Exome sequencing identifies a de novo frameshift mutation in the imprinted gene ZDBF2 in a sporadic patient with Nasopalpebral Lipoma-coloboma syndrome
Nasopalpebral lipoma‐coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have b...
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| Published in | American journal of medical genetics. Part A Vol. 170A; no. 7; pp. 1934 - 1937 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Blackwell Publishing Ltd
01.07.2016
Wiley Subscription Services, Inc |
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| Online Access | Get full text |
| ISSN | 1552-4825 1552-4833 1552-4833 |
| DOI | 10.1002/ajmg.a.37683 |
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| Abstract | Nasopalpebral lipoma‐coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have been associated with familial or sporadic NPLCS cases and the etiology of the disease remains unknown. In this work, the results of whole exome sequencing in a sporadic NPLCS patient are presented. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in ZDBF2 (zinc finger, DBF‐type containing 2), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases. This is the first genetic variant identified in a NPLCS patient and evidence supporting the pathogenicity of the identified mutation is discussed. © 2016 Wiley Periodicals, Inc. |
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| AbstractList | Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM% 167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have been associated with familial or sporadic NPLCS cases and the etiology of the disease remains unknown. In this work, the results of whole exome sequencing in a sporadic NPLCS patient are presented. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in
ZDBF2
(
zinc finger, DBF-type containing 2
), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases. This is the first genetic variant identified in a NPLCS patient and evidence supporting the pathogenicity of the identified mutation is discussed. Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have been associated with familial or sporadic NPLCS cases and the etiology of the disease remains unknown. In this work, the results of whole exome sequencing in a sporadic NPLCS patient are presented. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in ZDBF2 (zinc finger, DBF-type containing 2), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases. This is the first genetic variant identified in a NPLCS patient and evidence supporting the pathogenicity of the identified mutation is discussed. © 2016 Wiley Periodicals, Inc. Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have been associated with familial or sporadic NPLCS cases and the etiology of the disease remains unknown. In this work, the results of whole exome sequencing in a sporadic NPLCS patient are presented. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in ZDBF2 (zinc finger, DBF-type containing 2), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases. This is the first genetic variant identified in a NPLCS patient and evidence supporting the pathogenicity of the identified mutation is discussed. © 2016 Wiley Periodicals, Inc.Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have been associated with familial or sporadic NPLCS cases and the etiology of the disease remains unknown. In this work, the results of whole exome sequencing in a sporadic NPLCS patient are presented. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in ZDBF2 (zinc finger, DBF-type containing 2), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases. This is the first genetic variant identified in a NPLCS patient and evidence supporting the pathogenicity of the identified mutation is discussed. © 2016 Wiley Periodicals, Inc. |
| Author | Piña-Aguilar, Raul E. You, Jing Chacón-Camacho, Oscar F. Villegas-Ruiz, Vanessa Sobreira, Nara Zenteno, Juan C. |
| AuthorAffiliation | 2 Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 1 Department of Genetics-Research Unit, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico 3 Division of Genomic Medicine, National Medical Center “20 de Noviembre”, ISSSTE, Mexico City, Mexico 4 Faculty of Medicine, Department of Biochemistry, National Autonomous University of Mexico (UNAM), Mexico City, Mexico |
| AuthorAffiliation_xml | – name: 2 Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland – name: 3 Division of Genomic Medicine, National Medical Center “20 de Noviembre”, ISSSTE, Mexico City, Mexico – name: 4 Faculty of Medicine, Department of Biochemistry, National Autonomous University of Mexico (UNAM), Mexico City, Mexico – name: 1 Department of Genetics-Research Unit, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico |
