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Recently, a founder <jats:italic>Alu<\/jats:italic> insertion in exon 4 of <jats:italic>RP1<\/jats:italic> has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the <jats:italic>Alu<\/jats:italic> insertion in exon 4 of <jats:italic>RP1<\/jats:italic> using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating <jats:italic>RP1<\/jats:italic> variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed <jats:italic>Alu<\/jats:italic>Y c.4052_4053ins328\/p.(Tyr1352Alafs*9) insertion in <jats:italic>RP1<\/jats:italic> exon 4. This <jats:italic>Alu<\/jats:italic>Y insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this <jats:italic>Alu<\/jats:italic>Y insertion in <jats:italic>RP1<\/jats:italic> exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232\u20130.383), with no false-positive results using 120 control samples. The MEI in <jats:italic>RP1<\/jats:italic> exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The <jats:italic>RP1<\/jats:italic>-<jats:italic>Alu<\/jats:italic> grep program efficiently detected the <jats:italic>Alu<\/jats:italic>Y insertion, without the preprocessing of raw data or complex installation processes.<\/jats:p>","DOI":"10.1038\/s41598-021-92834-4","type":"journal-article","created":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T10:03:17Z","timestamp":1624874597000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["In Silico identification of a common mobile element insertion in exon 4 of RP1"],"prefix":"10.1038","volume":"11","author":[{"given":"Dongju","family":"Won","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joo-Yeon","family":"Hwang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yeeun","family":"Shim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suk Ho","family":"Byeon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junwon","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher Seungkyu","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyun Taek","family":"Lim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jong Rak","family":"Choi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seung-Tae","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinu","family":"Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,6,28]]},"reference":[{"key":"92834_CR1","doi-asserted-by":"publisher","first-page":"500","DOI":"10.3341\/kjo.2020.0087","volume":"34","author":"DH Shin","year":"2020","unstructured":"Shin, D. 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