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Novel Splicing Mutation in B3GAT3 Associated with Short Stature, GH Deficiency, Hypoglycaemia, Developmental Delay, and Multiple Congenital Anomalies

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Novel Splicing Mutation in B3GAT3 Associated with Short Stature, GH Deficiency, Hypoglycaemia, Developmental Delay, and Multiple Congenital Anomalies Hindawi Case Reports in Genetics Volume 2017, Article ID 3941483, 5 pages https://doi.org/10.1155/2017/3941483 Case Report Novel Splicing Mutation in B3GAT3 Associated with Short Stature, GH Deficiency, Hypoglycaemia, Developmental Delay, and Multiple Congenital Anomalies Samuel Bloor,1 Dinesh Giri,2,3 Mohammed Didi,3 and Senthil Senniappan2,3 1 School of Life Sciences, University of Liverpool, Liverpool, UK 2Institute of Child Health, University of Liverpool, Liverpool, UK 3Department of Endocrinology, Alder Hey Children’s NHS Foundation Trust, Liverpool, UK Correspondence should be addressed to Senthil Senniappan; [email protected] Received 18 August 2017; Revised 31 October 2017; Accepted 7 November 2017; Published 28 November 2017 Academic Editor: Yoshiyuki Ban Copyright © 2017 Samuel Bloor et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. B3GAT3, encoding -1,3-glucuronyltransferase 3, has an important role in proteoglycan biosynthesis. Homozygous B3GAT3 mutations have been associated with short stature, skeletal deformities, and congenital heart defects. We describe for the first time a novel heterozygous splice site mutation in B3GAT3 contributing to severe short stature, growth hormone (GH) deficiency, recurrent ketotic hypoglycaemia, facial dysmorphism, and congenital heart defects. A female infant, born at 34 weeks’ gestation to nonconsanguineous Caucasian parents with a birth weight of 1.9 kg, was noted to have cloacal abnormality, ventricular septal defect, pulmonary stenosis, and congenital sensorineural deafness. At 4 years of age, she was diagnosed with GH deficiency due to her short stature (height < 2.5 SD). MRI of the pituitary gland revealed a small anterior pituitary. She has multiple dysmorphic features: anteverted nares, small upturned nose, hypertelorism, slight frontal bossing, short proximal bones, hypermobile joints, and downslanting palpebral fissures. Whole exome sequencing (WES) was performed on the genomic DNA from the patient and biological mother. A heterozygous mutation in B3GAT3 (c.888+262T>G) in the invariant “GT” splice donor site was identified. This variant is considered to be pathogenic as it decreases the splicing efficiency in themRNA. 1. Introduction -1,3-Glucuronyltransferase 3 (GlcAT-I), encoded by B3GAT3, is located on chromosome 11q12.3 [4] and consists of Proteoglycans are an influential component of the extra- 335 amino acids with one N-linked glycan chain [5]. GlcAT- cellular matrix, orchestrating the cell-cell and cell-matrix I is a glucuronyltransferase involved in the biosynthesis of interactions [1]. Defects in the biochemical machinery, which GAG-protein linkers for proteoglycans. Specifically, GlcAT- produce proteoglycans, can lead to severe multisystem disor- I contributes to the addition of the terminal four saccha- ders. Cell signalling pathways, most notably developmental rides, xylose-galactose-galactose-glucuronic acid, hence its pathways, may become disrupted and processes such as presence in the cis-Golgi [6]. The addition of this tetrasac- skeletal development and cardiovascular maturation will charide provides an external face for binding by extracellular halt before they are fully complete [2]. Proteoglycans are produced through the secretory pathway in the endoplasmic signals. reticulum followed by the construction of the glycosamino- Homozygous mutations in B3GAT3 have previously been glycan (GAG) side chain within the Golgi complex. Multiple reported throughout the literature in patients with Larsen- posttranslational modifications occur in the Golgi complex, like syndrome. Larsen syndrome has previously been char- including the addition of disaccharides as well as epimerisa- acterised in association with proteoglycan synthesis related tion and sulfation of saccharide units, all performed by var- mutations, B4GALT7, and consists of phenotypic character- ious glycosyltransferases, epimerases, and sulfotransferases istics such as short stature, prominent forehead, and disloca- [3]. tions at multiple joints (knees, hips, elbows, and fingers) [7]. 