| Author_xml | – sequence: 1 givenname: Oscar F. surname: Chacón-Camacho fullname: Chacón-Camacho, Oscar F. organization: Department of Genetics-Research Unit, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico – sequence: 2 givenname: Nara surname: Sobreira fullname: Sobreira, Nara organization: Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Maryland, Baltimore – sequence: 3 givenname: Jing surname: You fullname: You, Jing organization: Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Maryland, Baltimore – sequence: 4 givenname: Raul E. surname: Piña-Aguilar fullname: Piña-Aguilar, Raul E. organization: Division of Genomic Medicine, National Medical Center "20 de Noviembre", ISSSTE, Mexico City, Mexico – sequence: 5 givenname: Vanessa surname: Villegas-Ruiz fullname: Villegas-Ruiz, Vanessa organization: Department of Genetics-Research Unit, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico – sequence: 6 givenname: Juan C. surname: Zenteno fullname: Zenteno, Juan C. email: Correspondence to:Dr. Juan C. Zenteno, Research Unit, Institute of Ophthalmology, "Conde de Valenciana," Chimalpopoca 14, Col. Obrera, Mexico City, CP 06800, Mexico., jczenteno@institutodeoftalmologia.org organization: Department of Genetics-Research Unit, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico |
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| Cites_doi | 10.1002/ajmg.a.35916 10.1038/ng.806 10.1093/bioinformatics/btp324 10.1101/gr.107524.110 10.1007/s00238-003-0523-8 10.1101/gad.232058.113 10.1016/j.ygeno.2008.12.012 10.4103/0301-4738.83615 10.1093/bioinformatics/btp352 10.1111/j.1399-0004.1991.tb03106.x 10.1016/j.febslet.2012.01.059 10.1002/humu.22769 10.1002/ajmg.1320110404 10.1001/jama.2014.6511 |
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| Keywords | ZDBF2 nasopalpebral lipoma exome sequencing coloboma |
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| References | SIGMA Type 2 Diabetes Consortium, Estrada K, Aukrust I, Bjørkhaug L, Burtt NP, Mercader JM, García-Ortiz H, Huerta-Chagoya A, Moreno-Macías H, Walford G, Flannick J, Williams AL, Gómez-Vázquez MJ, Fernandez-Lopez JC, Martínez-Hernández A, Centeno-Cruz F, Mendoza-Caamal E, Revilla-Monsalve C, Islas-Andrade S, Córdova EJ, Soberón X, González-Villalpando ME, Henderson E, Wilkens LR, Le Marchand L, Arellano-Campos O, Ordóñez-Sánchez ML, Rodríguez-Torres M, Rodríguez-Guillén R, Riba L, Najmi LA, Jacobs SB, Fennell T, Gabriel S, Fontanillas P, Hanis CL, Lehman DM, Jenkinson CP, Abboud HE, Bell GI, Cortes ML, Boehnke M, González-Villalpando C, Orozco L, Haiman CA, Tusié-Luna T, Aguilar-Salinas CA, Altshuler D, Njølstad PR, Florez JC, MacArthur DG, Jiménez-Morales S. 2014. Association of a low-frequency variant in HNF1A with type 2 diabetes in a Latino population. JAMA 311:2305-2314. Kobayashi H, Yamada K, Morita S, Hiura H, Fukuda A, Kagami M, Ogata T, Hata K, Sotomaru Y, Kono T. 2009. Identification of the mouse paternally expressed imprinted gene ZDBF2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2. Genomics 93:461-472. Duffie R, Ajjan S, Greenberg MV, Zamudio N, Escamilla del Arenal M, Iranzo J, Okamoto I, Barbaux S, Fauque P, Bourc'his D. 2014. The Gpr1/ZDBF2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals. Genes Dev 28:463-478. Bock-Kunz AL, Lyon DB, Singhal VK, Grin TR. 2000. Nasopalpebral lipoma-coloboma. Arch Ophthalmol 118:1699-1701. Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. 2015. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and genematcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat 36:425-431. Babu NS, Raviprakash D, Kumar R. 2011. Nasopalpebral lipoma coloboma syndrome. Indian J Ophthalmol 59:379-380. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498. Penchaszadeh VB, Velasquez D, Arrivillaga R. 1982. The nasopalpebral lipoma-coloboma syndrome: A new autosomal dominant dysplasia malformation syndrome with congenital nasopalpebral lipomas, eyelid colobomas, telecanthus, and maxillary hypoplasia. Am J Med Genet 11:397-410. Kobayashi H, Sakurai T, Sato S, Nakabayashi K, Hata K, Kono T. 2012. Imprinted DNA methylation reprogramming during early mouse embryogenesis at the Gpr1-ZDBF2 locus is linked to long cis-intergenic transcription. FEBS Lett 586:827-833. Akarsu AN, Sayli BS. 1991. Nasopalpebral lipoma-coloboma syndrome. Clin Genet 40:342-344. Moreira Gonzalez A, Jackson IT. 2003. Surgical correction of the nasopalpebral lipoma-coloboma syndrome. Eur J Plast Surg 26:263-267. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. Chacon-Camacho OF, Lopez-Martinez MS, Vázquez J, Nava-Castañeda A, Martin-Biasotti F, Piña-Aguilar RE, Iñiguez-Soto M, Acosta-García J, Zenteno JC. 2013. Nasopalpebral lipoma-coloboma syndrome: Clinical, radiological, and histopathological description of a novel sporadic case. Am J Med Genet A 161A:1470-1474. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. 2009; 25 2010; 20 2015; 36 2012; 586 2009; 93 2000; 118 1991; 40 1982; 11 2003; 26 2011; 43 2011; 59 2013; 161A 2014; 28 2014; 311 e_1_2_6_10_1 e_1_2_6_9_1 e_1_2_6_8_1 Bock‐Kunz AL (e_1_2_6_4_1) 2000; 118 e_1_2_6_5_1 e_1_2_6_7_1 e_1_2_6_6_1 e_1_2_6_13_1 e_1_2_6_14_1 e_1_2_6_3_1 e_1_2_6_11_1 e_1_2_6_2_1 e_1_2_6_12_1 e_1_2_6_15_1 e_1_2_6_16_1 21836344 - Indian J Ophthalmol. 2011 Sep-Oct;59(5):379-80 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 24589776 - Genes Dev. 2014 Mar 1;28(5):463-78 20644199 - Genome Res. 2010 Sep;20(9):1297-303 19200453 - Genomics. 2009 May;93(5):461-72 22449967 - FEBS Lett. 2012 Mar 23;586(6):827-33 19505943 - Bioinformatics. 2009 Aug 15;25(16):2078-9 7091184 - Am J Med Genet. 1982 Apr;11(4):397-410 11115270 - Arch Ophthalmol. 2000 Dec;118(12 ):1699-701 23636874 - Am J Med Genet A. 2013 Jun;161A(6):1470-4 1756608 - Clin Genet. 1991 Nov;40(5):342-4 24915262 - JAMA. 2014 Jun 11;311(22):2305-14 21478889 - Nat Genet. 2011 May;43(5):491-8 25684268 - Hum Mutat. 2015 Apr;36(4):425-31 |
