The breast cancer risk conferred by germline protein truncating variants (PTVs) in known and putative breast cancer genes has been extensively investigated. However, the effect of FANCM PTVs on breast cancer risk remains unclear. Our previous clinical, genetic and functional results on the N-terminal p.Arg658∗ and the two C-terminal p.Gln1701∗ and p.Gly1906Alafs∗12 variants suggested that FANCM PTVs may confer different risks for ER-negative (ER-neg) and triple-negative (TN) breast cancer subtypes. Here, we performed meta-analyses of seven studies totaling 144 681 breast cancer cases and 123 632 controls. FANCM PTVs were tested for association with breast cancer risk overall and the disease clinical subtypes by single variant and burden analyses. Two CRISPR-Cas9-based functional assays were also conducted to test the fitness of cells after knock-in of the p.Arg658∗, p.Gln1701∗ and p.Gly1906Alafs∗12 PTVs and the sensitivity of different FANCM regions to genome editing. Our results suggest that the N-terminal FANCM region upstream of p.Tyr725 harbors essential functions, whereas downstream regions appear dispensable. This is supported by our genetic data which indicate that all FANCM PTVs, excluding the two C-terminal p.Gln1701∗ and p.Gly1906Alafs∗12, are associated with an increased risk of ER-neg (OR = 1.41, P = 0.023) and TN (OR = 1.64, P = 0.0023). Notably, PTVs upstream of AA position 670 are associated with a moderate risk of developing TN breast cancer, and that even when the p.Arg658∗ carriers were excluded from the analysis. Importantly, our results confirm previous data indicating that p.Arg658∗ carriers are at moderate risk of developing ER-neg (OR = 2.08, P = 0.030) and TN (OR = 3.26; P = 0.0034), whereas carriers of p.Gln1701∗ and p.Gly1906Alafs∗12 should not be considered at increased risk. Our data are useful for counseling carriers of FANCM PTVs, but further analyses are warranted to obtain more precise risk estimates.

Beckman Research Institute of City of Hope Duarte USA

Biostatistics and Computational Biology Branch National Institute of Environmental Health Sciences NIH Durham NC USA

Biotech Research and Innovation Centre University of Copenhagen Copenhagen Denmark

Biotech Research and Innovation Centre University of Copenhagen Copenhagen Denmark; Department of Pharmacy and Biotechnology University of Bologna Bologna Italy

Cancer Epidemiology Division Cancer Council Victoria Melbourne Victoria Australia; Centre for Epidemiology and Biostatistics Melbourne School of Population and Global Health The University of Melbourne Melbourne Victoria Australia; Precision Medicine School of Clinical Sciences at Monash Health Monash University Clayton Victoria Australia

Cancer Epidemiology Division Cancer Council Victoria Melbourne Victoria Australia; Precision Medicine School of Clinical Sciences at Monash Health Monash University Clayton Victoria Australia; Department of Clinical Pathology The University of Melbourne Melbourne Australia

Cancer Genetics and Epidemiology Group Genomic Medicine Group Fundación Instituto de Investigación Sanitaria de Santiago de Compostela Complejo Hospitalario Universitario de Santiago SERGAS Santiago de Compostela Spain

Center for Familial Breast and Ovarian Cancer Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany; Center for Integrated Oncology Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany

Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge UK

Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Cambridge UK

Centre for Epidemiology and Biostatistics Melbourne School of Population and Global Health The University of Melbourne Melbourne Victoria Australia

Centre for Genomic and Experimental Medicine Institute of Genetics and Cancer University of Edinburgh Edinburgh UK

Department of Cancer Genetics Therapeutics and Ultrastructural Pathology The Cyprus Institute of Neurology and Genetics Nicosia Cyprus

Department of Cancer Genetics Therapeutics and Ultrastructural Pathology The Cyprus Institute of Neurology and Genetics Nicosia Cyprus; Department of Comparative Biomedical Sciences College of Veterinary Medicine Mississippi State University Starkville Mississippi USA

