Skip to main content
Top
Published in: BMC Medical Genetics 1/2017

Open Access 01-12-2017 | Case report

Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration

Authors: Zöe Powis, Alexa Hart, Sara Cherny, Igor Petrik, Erika Palmaer, Sha Tang, Carolyn Jones

Published in: BMC Medical Genetics | Issue 1/2017

Login to get access

Abstract

Background

Diagnostic Exome Sequencing (DES) has been shown to be an effective tool for diagnosis individuals with suspected genetic conditions.

Case Presentation

We report a male infant born with multiple anomalies including bilateral dysplastic kidneys, cleft palate, bilateral talipes, and bilateral absence of thumbs and first toes. Prenatal testing including chromosome analysis and microarray did not identify a cause for the multiple congenital anomalies. Postnatal diagnostic exome studies (DES) were utilized to find a molecular diagnosis for the patient.
Exome sequencing of the proband, mother, and father showed a previously unreported maternally inherited RNA binding motif protein 10 (RBM10) c.1352_1353delAG (p.E451Vfs*66) alteration. Mutations in RBM10 are associated with TARP syndrome, an X-linked recessive disorder originally described with cardinal features of talipes equinovarus, atrial septal defect, Robin sequence, and persistent left superior vena cava.

Conclusion

DES established a molecular genetic diagnosis of TARP syndrome for a neonatal patient with a poor prognosis in whom traditional testing methods were uninformative and allowed for efficient diagnosis and future reproductive options for the parents. Other reported cases of TARP syndrome demonstrate significant variability in clinical phenotype. The reported features in this infant including multiple hemivertebrae, imperforate anus, aplasia of thumbs and first toes have not been reported in previous patients, thus expanding the clinical phenotype for this rare disorder.
Appendix
Available only for authorised users
Literature
1.
go back to reference Directors ABo. Points to consider in the clinical application of genomic sequencing. Genet Med. 2012;14((8):759–61. Directors ABo. Points to consider in the clinical application of genomic sequencing. Genet Med. 2012;14((8):759–61.
2.
go back to reference Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010;11(6):R62.CrossRefPubMedPubMedCentral Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010;11(6):R62.CrossRefPubMedPubMedCentral
3.
go back to reference Beaulieu CL, Majewski J, Schwartzentruber J, Samuels ME, Fernandez BA, Bernier FP, Brudno M, Knoppers B, Marcadier J, Dyment D, et al. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am J Hum Genet. 2014;94(6):809–17.CrossRefPubMedPubMedCentral Beaulieu CL, Majewski J, Schwartzentruber J, Samuels ME, Fernandez BA, Bernier FP, Brudno M, Knoppers B, Marcadier J, Dyment D, et al. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am J Hum Genet. 2014;94(6):809–17.CrossRefPubMedPubMedCentral
4.
go back to reference Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Davis BT, Baxter RM, Zeng W, Mroske C, Parra MC, et al. Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med. 2014;17(7):578–86.CrossRefPubMed Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Davis BT, Baxter RM, Zeng W, Mroske C, Parra MC, et al. Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med. 2014;17(7):578–86.CrossRefPubMed
5.
go back to reference Iglesias A, Anyane-Yeboa K, Wynn J, Wilson A, Truitt Cho M, Guzman E, Sisson R, Egan C, Chung WK. The usefulness of whole-exome sequencing in routine clinical practice. Genet Med. 2014;16(12):922–31.CrossRefPubMed Iglesias A, Anyane-Yeboa K, Wynn J, Wilson A, Truitt Cho M, Guzman E, Sisson R, Egan C, Chung WK. The usefulness of whole-exome sequencing in routine clinical practice. Genet Med. 2014;16(12):922–31.CrossRefPubMed
6.
go back to reference Soden S, Saunders CJ, Willig LK, FArrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddle DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Trans Med. 2014;6(265):265ra168.CrossRef Soden S, Saunders CJ, Willig LK, FArrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddle DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Trans Med. 2014;6(265):265ra168.CrossRef
7.
go back to reference Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011;13(3):255–62.CrossRefPubMed Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011;13(3):255–62.CrossRefPubMed
8.
