A systematic review of hereditary neurological disorders diagnosed by whole exome sequencing in Pakistani population: updates from 2014 to November 2024

Whole exome sequencing: Unlocking the molecular diagnostic odyssey in Pakhtun ethnic group of Pakistani population

The Pakhtuns are 40.86 million people, accounting for 16.9 % of the Pakistani population, and primarily reside in the Khyber Pakhtunkhwa province. The Pakistani population in general, and the Pakhtun belt in particular, is divided into small, isolated tribes where inbreeding is very high (>55 %). This leads to high frequency of rare genetic diseases, making "Rare" conditions relatively common in this population. Due to the high frequency and overlapping phenotypes of affected individuals, molecular diagnostics are often difficult and time consuming. We investigated 1374 individuals from 272 families, including those with skin disorders (n = 52), vision disorders (n = 50), deafness (n = 26), neurological disorders (n = 102), and skeletal disorders (n = 42). Whole exome sequencing of the index patient was performed, and causative variant prioritization was carried out using an autosomal recessive model, following the ACMG 2015 guidelines and confirming segregation with the disease phenotypes via Sanger sequencing. Successfully resolved cases comprised of 69.5 %, of which 70.8 % (n = 136) had homozygous variants, while 6.3 % (n = 12) had compound heterozygous variations. This is a comprehensive study of the Pakhtun ethnic group, addressing the most common genetic disorders within this population. It has implications for the policy already approved by the local government to conduct pre-marital testing, aiming to reduce the disease burden in future generations. However, the study had limitations: we could not perform whole genome sequencing for the unresolved 30.5 % families (n = 83), and the sample size was not representative of the entire 40.86 million population. Nonetheless, the alarming incidence of rare diseases in this population supports the assertion that "rare" conditions are indeed common here.

QARS1 associated developmental epileptic encephalopathy: first report of a rare homozygous missense variant from Pakistan causing nonepileptic phenotype in a family of seven patients and a comprehensive review of the literature

BACKGROUND

Pathogenic variants in QARS1 (MIM:603727; Glutaminyl-TRNA Synthetase 1), which encodes Glutaminyl-tRNA synthetase 1, have been associated with rare progressive microcephaly with seizures and cerebral and cerebellar atrophy (MSCCA MIM:615760). Only a handful of MSCCA patients have been reported in the literature mostly associated with compound heterozygous QARS1 variants. In the current study, we aimed molecular characterization of a large consanguineous Pakistani family affected with microcephaly, severe intellectual and developmental disability.

METHODS

We isolated genomic DNA from blood samples collected from the two affected and three normal individuals of the family. We employed whole exome sequencing, homozygosity mapping, Sanger sequencing and in silico protein modelling tools to characterize the pathogenic variant causing the disease phenotype. Moreover, we collected data of 26 MSCCA patients previously reported in the literature.

RESULTS

The phenotype in the affected individuals of the family was characterized by microcephaly, severe intellectual and developmental disability, but no epilepsy. We found a rare QARS1 variant NM_005051.3:c.1133G > A, p.(Arg378His) in homozygous state in the family. This variant was recently cited in a patient of Turkish ethnicity, the only MSCCA patient reported with nonepileptic phenotype. This variant lying in the catalytic domain of glutaminyl-tRNA synthetase 1 showed deleterious structure and functional impacts on the protein predicted by in silico tools. The variant was classified as 'likely pathogenic' following ACMG guidelines.

CONCLUSIONS

We present first report of QARS1 associated developmental encephalopathy from Pakistan. Our study adds to the restricted clinical and mutational database of this rare disorder supporting the growing evidence that homozygous missense QARS1 genotypes may lead to the milder phenotype. The reports of more patients with molecular studies will enhance the understanding of the genotype-phenotype correlations.