This study focused on single nucleotide polymorphisms (SNPs) of the CNTNAP2 gene, which is closely associated with the adhesion between glial cells and neurons. Twenty children of the same age and sex (ten with ASD and ten healthy) were selected. DNA was extracted from the marked samples for both targeted groups of patients and healthy individuals then the process of tests is confirmed by electrophoresis. The samples have been sent to international lab (Macrogen Korea) for making the tests for analysis whole-exome. For performing the Illumina NovaSeq 6000 platform to identify genetic variants. The required analysis is focused on the main variants which located in/near exons or regulatory regions of CNTNAP2 gene to determine the functional impact for number of gene mutations. There are no deviations have been appearing through adopting both of Hardy-Weinberg equilibrium and chi-square test that reflect highly percentage of validating of studied data and that making valuable interpreting the potential genetic contribution to susceptibility to autism spectrum disorder. The validating the genotype data and ensuring the absence of systematic errors in genotype determination or selection bias. In term of outcomes of analysis has been highlighted several number for (non-coding and synonymous mutations) has been identify them during the period of the study. Finally, the paper display that mutations do not alter the protein sequence and contributed to autism through gene accumulation, transcriptional stability, and activation of neural pathways.