go back to reference Yang JW, Han JY, Seong MW, Sung JJ, Park SS, Lee KW. Hereditary Spastic Paraplegia with a Novel SPAST Mutation Misdiagnosed with Subacute Combined Degeneration. Experimental neurobiology. 2013;22(2):128–31.CrossRefPubMedPubMedCentral Yang JW, Han JY, Seong MW, Sung JJ, Park SS, Lee KW. Hereditary Spastic Paraplegia with a Novel SPAST Mutation Misdiagnosed with Subacute Combined Degeneration. Experimental neurobiology. 2013;22(2):128–31.CrossRefPubMedPubMedCentral
10.
go back to reference Bhattacharjee A, Sokolsky T, Wyman, S.K. Reese, M.G. Puffenberger E, Strauss K, Morton H. Parad R.B. Naylor, E.W. Development of DNA Confirmatory and High-Risk Diagnostic Testing for Newborns Using Targeted Next-Generation DNA Sequencing. Genetics in Medicine 2014(doi:10.1038/gim.2014.117):11. Bhattacharjee A, Sokolsky T, Wyman, S.K. Reese, M.G. Puffenberger E, Strauss K, Morton H. Parad R.B. Naylor, E.W. Development of DNA Confirmatory and High-Risk Diagnostic Testing for Newborns Using Targeted Next-Generation DNA Sequencing. Genetics in Medicine 2014(doi:10.​1038/​gim.​2014.​117):​11.
11.
go back to reference Might M, Wilsey, M. The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated. Genet Med. 2014;doi:10.1038/gim.2014.23:2. Might M, Wilsey, M. The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated. Genet Med. 2014;doi:10.​1038/​gim.​2014.​23:​2.
12.
go back to reference Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014;312(18):1870–9.CrossRefPubMedPubMedCentral Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA. 2014;312(18):1870–9.CrossRefPubMedPubMedCentral
13.
go back to reference Alamillo CL, Powis Z, Farwell K, Shahmirzadi L, Weltmer EC, Turocy J, Lowe T, Kobelka C, Chen E, Basel D, et al. Exome sequencing positively identified relevant alterations in more than half of cases with an indication of prenatal ultrasound anomalies. Prenat Diagn. 2015;35(11):1073–8.CrossRefPubMed Alamillo CL, Powis Z, Farwell K, Shahmirzadi L, Weltmer EC, Turocy J, Lowe T, Kobelka C, Chen E, Basel D, et al. Exome sequencing positively identified relevant alterations in more than half of cases with an indication of prenatal ultrasound anomalies. Prenat Diagn. 2015;35(11):1073–8.CrossRefPubMed
14.
go back to reference Carss KJHS, Parthiban V, McMullan DJ, Maher ER, Kilby MD, Hurles ME. Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound. Hum Mol Genet. 2014;23(12):9.CrossRef Carss KJHS, Parthiban V, McMullan DJ, Maher ER, Kilby MD, Hurles ME. Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound. Hum Mol Genet. 2014;23(12):9.CrossRef
15.
go back to reference Westerfield LE, Stover SR, Mathur VS, Nassef SA, Carter TG, Yang Y, Eng CM, Van den Veyver IB. Reproductive genetic counseling challenges associated with diagnostic exome sequencing in a large academic private reproductive genetic counseling practice. Prenat Diagn. 2015;35(10):1022–9.CrossRefPubMed Westerfield LE, Stover SR, Mathur VS, Nassef SA, Carter TG, Yang Y, Eng CM, Van den Veyver IB. Reproductive genetic counseling challenges associated with diagnostic exome sequencing in a large academic private reproductive genetic counseling practice. Prenat Diagn. 2015;35(10):1022–9.CrossRefPubMed
16.
go back to reference Farwell Gonzalez KD, Li X, Lu HM, Lu H, Pellegrino JE, Miller RT, Zeng W, Chao EC. Diagnostic Exome Sequencing and Tailored Bioinformatics of the Parents of a Deceased Child with Cobalamin Deficiency Suggests Digenic Inheritance of the MTR and LMBRD1 Genes. JIMD Rep. 2015;15:29–37.PubMed Farwell Gonzalez KD, Li X, Lu HM, Lu H, Pellegrino JE, Miller RT, Zeng W, Chao EC. Diagnostic Exome Sequencing and Tailored Bioinformatics of the Parents of a Deceased Child with Cobalamin Deficiency Suggests Digenic Inheritance of the MTR and LMBRD1 Genes. JIMD Rep. 2015;15:29–37.PubMed
17.
go back to reference Butterfield RJ, Stevenson TJ, Xing L, Newcomb TM, Nelson B, Zeng W, Li X, Lu HM, Lu H, Farwell Gonzalez KD, et al. Congenital lethal motor neuron disease with a novel defect in ribosome biogenesis. Neurology. 2014;82(15):1322–30.CrossRefPubMedPubMedCentral Butterfield RJ, Stevenson TJ, Xing L, Newcomb TM, Nelson B, Zeng W, Li X, Lu HM, Lu H, Farwell Gonzalez KD, et al. Congenital lethal motor neuron disease with a novel defect in ribosome biogenesis. Neurology. 2014;82(15):1322–30.CrossRefPubMedPubMedCentral
18.
