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A gene promoter plays pivotal role in the disease development. This study was designed to investigate the pathological role of variants of the <jats:italic>ISL1<\/jats:italic> gene promoter region in ASD patients.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Total DNA extracted from 625 subjects, including 332 ASD patients and 293 healthy controls, was sequenced to identify variants in the promoter region of <jats:italic>ISL1<\/jats:italic> gene. Further functional analyses of the variants were performed with dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA). All possible binding sites of transcription factor affected by the identified variants were predicted using the JASPAR database.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Four variants in the <jats:italic>ISL1<\/jats:italic> gene promoter were found only in patients with ASD by sequencing. Three of the four variants [g.4923\u2009G\u2009&gt;\u2009C (rs541081886), g.5079 A\u2009&gt;\u2009G (rs1371835943) and g.5309\u2009G\u2009&gt;\u2009A (rs116222082)] significantly decreased the transcriptional activities compared with the wild\u2010type <jats:italic>ISL1<\/jats:italic> gene promoter (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). The EMSA revealed that these variants [g.4923\u2009G\u2009&gt;\u2009C (rs541081886), g.5079 A\u2009&gt;\u2009G (rs1371835943) and g.5309\u2009G\u2009&gt;\u2009A (rs116222082)] in the <jats:italic>ISL1<\/jats:italic> gene promoter affected the number and affinity of binding sites of transcription factors. Further analysis with the online JASPAR database demonstrated that a cluster of putative binding sites for transcription factors may be altered by these variants.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>These sequence variants identified from the promoter region of <jats:italic>ISL1<\/jats:italic> gene in ASD patients are probably involved in the development of ASD by affecting the transcriptional activity and altering <jats:italic>ISL1<\/jats:italic> levels. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of ASD.<\/jats:p><\/jats:sec>","DOI":"10.1002\/jgm.3450","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T17:34:41Z","timestamp":1664386481000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Identification and functional analysis of genetic variants of <i>ISL1<\/i> gene promoter in human atrial septal defects"],"prefix":"10.1002","volume":"24","author":[{"given":"Xiu\u2010Yun","family":"Yin","sequence":"first","affiliation":[{"name":"School of Pharmacy, Drug Research &amp; Development Center, Wannan Medical College, Wuhu, Anhui, China &amp; The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University &amp; Chinese Academy of Medical Sciences  Tianjin 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