Skip to main content
Top
Published in: BMC Medical Genetics 1/2019

Open Access 01-12-2019 | Disorders of Intellectual Development | Case report

A novel deletion mutation in KMT2A identified in a child with ID/DD and blood eosinophilia

Authors: Haixia Zhang, Bingwu Xiang, Hui Chen, Xiang Chen, Tao Cai

Published in: BMC Medical Genetics | Issue 1/2019

Login to get access

Abstract

Background

The KMT2A gene encoded lysine methyltransferase plays an essential role in regulating gene expression during early development and hematopoiesis. To date, 92 different mutations of KMT2A have been curated in the human gene mutation database (HGMD), resulting in Wiedemann-Steiner syndrome (WDSTS) and intellectual disability (ID)/developmental delay (DD).

Case presentation

In this report, we present a de novo heterozygous deletion mutation [c.74delG; p. (Gly26Alafs*2)] in the KMT2A gene, which was identified by trio-based whole exome sequencing from a 5.5-year-old boy with ID/DD, stereotypic hand movements and blood eosinophilia. Many deleterious germline mutations of KMT2A have been documented to affect development of central nervous system, oral and craniofacial tissues, but not blood eosinophils.

Conclusions

This is the first report of a rare case with ID/DD as well as eosinophilia, resulting from a previously undescribed null mutation of KMT2A. Our findings expand the phenotypical spectrum in affected individuals with KMT2A mutations, and may shed some insight into the role of KMT2A in eosinophil metabolism.
Appendix
Available only for authorised users
Literature
1.
go back to reference Tarlungeanu DC, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Exp Mol Med. 2018;50(8):100. Tarlungeanu DC, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Exp Mol Med. 2018;50(8):100.
2.
go back to reference Study DDD. Prevalence and architecture of de novo mutations in developmental disorders. Nature. 2017;542(7642):433–8. Study DDD. Prevalence and architecture of de novo mutations in developmental disorders. Nature. 2017;542(7642):433–8.
3.
go back to reference Boivin MJ, Kakooza AM, Warf BC, Davidson LL, Grigorenko EL. Reducing neurodevelopmental disorders and disability through research and interventions. Nature. 2015;527(7578):S155–60. Boivin MJ, Kakooza AM, Warf BC, Davidson LL, Grigorenko EL. Reducing neurodevelopmental disorders and disability through research and interventions. Nature. 2015;527(7578):S155–60.
4.
go back to reference Baer S, Afenjar A, Smol T, Piton A, Gerard B, Alembik Y, Bienvenu T, Boursier G, Boute O, Colson C, et al. Wiedemann-Steiner syndrome as a major cause of syndromic intellectual disability: a study of 33 French cases. Clin Genet. 2018;94(1):141–52. Baer S, Afenjar A, Smol T, Piton A, Gerard B, Alembik Y, Bienvenu T, Boursier G, Boute O, Colson C, et al. Wiedemann-Steiner syndrome as a major cause of syndromic intellectual disability: a study of 33 French cases. Clin Genet. 2018;94(1):141–52.
5.
go back to reference Min Ko J, Cho JS, Yoo Y, Seo J, Choi M, Chae JH, Lee HR, Cho TJ. Wiedemann-Steiner syndrome with 2 novel KMT2A mutations. J Child Neurol. 2017;32(2):237–42. Min Ko J, Cho JS, Yoo Y, Seo J, Choi M, Chae JH, Lee HR, Cho TJ. Wiedemann-Steiner syndrome with 2 novel KMT2A mutations. J Child Neurol. 2017;32(2):237–42.
6.
