A four year old boy was diagnosed with hypertrophic cardiomyopathy with moderate degree of obstruction of the left ventricular outflow tract, secondary to asymmetric septal hypertrophy and no features of congestive heart failure, at the age of the 7 months. He was also found to have myxomatous mitral valve, systolic anterior motion of anterior mitral leaflet and moderate mitral regurgitation. There was no evidence of ventricular septal defect at this point in time.In view of phenotypic features suggestive of Noonan syndrome, he underwent genetic evaluation with target gene sequencing and was detected to have a novel heterozygous mutation in exon 13 of LZTR 1 (Leucine- zipper-like transcriptional regulator 1) gene. Echocardiogram on follow up showed increase in left ventricular outflow tract obstruction and appearance of an aneurysm in the membranous portion of interventricular septum. There were no features of right ventricular outflow obstruction, tricuspid regurgitation or aortic regurgitation. The appearance of the membranous septal aneurysm may be related to the direction of jet arising from the point of contact of the anterior mitral leaflet with the hypertrophied basal septum and hitting this part of the interventricular septum. It is an unusual mechanism for formation of membranous septal aneurysm, given its absence in the earlier echocardiograms and absence of any left to right shunt across the aneurysm. He has been initiated on beta blockers due to severe left ventricular outflow tract obstruction and is planned for septal myomectomy, resection of membranous septal aneurysm and mitral valve repair.