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TBX6, LHX1 and copy number variations in the complex genetics of Müllerian aplasia

Maria Sandbacka12, Hannele Laivuori23, Érika Freitas4, Mervi Halttunen3, Varpu Jokimaa5, Laure Morin-Papunen6, Carla Rosenberg4 and Kristiina Aittomäki17*

Author Affiliations

1 Folkhälsan Institute of Genetics, Helsinki, Finland

2 Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland

3 Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland

4 Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil

5 Department of Obstetrics and Gynecology, University of Turku, Turku, Finland

6 Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland

7 Department of Clinical Genetics, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland

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Orphanet Journal of Rare Diseases 2013, 8:125  doi:10.1186/1750-1172-8-125

Published: 16 August 2013



Müllerian aplasia (MA) is a congenital disorder of the female reproductive tract with absence of uterus and vagina with paramount impact on a woman’s life. Despite intense research, no major genes have been found to explain the complex genetic etiology.

Methods and Results

We have used several genetic methods to study 112 patients with MA. aCGH identified CNVs in 8/50 patients (16%), including 16p11.2 and 17q12 deletions previously associated with MA. Subsequently, another four patients were shown to carry the ~0.53 Mb deletion in 16p11.2. More importantly, sequencing of TBX6, residing within 16p11.2, revealed two patients carrying a splice site mutation. Two previously reported TBX6 variants in exon 4 and 6 were shown to have a significantly higher frequency in patients (8% and 5%, respectively) than in controls (2% each). We also sequenced LHX1 and found three apparently pathogenic missense variants in 5/112 patients. Altogether, we identified either CNVs or variations in TBX6 or LHX1 in 30/112 (26.8%) MA patients. CNVs were found in 12/112 (10.7%), patients, novel variants in TBX6 or LHX1 in 7/112 (6.3%), and rare variants in TBX6 in 15/112 (13.4%) patients. Furthermore, four of our patients (4/112, 3.6%) were shown to carry variants in both TBX6 and LHX1 or a CNV in combination with TBX6 variants lending support to the complex genetic etiology of MA.


We have identified TBX6 as a new gene associated with MA. Our results also support the relevance of LHX1 and CNVs in the development of this congenital malformation.