Genes & Genomics

, Volume 39, Issue 4, pp 417–422 | Cite as

Whole-exome sequencing in Tricho-rhino-phalangeal syndrome (TRPS) type I in a Korean family

Research Article

Abstract

Tricho-rhino-phalangeal syndrome (TRPS) is a rare autosomal dominant and monogenic disease. Among three types of TRPS, it is known that TRPS type I and type III are caused by deletions or substitutions in the TRPS1 gene, located on chromosome 8 (8q23.3). Although the mutations in TRPS1 gene are responsible for human TRPS, some cases are not detected by the mutations of TRPS1 gene and several cases are presented with different genetic variations. The present case was a sporadic and without TRPS1 mutation. Therefore, we performed whole-exome sequencing (WES) with one patient and his family (father, mother, and brother) and validated novel mutations using PCR and Sanger sequencing. Through family-based WES, we found the two de novo mutations such as ZNF 134 and EXD 3 genes. Through functional effect prediction using disease association Ensembl database, we propose that the de novo mutation of ZNF134 (p.Ser207Arg) could be one of potential candidate genes for causing TRPS and develope the TRPS phenotype in the present case.

Keywords

TRPS1 Next generation sequencing Whole-exome sequencing ZNF134 EXD3 Tricho-rhino-phalangeal syndrome 

Abbreviations

TRPS

Tricho-rhino-phalangeal syndrome

NGS

Next-generation sequencing

WES

Whole-exome sequencing

EXD3

Exonuclease 3′–5′ domain containing 3

ZNF134

Zinc finger protein 134

SNVs

Single-nucleotide variants

InDels

Insertions/deletions

UTR

Untranslated region

Supplementary material

13258_2016_508_MOESM1_ESM.jpg (55 kb)
Supplementary Fig. 1 TRPS1 gene interaction network by GeneMANIA Co-expression, physical interactions, co-localization, genetic interactions, shared protein domains, and pathway with TRPS1 gene show purple, pink, blue, green, gray-yellow, and light blue lines, respectively (JPG 55 KB)
13258_2016_508_MOESM2_ESM.xlsx (15 kb)
Supplementary material 2 (XLSX 15 KB)

References

  1. Chen LH, Ning CC, Chao SC (2010) Mutations in TRPS1 gene in trichorhinophalangeal syndrome type I in Asian patients. Br J Dermatol 163:416–419CrossRefPubMedGoogle Scholar
  2. Cheon CK, Sohn YB, Ko JM, Lee YJ, Song JS, Moon JW, Yang BK, Ha IS, Bae EJ, Jin HS et al (2014) Identification of KMT2D and KDM6A mutations by exome sequencing in Korean patients with Kabuki syndrome. J Hum Genet 59:321–325CrossRefPubMedGoogle Scholar
  3. Hatamura I, Kanauchi Y, Takahara M, Fujiwara M, Muragaki Y, Ooshima A, Ogino T (2001) A nonsense mutation in TRPS1 in a Japanese family with tricho-rhino-phalangeal syndrome type I. Clin Genet 59:366–367CrossRefPubMedGoogle Scholar
  4. Jin HS, Lee JB, Kim K, Lee KY, Choi VN, Kim JS, Jeong SY, Yim SY (2014) Identification of the rare compound heterozygous variants in the NEB gene in a Korean family with intellectual disability, epilepsy and early-childhood-onset generalized muscle weakness. J Hum Genet 59:643–647CrossRefPubMedGoogle Scholar
  5. Ketting RF, Haverkamp TH, van Luenen HG, Plasterk RH (1999) Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99:133–141CrossRefPubMedGoogle Scholar
  6. Kobayashi H, Hino M, Shimodahira M, Iwakura T, Ishihara T, Ikekubo K, Ogawa Y, Nakao K, Kurahachi H (2002) Missense mutation of TRPS1 in a family of tricho-rhino-phalangeal syndrome type III. Am J Med Genet 107:26–29CrossRefPubMedGoogle Scholar
  7. Ku CS, Naidoo N, Pawitan Y (2011) Revisiting Mendelian disorders through exome sequencing. Hum Genet 129:351–370CrossRefPubMedGoogle Scholar
  8. Ludecke HJ, Schaper J, Meinecke P, Momeni P, Gross S, von Holtum D, Hirche H, Abramowicz MJ, Albrecht B, Apacik C et al (2001) Genotypic and phenotypic spectrum in tricho-rhino-phalangeal syndrome types I and III. Am J Hum Genet 68:81–91CrossRefPubMedGoogle Scholar
  9. Momeni P, Glockner G, Schmidt O, von Holtum D, Albrecht B, Gillessen-Kaesbach G, Hennekam R, Meinecke P, Zabel B, Rosenthal A et al (2000) Mutations in a new gene, encoding a zinc-finger protein, cause tricho-rhino-phalangeal syndrome type I. Nat Genet 24:71–74CrossRefPubMedGoogle Scholar
  10. Nan X, Dai S, Li CT, Chen XR, Zhao HS, Zhang FS, Song QH (2013) Novel deletion mutation of TRPS1 gene in a Chinese patient of trichorhinophalangeal syndrome type I. Gene 523:88–91CrossRefPubMedGoogle Scholar
  11. Piccione M, Niceta M, Antona V, Di Fiore A, Cariola F, Gentile M, Corsello G (2009) Identification of two new mutations in TRPS 1 gene leading to the tricho-rhino-phalangeal syndrome type I and III. Am J Med Genet A 149A:1837–1841CrossRefPubMedGoogle Scholar
  12. Tommerup N, Vissing H (1995) Isolation and fine mapping of 16 novel human zinc finger-encoding cDNAs identify putative candidate genes for developmental and malignant disorders. Genomics 27:259–264CrossRefPubMedGoogle Scholar
  13. Zhou S, Jin D, Song Y (2013) Identification of a new mutation in TRPS1 gene leading to tricho-rhino-phalangeal syndrome I in a Chinese patient. J Dermatol 40:277–278CrossRefPubMedGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2016

Authors and Affiliations

  1. 1.Department of Nanobiomedical ScienceDankook UniversityCheonanRepublic of Korea
  2. 2.BK21 PLUS NBM Global Research Center for RegenerativeDankook UniversityCheonanRepublic of Korea
  3. 3.DKU-Theragen Institute for NGS Analysis (DTiNa)CheonanRepublic of Korea
  4. 4.Department of Microbiology, College of Natural ScienceDankook UniversityCheonanRepublic of Korea
  5. 5.Department of Dermatology, College of MedicineDankook UniversityCheonanRepublic of Korea

Personalised recommendations