Human DNA contains several variations, which can affect the structure and normal functioning of a protein. These variations could be single nucleotide polymorphisms (SNPs) or insertion-deletions (InDels). SNPs, as opposed to InDels, are more commonly present in DNA and may cause genetic disorders. In the current study, several bioinformatic tools were used to prioritize the pathogenic variants in the SLITRK1 gene. Out of all of the variants, 16 were commonly predicted to be pathogenic by these tools. All the variants had very low frequency, i.e., <0.0001 in the global population. The secondary structure of all filtered variants was predicted, but no structural change was observed at the site of variation in any variant. Protein stability analysis of these variants was then performed, which determined a decrease in protein stability of 10 of the variants. Amino acid conservation analysis revealed that all the amino acids were highly conserved, indicating their structural and functional importance. Protein 3D structure of wildtype SLITRK1 and all of its variants was predicted using I-TASSER, and the effect of variation on 3D structure of the protein was observed using the Missense3D tool, which presented the probable structural loss in three variants, i.e., Asn529Lys, Leu496Pro and Leu94Phe. The wildtype SLITRK1 protein and these three variants were independently docked with their close interactor protein PTPRD, and remarkable differences were observed in the docking sites of normal and variants, which will ultimately affect the functional activity of the SLITRK1 protein. Previous studies have shown that mutations in SLITRK1 are involved in Tourette syndrome. The present study may assist a molecular geneticist in interpreting the variant pathogenicity in research as well as diagnostic setup.

Polydactyly is a rare autosomal dominant or recessive appendicular patterning defect of the hands and feet, phenotypically characterized by the duplication of digits. Postaxial polydactyly (PAP) is the most common form and includes two main types: PAP type A (PAPA) and PAP type B (PAPB). Type A involves a well-established extra digit articulated with the fifth or sixth metacarpal, while type B presents a rudimentary or poorly developed superfluous digit. Pathogenic variants in several genes have been identified in isolated and syndromic forms of polydactyly. The current study presents two Pakistani families with autosomal recessive PAPA with intra- and inter-familial phenotype variability. Whole-exome sequencing and Sanger analysis revealed a novel missense variant in KIAA0825 (c.3572C>T: p.Pro1191Leu) in family A and a known nonsense variant in GLI1 (c.337C>T: p.Arg113*) in family B. In silico studies of mutant KIAA0825 and GLI1 proteins revealed considerable structural and interactional modifications that suggest an abnormal function of the proteins leading to the disease phenotype. The present study broadens the mutational spectrum of KIAA0825 and demonstrates the second case of a previously identified GLI1 variant with variable phenotypes. These findings facilitate genetic counseling in Pakistani families with a polydactyly-related phenotype.

Intellectual disability (ID) is a neuro-developmental condition that affects a person’s cognitive ability and results in a learning defect. It affects 1–3% of the general population; however, the ratio may be expected to be more in a consanguineous population. Herein in the present study, we identified a nuclear family from Dera Ismail Khan City in Pakistan. Whole exome sequencing was performed to map the pathogenic variant. Protein structural modeling and interaction studies were carried out to validate the variant with disease association. Molecular modeling of normal and mutated proteins was performed through I-TASSER and Chimera tools, while docking and interaction analysis was carried out using Cluspro. Clinical analysis of the patient determined mild intellectual disability and gait problem. Candidate gene analysis in this family found a homozygous missense mutation NM_002508:c.C2512T (p.Arg838Cys) in the 12th exon of NID1 gene. Molecular modeling of wild-type and mutant NID1 proteins determined a significant effect on the protein’s secondary and tertiary structure. Hence, based on the exome sequence analysis, NID1 is proposed to be a strong novel candidate ID gene in this family. The genetic mapping of the present family led us to determine a novel candidate gene to be associated with intellectual disability. Linkage of additional ID families with genes would confirm its validity and strengthen our notion. Furthermore, expression studies and pathway analysis will help in exploring the biological mechanism of learning and memory.