GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome
Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Stan...
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| Published in | American journal of human genetics Vol. 104; no. 1; pp. 35 - 44 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
03.01.2019
Elsevier |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1, always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders. |
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| AbstractList | Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1, always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders. Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1, always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders.Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1, always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders. Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1 . We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1 , always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders. |
| Author | Kircher, Martin Sol-Church, Katia Kernan, Kelly Bamshad, Michael J. Anadiotis, George Dempsey, Jennifer C. LaCroix, Amy J. Akkari, Yassmine M. Robbins, Katherine M. Nickerson, Deborah A. Gripp, Karen W. Fagerstrom, Carrie Myers, Candace T. Doherty, Dan Adam, Margaret P. Mehaffey, Michele Baratela, Wagner A.R. Mefford, Heather C. Bober, Michael B. Stabley, Deborah Sahraoui, Rebecca Duker, Angela L. Miller, Daniel G. |
| AuthorAffiliation | 6 Legacy Health, Portland, OR 97227, USA 3 Biological Sciences, University of Delaware, Newark, DE 19716, USA 4 Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA 7 Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA 9 Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA 2 Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA 1 Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA 8 Instituto da Criança, Departamento de Pediatria, Universidade de São Paulo, São Paulo, SP Brazil 5 Seattle Children’s Hospital, Seattle, WA 98105, USA 10 Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA |
| AuthorAffiliation_xml | – name: 6 Legacy Health, Portland, OR 97227, USA – name: 1 Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – name: 7 Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – name: 5 Seattle Children’s Hospital, Seattle, WA 98105, USA – name: 8 Instituto da Criança, Departamento de Pediatria, Universidade de São Paulo, São Paulo, SP Brazil – name: 4 Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA – name: 9 Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA – name: 2 Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – name: 3 Biological Sciences, University of Delaware, Newark, DE 19716, USA – name: 10 Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA |
| Author_xml | – sequence: 1 givenname: Amy J. surname: LaCroix fullname: LaCroix, Amy J. organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 2 givenname: Deborah surname: Stabley fullname: Stabley, Deborah organization: Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 3 givenname: Rebecca surname: Sahraoui fullname: Sahraoui, Rebecca organization: Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 4 givenname: Margaret P. surname: Adam fullname: Adam, Margaret P. organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 5 givenname: Michele surname: Mehaffey fullname: Mehaffey, Michele organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 6 givenname: Kelly surname: Kernan fullname: Kernan, Kelly organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 7 givenname: Candace T. surname: Myers fullname: Myers, Candace T. organization: Seattle Children’s Hospital, Seattle, WA 98105, USA – sequence: 8 givenname: Carrie surname: Fagerstrom fullname: Fagerstrom, Carrie organization: Legacy Health, Portland, OR 97227, USA – sequence: 9 givenname: George surname: Anadiotis fullname: Anadiotis, George organization: Legacy Health, Portland, OR 97227, USA – sequence: 10 givenname: Yassmine M. surname: Akkari fullname: Akkari, Yassmine M. organization: Legacy Health, Portland, OR 97227, USA – sequence: 11 givenname: Katherine M. surname: Robbins fullname: Robbins, Katherine M. organization: Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 12 givenname: Karen W. surname: Gripp fullname: Gripp, Karen W. organization: Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 13 givenname: Wagner A.R. surname: Baratela fullname: Baratela, Wagner A.R. organization: Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 14 givenname: Michael B. surname: Bober fullname: Bober, Michael B. organization: Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 15 givenname: Angela L. surname: Duker fullname: Duker, Angela L. organization: Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA – sequence: 16 givenname: Dan surname: Doherty fullname: Doherty, Dan organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 17 givenname: Jennifer C. surname: Dempsey fullname: Dempsey, Jennifer C. organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 18 givenname: Daniel G. surname: Miller fullname: Miller, Daniel G. organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 19 givenname: Martin surname: Kircher fullname: Kircher, Martin organization: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA – sequence: 20 givenname: Michael J. surname: Bamshad fullname: Bamshad, Michael J. organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 21 givenname: Deborah A. surname: Nickerson fullname: Nickerson, Deborah A. organization: Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA – sequence: 22 givenname: Heather C. surname: Mefford fullname: Mefford, Heather C. email: hmefford@uw.edu organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 23 givenname: Katia surname: Sol-Church fullname: Sol-Church, Katia email: ks5uq@virginia.edu organization: Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30554721$$D View this record in MEDLINE/PubMed |
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| Copyright | 2018 American Society of Human Genetics Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. 2018 American Society of Human Genetics. 2018 American Society of Human Genetics |
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| Keywords | 16p13 deletion epigenetic repeat expansion methylation Desbuquois dysplasia XYLT1 trinucleotide repeat fragile site skeletal dysplasia |
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| Snippet | Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal... |
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| SubjectTerms | 16p13 deletion Abnormalities, Multiple - genetics Alleles Blotting, Southern Cohort Studies Desbuquois dysplasia DNA Methylation - genetics Epigenesis, Genetic - genetics epigenetic Exons - genetics Female fragile site Humans Infant Infant, Newborn Male methylation Mutation Pedigree Pentosyltransferases - genetics repeat expansion skeletal dysplasia Sulfites - metabolism Syndrome trinucleotide repeat Trinucleotide Repeat Expansion - genetics UDP Xylose-Protein Xylosyltransferase XYLT1 |
| Title | GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome |
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