Department of Clinical Pathology The University of Melbourne Melbourne Australia; Clinical Genomics School of Translational Medicine Monash University Melbourne Australia

Department of Genetics and Pathology International Hereditary Cancer Center Pomeranian Medical University Szczecin Poland

Department of Genetics and Pathology International Hereditary Cancer Center Pomeranian Medical University Szczecin Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics Pomeranian Medical University Szczecin Poland

Department of Gynecology and Obstetrics Comprehensive Cancer Center Erlangen EMN Friedrich Alexander University Erlangen Nuremberg University Hospital Erlangen Erlangen Germany

Department of Gynecology and Obstetrics Comprehensive Cancer Center Lower Saxony Hannover Medical School Hannover Germany

Department of Internal Medicine and Huntsman Cancer Institute University of Utah Salt Lake City UT USA

Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada; Laboratory Medicine Program University Health Network Toronto Ontario Canada

Department of Laboratory Medicine and Pathology Mayo Clinic Rochester USA

Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden

Department of Medical Oncology Erasmus MC Cancer Institute Rotterdam the Netherlands

Department of Medical Oncology Mayo Clinic Rochester USA

Department of Medical Oncology University Hospital of Heraklion Heraklion Greece

Department of Nutrition Harvard T H Chan School of Public Health Boston USA

Department of Oncology Old Road Campus Research Building University of Oxford Oxford UK

Department of Oncology Södersjukhuset Stockholm Sweden; Department of Clinical Science and Education Södersjukhuset Karolinska Institutet Stockholm Sweden

Department of Pathology Leiden University Medical Center Leiden the Netherlands; Department of Human Genetics Leiden University Medical Center Leiden the Netherlands

Department of Population and Public Health Sciences Keck School of Medicine University of Southern California USA

Department of Population Science American Cancer Society Atlanta USA

Department of Quantitative Health Sciences Mayo Clinic Rochester USA

Department of Radiation Oncology Hannover Medical School Hannover Germany

Department of Radiology University of Wisconsin School of Medicine and Public Health Madison USA

Departments of Epidemiology and Nutrition Harvard T H Chan School of Public Health Channing Division of Network Medicine Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston USA

Division of Biostatistics Data Science Institute and Cancer Center Medical College of Wisconsin Milwaukee WI USA

Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA

Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA; Usher Institute of Population Health Sciences and Informatics The University of Edinburgh Edinburgh UK; Cancer Research UK Edinburgh Centre The University of Edinburgh Edinburgh UK

Division of Cancer Epidemiology German Cancer Research Center Heidelberg Germany

Division of Cancer Epidemiology German Cancer Research Center University Medical Center Hamburg Eppendorf Hamburg Germany

Division of Evolution Infection and Genomics School of Biological Sciences Faculty of Biology Medicine and Health University of Manchester Manchester UK; Manchester Centre for Genomic Medicine St Mary's Hospital Manchester University NHS Foundation Trust Manchester UK

Division of Oncology Faculty of Medicine School of Health Sciences University of Thessaly Larissa Greece

Dr Margarete Fischer Bosch Institute of Clinical Pharmacology Stuttgart Germany; University of Tübingen Tübingen Germany

Epidemiology Branch National Institute of Environmental Health Sciences NIH Durham NC USA

Fred A Litwin Center for Cancer Genetics Lunenfeld Tanenbaum Research Institute of Mount Sinai Hospital Toronto Ontario Canada; Department of Molecular Genetics University of Toronto Toronto Ontario Canada

Genome Diagnostics Program IFOM ETS the AIRC Institute of Molecular Oncology Milan Italy

Genome Diagnostics Program IFOM ETS the AIRC Institute of Molecular Oncology Milan Italy; Department of Biomedical Sciences Humanitas University Pieve Emanuele Milan Italy; IRCCS Humanitas Research Hospital Rozzano Milan Italy

