ATR-16 syndrome: mechanisms linking monosomy to phenotype

J Med Genet. 2020 Jun;57(6):414-421. doi: 10.1136/jmedgenet-2019-106528. Epub 2020 Jan 31.


Background: Deletions removing 100s-1000s kb of DNA, and variable numbers of poorly characterised genes, are often found in patients with a wide range of developmental abnormalities. In such cases, understanding the contribution of the deletion to an individual's clinical phenotype is challenging.

Methods: Here, as an example of this common phenomenon, we analysed 41 patients with simple deletions of ~177 to ~2000 kb affecting one allele of the well-characterised, gene dense, distal region of chromosome 16 (16p13.3), referred to as ATR-16 syndrome. We characterised deletion extents and screened for genetic background effects, telomere position effect and compensatory upregulation of hemizygous genes.

Results: We find the risk of developmental and neurological abnormalities arises from much smaller distal chromosome 16 deletions (~400 kb) than previously reported. Beyond this, the severity of ATR-16 syndrome increases with deletion size, but there is no evidence that critical regions determine the developmental abnormalities associated with this disorder. Surprisingly, we find no evidence of telomere position effect or compensatory upregulation of hemizygous genes; however, genetic background effects substantially modify phenotypic abnormalities.

Conclusions: Using ATR-16 as a general model of disorders caused by CNVs, we show the degree to which individuals with contiguous gene syndromes are affected is not simply related to the number of genes deleted but depends on their genetic background. We also show there is no critical region defining the degree of phenotypic abnormalities in ATR-16 syndrome and this has important implications for genetic counselling.

Keywords: ATR16; CNV; developmental delay; thalassemia.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ataxia Telangiectasia Mutated Proteins / genetics*
  • Chromosome Deletion
  • Chromosomes, Human, Pair 16 / genetics
  • DNA Copy Number Variations / genetics*
  • Female
  • Gene Deletion
  • Humans
  • Intellectual Disability / diagnosis
  • Intellectual Disability / genetics*
  • Intellectual Disability / pathology
  • Male
  • Monosomy / diagnosis
  • Monosomy / genetics*
  • Monosomy / pathology
  • Phenotype
  • alpha-Thalassemia / diagnosis
  • alpha-Thalassemia / genetics*
  • alpha-Thalassemia / pathology


  • ATR protein, human
  • Ataxia Telangiectasia Mutated Proteins

Supplementary concepts

  • Alpha-Thalassemia Mental Retardation Syndrome, Deletion-Type