A Nonsense Mutation in HOXD13 Gene from A Chinese Family with Non-Syndromic Synpolydactyly

Tohoku J Exp Med. 2019 Oct;249(2):93-100. doi: 10.1620/tjem.249.93.


Synpolydactyly is a congenital limb malformation characterized by incomplete separation and duplication in fingers and/or toes, which is mainly caused by mutations in the homeobox D13 (HOXD13) gene. Here, a four-generation family with variant phenotypes of synpolydactyly was analyzed, in which the proband had bilateral preaxial synpolydactyly in toes with normal fingers, the father had clinodactyly in the fifth fingers, while the mother and grandma was normal. Trio whole-exome sequencing (trio-WES) is a high throughput sequencing targeting whole genome for detecting exonic variants from the proband and the parents in a family. Through trio-WES followed by Sanger sequencing and enzyme digestion, a heterozygous nonsense mutation (c.859 C>T/p.Gln287Ter) was newly identified in the homeodomain of the HOXD13 gene from the proband and the affected father, but not from the unaffected mother, the unaffected grandma, or the normal control. Mutation Taster, Human Splicing Finder and EX-SKIP predicted that the heterozygous mutation (c.859 C>T) would result in haploinsufficiency of HOXD13 protein through nonsense-mediated mRNA decay (NMD) and splicing abnormality, which might disrupt the integrity and reduce the expression level of the HOXD13 protein (loss-of-function). In short, a heterozygous nonsense mutation in the HOXD13 gene was newly identified in two patients with mild phenotypes of synpolydactyly, which extends the mutation spectrum in HOXD13 gene. Moreover, the findings we presented here deepen our understanding of the clinical consequences of non-syndromic synpolydactyly and may provide a new clue for further studies of the pathogenic mechanism of the mutation that causes aberrant splicing of HOXD13 gene.

Keywords: HOXD13 gene; exome sequencing; exonic splicing regulatory mutation; nonsense-mediated mRNA decay; synpolydactyly.

MeSH terms

  • Adult
  • Aged
  • Asian People / genetics*
  • Base Sequence
  • Child, Preschool
  • Codon, Nonsense / genetics*
  • Exome Sequencing
  • Female
  • Homeodomain Proteins / genetics*
  • Humans
  • Male
  • Middle Aged
  • Pedigree
  • Syndactyly / genetics*
  • Transcription Factors / genetics*


  • Codon, Nonsense
  • HOXD13 protein, human
  • Homeodomain Proteins
  • Transcription Factors

Supplementary concepts

  • Syndactyly, type 2