DNA damage can be induced by a variety of sources such as ionizing radiation and ultraviolet light. Cell cycle checkpoints are responsible for co-ordinating cell cycle and repair responses to such DNA damage. Defects in these checkpoints can result in the accumulation of DNA damage, leading to genomic instability and increase susceptibility to cancer development. An apical component of the cell cycle checkpoint and DNA damage repair response is the ataxia telangiectasia mutated (ATM) protein. ATM signals DNA damage checkpoint arrest and repair of double strand breaks by activation of downstream substrates such as CHK2 and p53. Mutations in ATM result in the human genetic disorder ataxia telangiectasia (AT) which is characterised by genomic instability, radiation sensitivity and cancer predisposition. A variant of ATM present in 1% of the European population, Ser49Cys, has been associated with a five-fold increased risk of melanoma development. However, the functional consequence of the ATM Ser49Cys alteration is yet to be defined. Here, patient-derived lymphoblastoid and primary human melanoblast strains containing the ATM Ser49Cys variant allele have been assessed for their ATM signalling following treatment with ionizing radiation (IR). These experiments demonstrate that this ATM variant is functionally defective for only the p53-dependent arm of DNA damage response signalling. This appears to be a direct effect of the Ser49Cys substitution, and this variant has a dominant effect on the wild type ATM expressed from the other allele. It does not affect the immediate cell cycle responses to IR. The lack of activation of the p53 arm of the ATM-dependent DNA damage response suggests loss of pro-apoptotic signalling and/or responses to longer term replicative stress, which in turn may lead to genomic instability and ultimately, a predisposition to cancer development That this variant confers only a small predisposition to cancer development suggests that other factors can compensate for the loss of this important signalling mechanism.