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Hum Mutat. 2020 Jan;41(1):122-128. doi: 10.1002/humu.23914. Epub 2019 Sep 26.

A founder variant in the South Asian population leads to a high prevalence of FANCL Fanconi anemia cases in India.

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Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.
Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India.
Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
School of Biotechnology and Bioinformatics, Level 6, D.Y. Patil Deemed to be University, Navi Mumbai, Maharashtra, India.
Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan.
Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Department of Regenerative Medicine Research, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo Onoda, Yamaguchi, Japan.
Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
Laboratory of Genome Maintenance, The Rockefeller University, New York, New York.
Apollo Specialty Hospital, Chennai, India.
Department of Pediatric Hematology, Institute of Child Health and Hospital for Children, Chennai, India.
Human Genetics and Hematology Program, The Rockefeller University, New York, New York.


Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure, predisposition to cancer, and congenital abnormalities. FA is caused by pathogenic variants in any of 22 genes involved in the DNA repair pathway responsible for removing interstrand crosslinks. FANCL, an E3 ubiquitin ligase, is an integral component of the pathway, but patients affected by disease-causing FANCL variants are rare, with only nine cases reported worldwide. We report here a FANCL founder variant, anticipated to be synonymous, c.1092G>A;p.K364=, but demonstrated to induce aberrant splicing, c.1021_1092del;p.W341_K364del, that accounts for the onset of FA in 13 cases from South Asia, 12 from India and one from Pakistan. We comprehensively illustrate the pathogenic nature of the variant, provide evidence for a founder effect, and propose including this variant in genetic screening of suspected FA patients in India and Pakistan, as well as those with ancestry from these regions of South Asia.


FANCL; Fanconi anemia; India; South Asia; founder variant


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