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Tidwell T, Deshotel M, Palumbos J, Miller C, Bayrak-Toydemir P, Carey JC. Novel de novo ARCN1 intronic variant causes rhizomelic short stature with microretrognathia and developmental delay. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005728. [PMID: 33154040 PMCID: PMC7784487 DOI: 10.1101/mcs.a005728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
The archain 1 (ARCN1) gene encodes the coatomer subunit delta protein and is a component of the COPI coatomer complex, which is involved in retrograde vesical trafficking from the Golgi complex to the endoplasmic reticulum. Variants in ARCN1 have recently been associated with rhizomelic short stature with microcephaly, microretrognathia, and developmental delay. Here we report a 3.5-yr-old boy with microcephaly, global developmental delay, and multiple congenital abnormalities and the ARCN1-related syndrome caused by a novel de novo intronic variant. Whole-exome sequencing of the proband and his parents was utilized to determine the genetic origin of the patient's disorder and identified a de novo variant, NM_001655.5:c.654-15A > G, in the ARCN1 gene. Follow-up functional characterization of mRNA from the patient demonstrated that this variant creates a splicing defect of the ARCN1 mRNA. ARCN1-related syndrome represents an emerging disorder of developmental delay, and this report represents the sixth described patient. Despite the few instances reported in literature, the phenotype is consistent between our patient and previously reported individuals.
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Affiliation(s)
| | | | - Janice Palumbos
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
| | - Chris Miller
- ARUP Laboratories, Salt Lake City, Utah 84108, USA
| | - Pinar Bayrak-Toydemir
- ARUP Laboratories, Salt Lake City, Utah 84108, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84113, USA
| | - John C Carey
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
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Zepeda-Mendoza CJ, Cousin MA, Basu S, Jenkinson G, Oliver G, Pittock ST, Baughn LB, Klee EW, Babovic-Vuksanovic D. An intragenic duplication of TRPS1 leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004655. [PMID: 31662300 PMCID: PMC6913153 DOI: 10.1101/mcs.a004655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Trichorhinophalangeal syndrome type I (TRPSI) is a rare disorder that causes distinctive ectodermal, facial, and skeletal features affecting the hair (tricho-), nose (rhino-), and fingers and toes (phalangeal) and is inherited in an autosomal dominant pattern. TRPSI is caused by loss of function variants in TRPS1, involved in the regulation of chondrocyte and perichondrium development. Pathogenic variants in TRPS1 include missense mutations and deletions with variable breakpoints, with only a single instance of an intragenic duplication reported to date. Here we report an affected individual presenting with a classic TRPSI phenotype who is heterozygous for a de novo intragenic ∼36.3-kbp duplication affecting exons 2–4 of TRPS1. Molecular analysis revealed the duplication to be in direct tandem orientation affecting the splicing of TRPS1. The aberrant transcripts are predicted to produce a truncated TRPS1 missing the nuclear localization signal and the GATA and IKAROS-like zinc-finger domains resulting in functional TRPS1 haploinsufficiency. Our study identifies a novel intragenic tandem duplication of TRPS1 and highlights the importance of molecular characterization of intragenic duplications.
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Affiliation(s)
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gavin Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Siobhan T Pittock
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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3
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Allanson J, Smith A, Forzano F, Lin AE, Raas-Rothschild A, Howley HE, Boycott KM. Nablus syndrome: Easy to diagnose yet difficult to solve. Am J Med Genet C Semin Med Genet 2019; 178:447-457. [PMID: 30580486 DOI: 10.1002/ajmg.c.31660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022]
Abstract
Nablus syndrome was first described by the late Ahmad Teebi in 2000, and 13 individuals have been reported to date. Nablus syndrome can be clinically diagnosed based on striking facial features, including tight glistening skin with reduced facial expression, blepharophimosis, telecanthus, bulky nasal tip, abnormal external ear architecture, upswept frontal hairline, and sparse eyebrows. However, the precise genetic etiology for this rare condition remains elusive. Comparative microarray analyses of individuals with Nablus syndrome (including two mother-son pairs) reveal an overlapping 8q22.1 microdeletion, with a minimal critical region of 1.84 Mb (94.43-96.27 Mb). Whereas this deletion is present in all affected individuals, 13 individuals without Nablus syndrome (including two mother-child pairs) also have the 8q22.1 microdeletion that partially or fully overlaps the minimal critical region. Thus, the 8q22.1 microdeletion is necessary but not sufficient to cause the clinical features characteristic of Nablus syndrome. We discuss possible explanations for Nablus syndrome, including one-locus, two-locus, epigenetic, and environmental mechanisms. We performed exome sequencing for five individuals with Nablus syndrome. Although we failed to identify any deleterious rare coding variants in the critical region that were shared between individuals, we did identify one common SNP in an intronic region that was shared. Clearly, unraveling the genetic mechanism(s) of Nablus syndrome will require additional investigation, including genomic and RNA sequencing of a larger cohort of affected individuals. If successful, it will provide important insights into fundamental concepts such as variable expressivity, incomplete penetrance, and complex disease relevant to both Mendelian and non-Mendelian disorders.
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Affiliation(s)
| | - Amanda Smith
- Department of Genetics, CHEO, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine University of Ottawa, Ottawa, Ontario, Canada
| | - Francesca Forzano
- Department of Clinical Genetics, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust London, London, United Kingdom.,Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - Angela E Lin
- Genetics Unit, MassGeneral Hospital for Children, Boston, Massachusetts
| | - Annick Raas-Rothschild
- Institute of Rare Disease, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Heather E Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Department of Genetics, CHEO, Ottawa, Ontario, Canada.,CHEO Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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