go back to reference Gandomi SK, Farwell Gonzalez KD, Parra M, Shahmirzadi L, Mancuso J, Pichurin P, Temme R, Dugan S, Zeng W, Tang S. Diagnostic exome sequencing identifies two novel IQSEC2 mutations associated with X-linked intellectual disability with seizures: implications for genetic counseling and clinical diagnosis. J Genet Couns. 2014;23(3):289–98.CrossRefPubMed Gandomi SK, Farwell Gonzalez KD, Parra M, Shahmirzadi L, Mancuso J, Pichurin P, Temme R, Dugan S, Zeng W, Tang S. Diagnostic exome sequencing identifies two novel IQSEC2 mutations associated with X-linked intellectual disability with seizures: implications for genetic counseling and clinical diagnosis. J Genet Couns. 2014;23(3):289–98.CrossRefPubMed
19.
go back to reference Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865–71.CrossRefPubMedPubMedCentral Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865–71.CrossRefPubMedPubMedCentral
20.
go back to reference Laduca H, Stuenkel AJ, Dolinsky JS, Keiles S, Tandy S, Pesaran T, Chen E, Gau CL, Palmaer E, Shoaepour K, et al. Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients. Genet Med. 2014;16(11):830–7.CrossRefPubMedPubMedCentral Laduca H, Stuenkel AJ, Dolinsky JS, Keiles S, Tandy S, Pesaran T, Chen E, Gau CL, Palmaer E, Shoaepour K, et al. Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients. Genet Med. 2014;16(11):830–7.CrossRefPubMedPubMedCentral
21.
go back to reference International HapMap C. The International HapMap Project. Nature. 2003;426(6968):789–96.CrossRef International HapMap C. The International HapMap Project. Nature. 2003;426(6968):789–96.CrossRef
23.
go back to reference Callebaut I, Mornon JP. OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats. Bioinformatics. 2005;21(6):699–702.CrossRefPubMed Callebaut I, Mornon JP. OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats. Bioinformatics. 2005;21(6):699–702.CrossRefPubMed
24.
go back to reference Bonnal S, Martinez C, Forch P, Bachi A, Wilm M, Valcarcel J. RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition. Mol Cell. 2008;32(1):81–95.CrossRefPubMed Bonnal S, Martinez C, Forch P, Bachi A, Wilm M, Valcarcel J. RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition. Mol Cell. 2008;32(1):81–95.CrossRefPubMed
25.
go back to reference Mourao A, Bonnal S, Soni K, Warner L, Bordonne R, Valcarcel J, Sattler M. Structural basis for the recognition of spliceosomal SmN/B/B' proteins by the RBM5 OCRE domain in splicing regulation. Elife. 2016;29:5. Mourao A, Bonnal S, Soni K, Warner L, Bordonne R, Valcarcel J, Sattler M. Structural basis for the recognition of spliceosomal SmN/B/B' proteins by the RBM5 OCRE domain in splicing regulation. Elife. 2016;29:5.
26.
go back to reference Johnston JJ, Sapp JC, Curry C, Horton M, Leon E, Cusmano-Ozog K, Dobyns WB, Hudgins L, Zackai E, Biesecker LG. Expansion of the TARP syndrome phenotype associated with de novo mutations and mosaicism. Am J Med Genet A. 2014;164A(1):120–8.CrossRefPubMed Johnston JJ, Sapp JC, Curry C, Horton M, Leon E, Cusmano-Ozog K, Dobyns WB, Hudgins L, Zackai E, Biesecker LG. Expansion of the TARP syndrome phenotype associated with de novo mutations and mosaicism. Am J Med Genet A. 2014;164A(1):120–8.CrossRefPubMed
27.
go back to reference Inoue A, Yamamoto N, Kimura M, Nishio K, Yamane H, Nakajima K. RBM10 regulates alternative splicing. FEBS Lett. 2014;588(6):942–7.CrossRefPubMed Inoue A, Yamamoto N, Kimura M, Nishio K, Yamane H, Nakajima K. RBM10 regulates alternative splicing. FEBS Lett. 2014;588(6):942–7.CrossRefPubMed
28.
go back to reference Gorlin RJ, Cervenka J, Anderson RC, Sauk JJ, Bevis WD. Robin's syndrome. A probably X-linked recessive subvariety exhibiting persistence of left superior vena cava and atrial septal defect. Am J Dis Child. 1970;119(2):176–8.CrossRefPubMed Gorlin RJ, Cervenka J, Anderson RC, Sauk JJ, Bevis WD. Robin's syndrome. A probably X-linked recessive subvariety exhibiting persistence of left superior vena cava and atrial septal defect. Am J Dis Child. 1970;119(2):176–8.CrossRefPubMed
29.
go back to reference Gripp KW, Hopkins E, Johnston JJ, Krause C, Dobyns WB, Biesecker LG. Long-term survival in TARP syndrome and confirmation of RBM10 as the disease-causing gene. Am J Med Genet A. 2011;155A(10):2516–20.CrossRefPubMed Gripp KW, Hopkins E, Johnston JJ, Krause C, Dobyns WB, Biesecker LG. Long-term survival in TARP syndrome and confirmation of RBM10 as the disease-causing gene. Am J Med Genet A. 2011;155A(10):2516–20.CrossRefPubMed
Metadata
Title
Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration
Authors
Zöe Powis
Alexa Hart
Sara Cherny
Igor Petrik
Erika Palmaer
Sha Tang
Carolyn Jones
Publication date
01-12-2017
Publisher
BioMed Central
Published in
BMC Medical Genetics / Issue 1/2017
Electronic ISSN: 1471-2350
DOI
https://doi.org/10.1186/s12881-017-0426-3

Other articles of this Issue 1/2017

BMC Medical Genetics 1/2017 Go to the issue