go back to reference Lelieveld SH, Reijnders MR, Pfundt R, Yntema HG, Kamsteeg EJ, de Vries P, de Vries BB, Willemsen MH, Kleefstra T, Lohner K, et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat Neurosci. 2016;19(9):1194–6. Lelieveld SH, Reijnders MR, Pfundt R, Yntema HG, Kamsteeg EJ, de Vries P, de Vries BB, Willemsen MH, Kleefstra T, Lohner K, et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat Neurosci. 2016;19(9):1194–6.
7.
go back to reference Jones WD, Dafou D, McEntagart M, Woollard WJ, Elmslie FV, Holder-Espinasse M, Irving M, Saggar AK, Smithson S, Trembath RC, et al. De novo mutations in MLL cause Wiedemann-Steiner syndrome. Am J Hum Genet. 2012;91(2):358–64. Jones WD, Dafou D, McEntagart M, Woollard WJ, Elmslie FV, Holder-Espinasse M, Irving M, Saggar AK, Smithson S, Trembath RC, et al. De novo mutations in MLL cause Wiedemann-Steiner syndrome. Am J Hum Genet. 2012;91(2):358–64.
8.
go back to reference Cai T, Chen X, Li J, Xiang B, Yang L, Liu Y, Chen Q, He Z, Sun K, Liu PP. Identification of novel mutations in the HbF repressor gene BCL11A in patients with autism and intelligence disabilities. Am J Hematol. 2017;92(12):E653–6. Cai T, Chen X, Li J, Xiang B, Yang L, Liu Y, Chen Q, He Z, Sun K, Liu PP. Identification of novel mutations in the HbF repressor gene BCL11A in patients with autism and intelligence disabilities. Am J Hematol. 2017;92(12):E653–6.
9.
go back to reference Guo S, Yang L, Liu H, Chen W, Li J, Yu P, Sun ZS, Chen X, Du J, Cai T. Identification of novel compound mutations in PLA2G6-associated neurodegeneration patient with characteristic MRI imaging. Mol Neurobiol. 2017;54(6):4636–43. Guo S, Yang L, Liu H, Chen W, Li J, Yu P, Sun ZS, Chen X, Du J, Cai T. Identification of novel compound mutations in PLA2G6-associated neurodegeneration patient with characteristic MRI imaging. Mol Neurobiol. 2017;54(6):4636–43.
10.
go back to reference Bi C, Wu J, Jiang T, Liu Q, Cai W, Yu P, Cai T, Zhao M, Jiang YH, Sun ZS. Mutations of ANK3 identified by exome sequencing are associated with autism susceptibility. Hum Mutat. 2012;33(12):1635–8. Bi C, Wu J, Jiang T, Liu Q, Cai W, Yu P, Cai T, Zhao M, Jiang YH, Sun ZS. Mutations of ANK3 identified by exome sequencing are associated with autism susceptibility. Hum Mutat. 2012;33(12):1635–8.
11.
go back to reference Wang Y, Zeng C, Li J, Zhou Z, Ju X, Xia S, Li Y, Liu A, Teng H, Zhang K, et al. PAK2 Haploinsufficiency results in synaptic cytoskeleton impairment and autism-related behavior. Cell Rep. 2018;24(8):2029–41. Wang Y, Zeng C, Li J, Zhou Z, Ju X, Xia S, Li Y, Liu A, Teng H, Zhang K, et al. PAK2 Haploinsufficiency results in synaptic cytoskeleton impairment and autism-related behavior. Cell Rep. 2018;24(8):2029–41.
12.
go back to reference Brito-Babapulle F. The eosinophilias, including the idiopathic hypereosinophilic syndrome. Br J Haematol. 2003;121(2):203–23. Brito-Babapulle F. The eosinophilias, including the idiopathic hypereosinophilic syndrome. Br J Haematol. 2003;121(2):203–23.
13.
go back to reference Li J, Cai T, Jiang Y, Chen H, He X, Chen C, Li X, Shao Q, Ran X, Li Z, et al. Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database. Mol Psychiatry. 2016;21(2):290–7. Li J, Cai T, Jiang Y, Chen H, He X, Chen C, Li X, Shao Q, Ran X, Li Z, et al. Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database. Mol Psychiatry. 2016;21(2):290–7.
14.