Genome Diagnostics Program IFOM ETS the AIRC Institute of Molecular Oncology Milan Italy; Unité de Génomique Fonctionnelle Institut de Cancérologie de l'Ouest Nantes Angers Angers France; Univ Angers Nantes Université Inserm CNRS CRCI2NA SFR ICAT Angers France

Human Genotyping Unit CeGen Spanish National Cancer Research Centre Instituto de Salud Carlos 3 Madrid Spain

Human Genotyping Unit CeGen Spanish National Cancer Research Centre Madrid Spain

IEO European Institute of Oncology IRCCS Division of Cancer Prevention and Genetics Milan Italy

Inserm U1331 Paris France; Institut Curie Paris France; Mines Paris Fontainebleau France; PSL Research University Paris France

Institut Curie Service de Génétique Paris France; Inserm U1339 Paris France; Université Paris Cité Paris France

Institute for Medical Biometry and Epidemiology University Medical Center Hamburg Eppendorf Hamburg Germany; Institute for Occupational and Maritime Medicine University Medical Center Hamburg Eppendorf Hamburg Germany

Institute for Prevention and Occupational Medicine of the German Social Accident Insurance Institute of the Ruhr University Bochum Bochum Germany

Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences Ufa Russia

Institute of Clinical Medicine Faculty of Medicine University of Oslo Oslo Norway; Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway

Institute of Medical Biochemistry and Laboratory Diagnostics 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic

Institute of Medical Biochemistry and Laboratory Diagnostics 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic; Institute of Biology and Medical Genetics 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic

Institute of Medical Biochemistry and Laboratory Diagnostics 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic; Institute of Pathological Physiology 1st Faculty of Medicine Charles University Prague Czech Republic

Intermountain Healthcare Salt Lake City UT USA

Laboratory of Hematology Oncology IEO European Institute of Oncology IRCCS Milan Italy

Mayo Clinic Rochester USA

Molecular Genetics of Breast Cancer German Cancer Research Center Heidelberg Germany

Molecular Genetics of Breast Cancer German Cancer Research Center Lahore Pakistan

Molecular Oncology Laboratory Hospital Clinico San Carlos Instituto de Investigación Sanitaria San Carlos Madrid Spain

Oncólogy and Genétics Group Instituto Investigación Sanitaria Galicia Sur SERGAS Vigo Spain

Perelman School of Medicine University of Pennsylvania Philadelphia USA

Peter MacCallum Cancer Centre Melbourne Victoria Australia

Peter MacCallum Cancer Centre Melbourne Victoria Australia; Sir Peter MacCallum Department of Oncology The University of Melbourne Melbourne Victoria Australia

Public Health Program QIMR Berghofer Brisbane Queensland Australia

Roswell Park Cancer Center Buffalo USA

School of Cancer and Pharmaceutical Sciences Comprehensive Cancer Centre Guy's Campus King's College London London UK

Sir Peter MacCallum Department of Oncology The University of Melbourne Melbourne Victoria Australia; Parkville Familial Cancer Centre Peter MacCallum Cancer Centre and Royal Melbourne Hospital Melbourne Australia

Slone Epidemiology Center Boston University Chobanian and Avedisian School of Medicine Boston USA

Team Exposome and Heredity CESP Gustave Roussy INSERM University Paris Saclay UVSQ Villejuif France

The University of Kansas Cancer Center Kansas City KS USA

Unit of Medical Genetics Department of Medical Oncology and Hematology Fondazione IRCCS Istituto Nazionale dei Tumori di Milano Italy

Unit of Predictive Medicine Molecular Bases of Genetic Risk Department of Experimental Oncology Fondazione IRCCS Istituto Nazionale dei Tumori Milan Italy

University of California San Diego La Jolla California USA

University of Washington Seattle USA

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