2 Case Reports in Genetics In this report, we describe, for the first time, a novel Total variants 55,355 heterozygous splice site mutation in B3GAT3 contributing to severe short stature, growth hormone (GH) deficiency, facial Condence 41,700 dysmorphisms, and congenital heart defects amongst other symptoms. Common variants 2,533 Predicted deleterious 2. Case Presentation 645 variants A female child born at 34 weeks’ gestation to nonconsan- Genetic analysis 203 guineous Caucasian parents with unremarkable antenatal history was noted to have a posterior cloaca requiring Phenotypic analysis 8 reconstructive surgery at 2 years of age. She has multiple dysmorphic features such as anteverted nares, small upturned nose, hypertelorism, slight frontal bossing, short proximal Figure 1: Ingenuity Variant Analysis (IVA) filtering schematic to determine genes of interest in the patient. Genes were filtered based bones (femur, humerus) hypermobile joints, and downslant- upon confidence that the sequence was correctly sequenced, how ing palpebral fissures. She also has congenital sensorineural common the gene is in the wider gene pool, a prediction of the deafness, ventricular septal defect, and pulmonary stenosis, variants’ deleterious effect, and then the type of genetic mutation which required surgical correction. The phenotypic features that it is. Genecards.org was then used to determine the phenotypic aresummarisedinTable1. relevance of the gene to the symptoms of our patient. At 4 years of age, she was diagnosed with growth hor- mone (GH) deficiency due to her severe short stature (<2.5SDS)andsubsequentlyshewascommencedonGH and NHLBI ESP exomes were excluded. The predicted treatment. An MRI of her pituitary gland showed a small deleterious variants included nonsynonymous coding, splice anterior pituitary and the other pituitary hormones were site, frameshift, and stop gain variants. within the normal range. Investigations into her recurrent Ingenuity Variant Analysis (IVA) bioinformatic software hypoglycaemic episodes following a prolonged fasting for 19 was used to develop a filtering system (Figure 1) in order to hours were consistent with ketotic hypoglycaemia (Table 2). determine a small pool of genes, which are suspected to be There is a history of short stature and dysmorphism pathogenic, causing the phenotypic features of the patient. present on the paternal side. There was also a previous Confidence values were set to a call quality of 20. Common stillborn elder sibling with midline cleft palate, absent uvula, variants included variants present in at least 1% minor small jaw, depressed nasal bridge, abnormalities on MRI allele frequency in the following databases: Allele Frequency brain such as absence of the inferior cerebellar vermis, partial Community, 1000 Genomes Project, ExAC, and the NHLBI agenesis of corpus callosum, congenital heart defects, and ESP exomes. Followed by a prediction of the deleterious short bones. effect of the mutation using in silico tools such as PolyPhen, CGH microarray did not reveal any copy number vari- SIFTforSNPs,andMaxENTscansplicesitemutations, ants. A targeted exome sequencing of 70 genes associ- the variants were categorised as either pathogenic or likely ated with disorders of ketogenesis, ketolysis, carbohydrate pathogenic. Finally, a genetic analysis was performed looking metabolism, fatty acid oxidation defects, and hyperammon- for homozygous, compound heterozygous, haploinsufficient, aemia did not identify any pathogenic mutations. hemizygous, het-ambiguous, and heterozygous mutations. Subsequent research was performed upon the filtrate with 3. Methods genecards.org to determine any relevance to the symptoms of the patient. Whole exome sequencing (WES) was performed on the genomic DNA of the patient and biological mother after 4. Results obtaining written and informed consent. We were unable to obtain samples from the father. The study was given Ofthe203geneticvariantsthatIVAfilteredaslikelyto favourable ethical opinion by the North West-Liverpool be pathogenic, genes such as COL24A1, PLXND1, TECRL, Central Research Ethics Committee (REC Reference: EBF2, ABLIM1, PRDM10,andPOSTN were filtered out as 15/NW/0758) and the Clinical Research Business Unit at they did not segregate with the patient phenotype following Alder Hey Children’s NHS Foundation Trust, Liverpool, a detailed review of the biological information available from UK, granted site study approval. Informed and written the current literature [8–14]. consent were obtained from the parents. Genomic DNA A heterozygous mutation in B3GAT3 (c.888+262T>G) was extracted from the child and her biological mother. in the invariant “GT” splice donor site was identified. In Exons were captured using SureSelect XT Human All Exon silico modelling of this variant categorised the variant as V5 capture library and DNA sequencing was carried out pathogenic. This variant decreases the splicing efficiency of using the Illumina HiSeq4000 at 2 × 150 bp paired-end the mRNA as predicted by a MaxEntScan score decrease of sequencer. The sequence data were aligned to the reference 100% (from 11.01 to −0.14). MaxEntScan is an in silico splicing genome (GRCh37/hg19). The variants present in at least 1% defect prediction tool used to analyse the affinity of an minor
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