The aim of current study was to recruit the samples (blood/buccal swab) from Pakistani pediatric patients with isolated ventricular septal defect (VSD) and age/gender matched controls from the same population and investigate the selected SNPs 1) MTRR; NM_002454; rs1532268; c.524C > T; p.Ser175Leu, 2) GATA4; NM_001308093; rs104894073; c.886G > A; p.Gly296Ser, 3) VEGF; NM_003377; rs699947; c.-2578C > A, 4) ISL1; rs6867206; intergenic; g.51356860 T > C in the recruited cohort. This evidence concerns the gene ISL1 and ventricular septal defect.