Functional & Integrative Genomics

, Volume 13, Issue 3, pp 285–293 | Cite as

Copy number variation-based polymorphism in a new pseudoautosomal region 3 (PAR3) of a human X-chromosome-transposed region (XTR) in the Y chromosome

  • Avinash M. Veerappa
  • Prakash Padakannaya
  • Nallur B. RamachandraEmail author
Original Paper


A 3.5-Mb region of the X chromosome underwent duplication and transposition to the Y chromosome ~5–6 Mya. This X-transposed-region (XTR) originated at Xq21.3 and was inserted at Yp11.2. The two locations have 98.78 % homology and a high concentration of tandem repeats. In whole-genome scans of ten large families with dyslexic members, we identified transposed blocks comprising >102 kb of the Yp11.2 region in its homologous region at Xq21.3 in three females from three different families. Although recombination is known to be limited only to the pseudoautosomal regions (PARs) of the X and Y chromosomes, we report allelic unequal recombination between the XTR region Yp11.2 and Xq21.3, indicating the presence of a new PAR, which we named PAR3. This PAR3 region was also found in 2 % of the general population. An additional layer of justification could be provided from six other dyslexic cases which harbored duplications and deletions in the same Xq21.3 and Yp11.2 regions through allelic unequal recombination.


PAR1 PAR2 CNV X-transposed region Yp11.2 Xq21.3 PAR3 



We thank the subjects and their families for participating in this study; Prof. H. A. Ranganath for his help and encouragement; Marita J, Anand S, and Shyamala K.V. for their help in sample collection; the services of Vimta Labs Ltd.; University of Mysore for providing facility to conduct this work; and the Department of Science and Technology—Health Science (SR/SO/HS-103/2007) for funding, Government of India, New Delhi.

Ethics statement

Written consent was obtained from all participants involved in this study and the Institutional Human Ethical Committee (IHEC no. 3/RI/2008-09) approved the consent procedure.

Supplementary material

10142_2013_323_MOESM1_ESM.jpg (913 kb)
Supplementary Fig. 1 Illustration of three pedigrees under study. a, b and c are the pedigrees of three dyslexic families showing the recombined blocks of Yp11.2 in one of the X-chromosome Xq21.3 region (a-IV-2; b-III-11 and c-III-6). The arrows indicate the probands which shows the duplicated and deleted blocks found in Xq21.3/PCDH11X/TGIF2LX region (a-V-2 and b-III-10). (JPEG 912 kb)
10142_2013_323_MOESM2_ESM.jpg (178 kb)
Supplementary Fig. 2 (JPEG 177 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Avinash M. Veerappa
    • 1
  • Prakash Padakannaya
    • 2
  • Nallur B. Ramachandra
    • 1
    Email author
  1. 1.Genomics Laboratory, DOS in ZoologyUniversity of MysoreMysore-06India
  2. 2.DOS in PsychologyUniversity of MysoreMysore-06India

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