| References_xml | – reference: Duffie R, Ajjan S, Greenberg MV, Zamudio N, Escamilla del Arenal M, Iranzo J, Okamoto I, Barbaux S, Fauque P, Bourc'his D. 2014. The Gpr1/ZDBF2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals. Genes Dev 28:463-478. – reference: Kobayashi H, Yamada K, Morita S, Hiura H, Fukuda A, Kagami M, Ogata T, Hata K, Sotomaru Y, Kono T. 2009. Identification of the mouse paternally expressed imprinted gene ZDBF2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2. Genomics 93:461-472. – reference: Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. 2015. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and genematcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat 36:425-431. – reference: McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303. – reference: DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498. – reference: Akarsu AN, Sayli BS. 1991. Nasopalpebral lipoma-coloboma syndrome. Clin Genet 40:342-344. – reference: Kobayashi H, Sakurai T, Sato S, Nakabayashi K, Hata K, Kono T. 2012. Imprinted DNA methylation reprogramming during early mouse embryogenesis at the Gpr1-ZDBF2 locus is linked to long cis-intergenic transcription. FEBS Lett 586:827-833. – reference: Moreira Gonzalez A, Jackson IT. 2003. Surgical correction of the nasopalpebral lipoma-coloboma syndrome. Eur J Plast Surg 26:263-267. – reference: Bock-Kunz AL, Lyon DB, Singhal VK, Grin TR. 2000. Nasopalpebral lipoma-coloboma. Arch Ophthalmol 118:1699-1701. – reference: SIGMA Type 2 Diabetes Consortium, Estrada K, Aukrust I, Bjørkhaug L, Burtt NP, Mercader JM, García-Ortiz H, Huerta-Chagoya A, Moreno-Macías H, Walford G, Flannick J, Williams AL, Gómez-Vázquez MJ, Fernandez-Lopez JC, Martínez-Hernández A, Centeno-Cruz F, Mendoza-Caamal E, Revilla-Monsalve C, Islas-Andrade S, Córdova EJ, Soberón X, González-Villalpando ME, Henderson E, Wilkens LR, Le Marchand L, Arellano-Campos O, Ordóñez-Sánchez ML, Rodríguez-Torres M, Rodríguez-Guillén R, Riba L, Najmi LA, Jacobs SB, Fennell T, Gabriel S, Fontanillas P, Hanis CL, Lehman DM, Jenkinson CP, Abboud HE, Bell GI, Cortes ML, Boehnke M, González-Villalpando C, Orozco L, Haiman CA, Tusié-Luna T, Aguilar-Salinas CA, Altshuler D, Njølstad PR, Florez JC, MacArthur DG, Jiménez-Morales S. 2014. Association of a low-frequency variant in HNF1A with type 2 diabetes in a Latino population. JAMA 311:2305-2314. – reference: Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. – reference: Chacon-Camacho OF, Lopez-Martinez MS, Vázquez J, Nava-Castañeda A, Martin-Biasotti F, Piña-Aguilar RE, Iñiguez-Soto M, Acosta-García J, Zenteno JC. 2013. Nasopalpebral lipoma-coloboma syndrome: Clinical, radiological, and histopathological description of a novel sporadic case. Am J Med Genet A 161A:1470-1474. – reference: Penchaszadeh VB, Velasquez D, Arrivillaga R. 1982. The nasopalpebral lipoma-coloboma syndrome: A new autosomal dominant dysplasia malformation syndrome with congenital nasopalpebral lipomas, eyelid colobomas, telecanthus, and maxillary hypoplasia. Am J Med Genet 11:397-410. – reference: Babu NS, Raviprakash D, Kumar R. 2011. Nasopalpebral lipoma coloboma syndrome. Indian J Ophthalmol 59:379-380. – reference: Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. 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| Snippet | Nasopalpebral lipoma‐coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the... Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the... Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM% 167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the... |
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| SubjectTerms | Abnormalities, Multiple - genetics Abnormalities, Multiple - physiopathology Base Sequence - genetics Child, Preschool coloboma Coloboma - genetics Coloboma - physiopathology DNA-Binding Proteins - genetics Exome - genetics exome sequencing Eyelid Neoplasms - genetics Eyelid Neoplasms - physiopathology Female Frameshift Mutation Genomic Imprinting Humans Lipoma - genetics Lipoma - physiopathology nasopalpebral lipoma Pedigree ZDBF2 |
| Title | Exome sequencing identifies a de novo frameshift mutation in the imprinted gene ZDBF2 in a sporadic patient with Nasopalpebral Lipoma-coloboma syndrome |
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