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Updated: Sep 3, 2025

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
07:15

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

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Study of variants associated with ventricular septal defects (VSDs) highlights the unique genetic structure of the

Sumbal Sarwar1, Shabana2, Amna Tahir3

  • 1Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, 54590, Pakistan. sumbal.sarwar@ymail.com.

Italian Journal of Pediatrics
|July 23, 2022
PubMed

Insights

Genetic variants in ISL1, NFATc1, TBX5, and MTHFR genes are associated with congenital heart defects (ventricular septal defects) in Pakistani children. This finding aids in understanding the genetic basis of VSDs and potential screening strategies.

Area of Science:

  • Cardiovascular Genetics
  • Pediatric Cardiology
  • Molecular Biology

Background:

  • Ventricular septal defects (VSDs) are a leading cause of infant mortality from cardiac anomalies, affecting up to 4% of neonates.
  • The complex interplay of genetic and environmental factors in VSD etiology remains incompletely understood.

Purpose of the Study:

  • To investigate the association between specific gene variants and the occurrence of VSDs in a Pakistani pediatric cohort.
  • To identify potential genetic markers for VSD risk in the Pakistani population.

Main Methods:

  • Genotyping of six gene variants (ISL1, NFATc1, VEGF, HEY2, TBX5, MTHFR) in 200 VSD children and 150 healthy controls using tetra-ARMS PCR and PCR-RFLP.
  • Collection of pediatric clinical and demographic data.

Main Results:

  • Significant associations were found between VSD and variants in ISL1 (rs1017), NFATc1 (rs7240256), TBX5 (rs11067075), and MTHFR (rs1801133) in the Pakistani cohort.
  • VEGF and HEY2 gene variants were not detected in the study population.
  • Allele and genotype frequencies differed significantly between VSD cases and controls for the associated genes.

Conclusions:

  • ISL1, NFATc1, TBX5, and MTHFR gene variants are implicated in the pathogenesis of VSDs in Pakistani children.
  • Wider genetic screening programs targeting these markers could help reduce VSD risk in the Pakistani population.
Abstract

Keywords:
Genetic variationsPakistani populationRFLPTetra ARMS PCRVentricular septal defects

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