Left Ventricular Outflow Tract Obstruction (LVOTO) is a significant subtype of Congenital Heart Disease (CHD) with these lesions accounting for 14% of all CHD. The associated mortality and morbidity associated with these lesions is significant with severe cases frequently fatal. Although a multifactorial aetiology for LVOTO has been proposed, there are multiple strands of evidence to suggest that LVOTO is in at least some cases monogenic. The use of chromosomal abnormalities such as balanced translocations is a recognised tool in the identification of disease genes. A patient was identified with LVOTO in association with a de novo balanced translocation, 46,XY,t(14;15)(q23;q26.3) dn and the regions surrounding the breakpoints on both chromosomes were considered candidate loci for a causative gene. Investigation of the breakpoints by FISH and by mapping of the breakpoint on derived chromosome 14 showed that NR2F2, a transcription factor with a role in development, was interrupted by the translocation. However, sequencing of NR2F2 in 112 DNA samples from patients with isolated LVOTO failed to show any additional mutations. Due to the possibility of a position effect, additional genes up to 2 Mb from the breakpoints were considered candidate genes and the mRNA expression in murine embryos was studied. mRNA expression patterns of Nr2f2 and Mctp2were identified consistent with a role in cardiac development. Subsequent sequencing of MCTP2 identified a single missense mutation in the LVOTO patient cohort, suggesting both genes may be involved in the aetiology of LVOTO. Immunohistochemistry of NR2F2 and MCTP2 also showed patterns consistent with a role for both proteins in cardiogenesis; NR2F2 expression included atrial myocardium and heart valves and MCTP2 in the ventricular myocardium. As copy number variation of NR2F2 and MCTP2 remained a further possible cause for LVOTO, DNA from 36 cases of isolated LVOTO with a normal karyotype and negative for mutations in NR2F2 or MCTP2, was interrogated using array Comparative Genomic Hybridisation. Although no CNVs of the region containing these genes were identified, the interruption of NR2F2 by a translocation and discovery of a mutation in MCTP2 suggests that variation in either gene may be a low frequency cause of LVOTO.