go back to reference Ma D, Wang X, Guo J, Zhang J, Cai T. Identification of a novel mutation of RUNX2 in a family with supernumerary teeth and craniofacial dysplasia by whole-exome sequencing: a case report and literature review. Medicine (Baltimore). 2018;97(32):e11328. Ma D, Wang X, Guo J, Zhang J, Cai T. Identification of a novel mutation of RUNX2 in a family with supernumerary teeth and craniofacial dysplasia by whole-exome sequencing: a case report and literature review. Medicine (Baltimore). 2018;97(32):e11328.
15.
go back to reference Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J. mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing. J Med Genet. 2015;52(4):275–81. Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J. mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing. J Med Genet. 2015;52(4):275–81.
16.
go back to reference Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.
17.
go back to reference Lebrun N, Giurgea I, Goldenberg A, Dieux A, Afenjar A, Ghoumid J, Diebold B, Mietton L, Briand-Suleau A, Billuart P, et al. Molecular and cellular issues of KMT2A variants involved in Wiedemann-Steiner syndrome. Eur J Hum Genet. 2018;26(1):107–16. Lebrun N, Giurgea I, Goldenberg A, Dieux A, Afenjar A, Ghoumid J, Diebold B, Mietton L, Briand-Suleau A, Billuart P, et al. Molecular and cellular issues of KMT2A variants involved in Wiedemann-Steiner syndrome. Eur J Hum Genet. 2018;26(1):107–16.
18.
go back to reference Ronan JL, Wu W, Crabtree GR. From neural development to cognition: unexpected roles for chromatin. Nat Rev Genet. 2013;14(5):347–59. Ronan JL, Wu W, Crabtree GR. From neural development to cognition: unexpected roles for chromatin. Nat Rev Genet. 2013;14(5):347–59.
19.
go back to reference Mishra BP, Zaffuto KM, Artinger EL, Org T, Mikkola HK, Cheng C, Djabali M, Ernst P. The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. Cell Rep. 2014;7(4):1239–47. Mishra BP, Zaffuto KM, Artinger EL, Org T, Mikkola HK, Cheng C, Djabali M, Ernst P. The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. Cell Rep. 2014;7(4):1239–47.
20.
go back to reference Ayton P, Sneddon SF, Palmer DB, Rosewell IR, Owen MJ, Young B, Presley R, Subramanian V. Truncation of the Mll gene in exon 5 by gene targeting leads to early preimplantation lethality of homozygous embryos. Genesis. 2001;30(4):201–12. Ayton P, Sneddon SF, Palmer DB, Rosewell IR, Owen MJ, Young B, Presley R, Subramanian V. Truncation of the Mll gene in exon 5 by gene targeting leads to early preimplantation lethality of homozygous embryos. Genesis. 2001;30(4):201–12.
21.
go back to reference Mohan M, Lin C, Guest E, Shilatifard A. Licensed to elongate: a molecular mechanism for MLL-based leukaemogenesis. Nat Rev Cancer. 2010;10(10):721–8. Mohan M, Lin C, Guest E, Shilatifard A. Licensed to elongate: a molecular mechanism for MLL-based leukaemogenesis. Nat Rev Cancer. 2010;10(10):721–8.
22.
go back to reference Urtishak KA, Robinson BW, Rappaport EF, Sarezky MD, Biegel JA, Nichols KE, Wilmoth DM, Wang LS, Stern JW, Felix CA. Unique familial MLL (KMT2A)-rearranged precursor B-cell infant acute lymphoblastic leukemia in non-twin siblings. Pediatr Blood Cancer. 2016;63(7):1175–80. Urtishak KA, Robinson BW, Rappaport EF, Sarezky MD, Biegel JA, Nichols KE, Wilmoth DM, Wang LS, Stern JW, Felix CA. Unique familial MLL (KMT2A)-rearranged precursor B-cell infant acute lymphoblastic leukemia in non-twin siblings. Pediatr Blood Cancer. 2016;63(7):1175–80.
23.
