Chromosomal Microarray Analysis Identifies a Novel SALL1 Deletion, Supporting the Association of Haploinsufficiency with a Mild Phenotype of Townes-Brocks Syndrome

Genes (Basel). 2023 Jan 19;14(2):258. doi: 10.3390/genes14020258.


SALL1 heterozygous pathogenic variants cause Townes-Brocks syndrome (TBS), a condition with variable clinical presentation. The main features are a stenotic or imperforate anus, dysplastic ears, and thumb malformations, and other common concerns are hearing impairments, foot malformations, and renal and heart defects. Most of the pathogenic SALL1 variants are nonsense and frameshift, likely escaping nonsense-mediated mRNA decay and causing disease via a dominant-negative mechanism. Haploinsufficiency may result in mild phenotypes, but only four families with distinct SALL1 deletions have been reported to date, with a few more being of larger size and also affecting neighboring genes. We report on a family with autosomal dominant hearing impairment and mild anal and skeletal anomalies, in whom a novel 350 kb SALL1 deletion, spanning exon 1 and the upstream region, was identified by array comparative genomic hybridization. We review the clinical findings of known individuals with SALL1 deletions and point out that the overall phenotype is milder, especially when compared with individuals who carry the recurrent p.Arg276Ter mutation, but with a possible higher risk of developmental delay. Chromosomal microarray analysis is still a valuable tool in the identification of atypical/mild TBS cases, which are likely underestimated.

Keywords: SALL1; Townes–Brocks syndrome; genotype–phenotype correlations; nonsense-mediated decay.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anus, Imperforate* / genetics
  • Comparative Genomic Hybridization
  • Haploinsufficiency
  • Humans
  • Microarray Analysis
  • Phenotype
  • Syndrome*
  • Thumb / abnormalities
  • Transcription Factors* / genetics


  • SALL1 protein, human
  • Transcription Factors

Supplementary concepts

  • Townes-Brocks syndrome