Fully mature hair and nails differ greatly in physical appearance but share common signaling events at the embryonic level during development and morphogenesis. Abnormalities in any crucial component of these signaling cascades can lead to either isolated hair and nail disorders or associated phenotypes such as pure hair and nail ectodermal dysplasia (PHNED). The current study was conducted to find out the genetic factors behind severe form of Ectodermal Dysplasia in Pakistani family. For the current study, we recruited large kindred with multiply affected individuals from a remote area of Pakistan. Approval for the study was obtained from the institutional review board of Quaid-i-Azam University, Islamabad, Pakistan, and written informed consent was obtained from all the available family participants. Haplotypes were constructed by typing microsatellite markers which revealed linkage to chromosome 12q13. Sequence analysis of HOXC13 revealed that all affected individuals were homozygous for a novel nonsense variant (c.265C/T, p.Gln89*). To date, only five sequence variants in the HOXC13gene causing PHNED have been reported. The presence of the mutated genes and the polymorphic nature of the variant (c.265C/T, p.Gln89*), detected in our family were excluded from a panel of 150 unrelated ethnically matched control individuals. In conclusion, we report a novel nonsense variant (c.265C/T, p.Gln89*) in the HOXC13 gene, which resulted in a premature termination codon and is predicted either to produce a truncated protein without an essential DNA binding homeodomain or more likely to undergo nonsense-mediated RNA decay ultimately producing the PHNED phenotype. These findings expand the spectrum of mutations related to the HOXC13 gene, which results in the PHNED phenotype.