go back to reference Peterson JF, Baughn LB, Pearce KE, Williamson CM, Benevides Demasi JC, Olson RM, Goble TA, Meyer RG, Greipp PT, Ketterling RP. KMT2A (MLL) rearrangements observed in pediatric/young adult T-lymphoblastic leukemia/lymphoma: a 10-year review from a single cytogenetic laboratory. Genes Chromosomes Cancer. 2018;57(11):541–6. Peterson JF, Baughn LB, Pearce KE, Williamson CM, Benevides Demasi JC, Olson RM, Goble TA, Meyer RG, Greipp PT, Ketterling RP. KMT2A (MLL) rearrangements observed in pediatric/young adult T-lymphoblastic leukemia/lymphoma: a 10-year review from a single cytogenetic laboratory. Genes Chromosomes Cancer. 2018;57(11):541–6.
24.
go back to reference Saarinen S, Kaasinen E, Karjalainen-Lindsberg ML, Vesanen K, Aavikko M, Katainen R, Taskinen M, Kytola S, Leppa S, Hietala M, et al. Primary mediastinal large B-cell lymphoma segregating in a family: exome sequencing identifies MLL as a candidate predisposition gene. Blood. 2013;121(17):3428–30. Saarinen S, Kaasinen E, Karjalainen-Lindsberg ML, Vesanen K, Aavikko M, Katainen R, Taskinen M, Kytola S, Leppa S, Hietala M, et al. Primary mediastinal large B-cell lymphoma segregating in a family: exome sequencing identifies MLL as a candidate predisposition gene. Blood. 2013;121(17):3428–30.
25.
go back to reference Gotlib J. World Health Organization-defined eosinophilic disorders: 2017 update on diagnosis, risk stratification, and management. Am J Hematol. 2017;92(11):1243–59. Gotlib J. World Health Organization-defined eosinophilic disorders: 2017 update on diagnosis, risk stratification, and management. Am J Hematol. 2017;92(11):1243–59.
26.
go back to reference Andersen CL, Siersma VD, Hasselbalch HC, Vestergaard H, Mesa R, Felding P, Olivarius ND, Bjerrum OW. Association of the blood eosinophil count with hematological malignancies and mortality. Am J Hematol. 2015;90(3):225–9. Andersen CL, Siersma VD, Hasselbalch HC, Vestergaard H, Mesa R, Felding P, Olivarius ND, Bjerrum OW. Association of the blood eosinophil count with hematological malignancies and mortality. Am J Hematol. 2015;90(3):225–9.
27.
go back to reference Anastasi J. The myeloproliferative neoplasms including the eosinophilia-related myeloproliferations associated with tyrosine kinase mutations: changes and issues in classification and diagnosis criteria. Semin Diagn Pathol. 2011;28(4):304–13. Anastasi J. The myeloproliferative neoplasms including the eosinophilia-related myeloproliferations associated with tyrosine kinase mutations: changes and issues in classification and diagnosis criteria. Semin Diagn Pathol. 2011;28(4):304–13.
28.
go back to reference Chen W, Li Q, Hudson WA, Kumar A, Kirchhof N, Kersey JH. A murine Mll-AF4 knock-in model results in lymphoid and myeloid deregulation and hematologic malignancy. Blood. 2006;108(2):669–77. Chen W, Li Q, Hudson WA, Kumar A, Kirchhof N, Kersey JH. A murine Mll-AF4 knock-in model results in lymphoid and myeloid deregulation and hematologic malignancy. Blood. 2006;108(2):669–77.
Metadata
Title
A novel deletion mutation in KMT2A identified in a child with ID/DD and blood eosinophilia
Authors
Haixia Zhang
Bingwu Xiang
Hui Chen
Xiang Chen
Tao Cai
Publication date
01-12-2019
Publisher
BioMed Central
Published in
BMC Medical Genetics / Issue 1/2019
Electronic ISSN: 1471-2350
DOI
https://doi.org/10.1186/s12881-019-0776-0

Other articles of this Issue 1/2019

BMC Medical Genetics 1/2019 Go to the issue