Deletion*
  • Chromosomes, Human, Pair 22*
  • DNA / genetics
  • DNA / isolation & purification
  • Female
  • Fluorescein-5-isothiocyanate / metabolism
  • Fluorescent Dyes / metabolism
  • France
  • Humans
  • In Situ Hybridization, Fluorescence
  • Indoles / metabolism
  • Nerve Tissue Proteins
  • Nucleic Acid Amplification Techniques
  • Polymerase Chain Reaction
  • Syndrome
  • Xanthenes / metabolism


  • Carrier Proteins
  • Fluorescent Dyes
  • Indoles
  • Nerve Tissue Proteins
  • SHANK3 protein, human
  • Xanthenes
  • DAPI
  • Texas red
  • DNA
  • Fluorescein-5-isothiocyanate