We report a novel germline Met53Val mutation in CDKN2A from a large melanoma-prone family; this mutation occurs in exon 2 of CDKN2A where p16 and alternative reading frame (ARF) both share transcript sequences. The previously reported Met53Ile and the current Met53Val mutations are coupled to distinct Asp68His and Asp67Gly alterations in ARF, respectively. The coincidence of second, independent p16 Met53 alteration that differentially alters ARF suggests that there may be selectivity for targeting the p16 transcript over the ARF transcript.