{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T23:45:26Z","timestamp":1783640726106,"version":"3.55.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,12,23]],"date-time":"2024-12-23T00:00:00Z","timestamp":1734912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006306","name":"Sigrid Jus\u00e9lius Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006306","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003125","name":"Finnish Cultural Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003125","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004756","name":"Emil Aaltonen Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004756","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011727","name":"Stockholm County Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011727","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006129","name":"Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005744","name":"Foundation for Pediatric Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005744","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Orion Research Foundation, and Folkh\u00e4lsan Research Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Hypophosphatemic rickets is a rare bone disease characterized by short stature, bone deformities, impaired bone mineralization, and dental problems. Most commonly, hypophosphatemic rickets is caused by pathogenic variants in the X-chromosomal PHEX gene, but autosomal dominant and recessive forms also exist. We investigated a Finnish family in which the son (index, 29\u00a0yr) and mother (56\u00a0yr) had hypophosphatemia since childhood. Both patients had typical clinical, radiographic, and biochemical features of hypophosphatemic rickets, including a pathological fracture in the son. Gene panels and whole-exome sequencing did not reveal any pathogenic variants in the known hypophosphatemia genes. Therefore, we performed whole genome sequencing and identified a deep intronic variant (c.2147\u2009+\u20091197A\u2009&amp;gt;\u2009G) in PHEX. Both the affected individuals, but none of the unaffected family members, had the same variant, as confirmed by Sanger sequencing. According to RT-PCR, whole transcriptomic data, and in silico analyses, the variant led to a new splice donor site in intron 21 and an 84 basepair pseudoexon between exons 21 and 22, likely leading to the synthesis of abnormal PHEX protein. Our study underscores the importance of intronic PHEX variants in X-linked hypophosphatemia (XLH). In patients with features of XLH but negative gene panel or whole-exome sequencing results, the combination of whole-genome sequencing and whole transcriptomics should be considered to detect possible deep intronic variants. The methodologies presented have the potential to be used more widely in other rare diseases.<\/jats:p>","DOI":"10.1093\/jbmrpl\/ziae169","type":"journal-article","created":{"date-parts":[[2024,12,23]],"date-time":"2024-12-23T19:44:13Z","timestamp":1734983053000},"source":"Crossref","is-referenced-by-count":3,"title":["A deep intronic <i>PHEX<\/i> variant associated with X-linked hypophosphatemia in a Finnish family"],"prefix":"10.1093","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8971-4306","authenticated-orcid":false,"given":"Laura","family":"Koponen","sequence":"first","affiliation":[{"name":"Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki , Helsinki 00014 ,","place":["Finland"]},{"name":"Folkh\u00e4lsan Research Center , Helsinki 00290 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2947-4683","authenticated-orcid":false,"given":"Minna","family":"Pekkinen","sequence":"additional","affiliation":[{"name":"Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki , Helsinki 00014 ,","place":["Finland"]},{"name":"Folkh\u00e4lsan Research Center , Helsinki 00290 ,","place":["Finland"]},{"name":"Children\u2019s Hospital, University of Helsinki and Helsinki University Hospital , Helsinki 00014 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1194-8959","authenticated-orcid":false,"given":"Jelmer","family":"Legebeke","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm 17177 ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mari","family":"Muurinen","sequence":"additional","affiliation":[{"name":"Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki , Helsinki 00014 ,","place":["Finland"]},{"name":"Folkh\u00e4lsan Research Center , Helsinki 00290 ,","place":["Finland"]},{"name":"Children\u2019s Hospital, University of Helsinki and Helsinki University Hospital , Helsinki 00014 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9197-1288","authenticated-orcid":false,"given":"Salla","family":"Rusanen","sequence":"additional","affiliation":[{"name":"Folkh\u00e4lsan Research Center , Helsinki 00290 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5744-4292","authenticated-orcid":false,"given":"Shabir","family":"Hussain","sequence":"additional","affiliation":[{"name":"Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki , Helsinki 00014 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4888-8793","authenticated-orcid":false,"given":"Fan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm 17177 ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7397-6122","authenticated-orcid":false,"given":"Pasi I","family":"Nevalainen","sequence":"additional","affiliation":[{"name":"Rare Diseases Unit and Endocrine Unit, Department of Internal Medicine, Tampere University Hospital, and Faculty of Medicine and Health Technology, Tampere University , Tampere 33101 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4547-001X","authenticated-orcid":false,"given":"Outi","family":"M\u00e4kitie","sequence":"additional","affiliation":[{"name":"Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki , Helsinki 00014 ,","place":["Finland"]},{"name":"Folkh\u00e4lsan Research Center , Helsinki 00290 ,","place":["Finland"]},{"name":"Children\u2019s Hospital, University of Helsinki and Helsinki University Hospital , Helsinki 00014 ,","place":["Finland"]},{"name":"Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm 17177 ,","place":["Sweden"]},{"name":"Clinical Genetics, Karolinska University Hospital , Stockholm 17177 ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,12,23]]},"reference":[{"key":"2025012806260079300_ref1","doi-asserted-by":"publisher","first-page":"1005189","DOI":"10.3389\/fendo.2022.1005189","article-title":"Osteocytes and the pathogenesis of hypophosphatemic rickets","volume":"13","author":"Yamazaki","year":"2022","journal-title":"Front Endocrinol (Lausanne)"},{"issue":"1","key":"2025012806260079300_ref2","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s13023-019-1014-8","article-title":"FGF23 and its role in X-linked hypophosphatemia-related morbidity","volume":"14","author":"Beck-Nielsen","year":"2019","journal-title":"Orphanet J Rare Dis"},{"issue":"1","key":"2025012806260079300_ref3","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1046\/j.1523-1755.2000.00807.x","article-title":"PHEX gene and hypophosphatemia","volume":"57","author":"Drezner","year":"2000","journal-title":"Kidney Int"},{"key":"2025012806260079300_ref4","doi-asserted-by":"publisher","first-page":"116135","DOI":"10.1016\/j.bone.2021.116135","article-title":"Genotype-phenotype analysis, and assessment of the importance of the zinc-binding site in PHEX in Japanese patients with X-linked hypophosphatemic rickets using 3D structure modeling","volume":"153","author":"Ishihara","year":"2021","journal-title":"Bone"},{"issue":"2","key":"2025012806260079300_ref5","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1002\/humu.24296","article-title":"Novel PHEX gene locus-specific database: comprehensive characterization of vast number of variants associated with X-linked hypophosphatemia (XLH)","volume":"43","author":"Sarafrazi","year":"2022","journal-title":"Hum Mutat"},{"issue":"8","key":"2025012806260079300_ref6","doi-asserted-by":"publisher","first-page":"3840","DOI":"10.1210\/jcem.86.8.7730","article-title":"X-linked hypophosphatemia attributable to pseudoexons of the PHEX gene","volume":"86","author":"Christie","year":"2001","journal-title":"J Clin Endocrinol Metab"},{"key":"2025012806260079300_ref7","doi-asserted-by":"publisher","first-page":"116839","DOI":"10.1016\/j.bone.2023.116839","article-title":"X-linked hypophosphatemia caused by a deep intronic variant in PHEX identified by PCR-based RNA analysis of urine-derived cells","volume":"176","author":"Grimbly","year":"2023","journal-title":"Bone"},{"issue":"7","key":"2025012806260079300_ref8","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/s41581-019-0152-5","article-title":"Clinical practice recommendations for the diagnosis and management of X-linked hypophosphataemia","volume":"15","author":"Haffner","year":"2019","journal-title":"Nat Rev Nephrol"},{"issue":"8","key":"2025012806260079300_ref9","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1002\/jbmr.3475","article-title":"A randomized, double-blind, placebo-controlled, phase 3 trial evaluating the efficacy of burosumab, an anti-FGF23 antibody, in adults with X-linked hypophosphatemia: week 24 primary analysis","volume":"33","author":"Insogna","year":"2018","journal-title":"J Bone Miner Res"},{"issue":"10","key":"2025012806260079300_ref10","doi-asserted-by":"publisher","first-page":"e998","DOI":"10.1210\/clinem\/dgad223","article-title":"Effects of burosumab treatment on mineral metabolism in children and adolescents with X-linked hypophosphatemia","volume":"108","author":"Ewert","year":"2023","journal-title":"J Clin Endocrinol Metab"},{"issue":"21","key":"2025012806260079300_ref11","doi-asserted-by":"publisher","first-page":"1987","DOI":"10.1056\/NEJMoa1714641","article-title":"Burosumab therapy in children with X-linked hypophosphatemia","volume":"378","author":"Carpenter","year":"2018","journal-title":"N Engl J Med"},{"issue":"10","key":"2025012806260079300_ref12","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1038\/s10038-023-01174-w","article-title":"Identification of a novel pathogenic deep intronic variant in PTEN resulting in pseudoexon inclusion in a patient with juvenile polyps","volume":"68","author":"Jelsig","year":"2023","journal-title":"J Hum Genet"},{"issue":"10","key":"2025012806260079300_ref13","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1038\/s10038-023-01159-9","article-title":"Genome sequencing identifies coding and non-coding variants for non-syndromic hearing loss","volume":"68","author":"Ramzan","year":"2023","journal-title":"J Hum Genet"},{"issue":"16","key":"2025012806260079300_ref14","doi-asserted-by":"publisher","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2025012806260079300_ref15","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet Med"},{"issue":"7","key":"2025012806260079300_ref16","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1016\/j.ajhg.2023.06.002","article-title":"Using the ACMG\/AMP framework to capture evidence related to predicted and observed impact on splicing: recommendations from the ClinGen SVI Splicing Subgroup","volume":"110","author":"Walker","year":"2023","journal-title":"Am J Hum Genet"},{"issue":"16","key":"2025012806260079300_ref17","doi-asserted-by":"publisher","first-page":"2745","DOI":"10.1093\/bioinformatics\/btv195","article-title":"PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels","volume":"31","author":"Choi","year":"2015","journal-title":"Bioinformatics"},{"issue":"10","key":"2025012806260079300_ref18","doi-asserted-by":"publisher","first-page":"e46688","DOI":"10.1371\/journal.pone.0046688","article-title":"Predicting the functional effect of amino acid substitutions and indels","volume":"7","author":"Choi","year":"2012","journal-title":"PLoS One"},{"issue":"3","key":"2025012806260079300_ref19","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1038\/ng.2892","article-title":"A general framework for estimating the relative pathogenicity of human genetic variants","volume":"46","author":"Kircher","year":"2014","journal-title":"Nat Genet"},{"issue":"1","key":"2025012806260079300_ref20","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1186\/1471-2105-11-548","article-title":"Protein structure analysis of mutations causing inheritable diseases. An e-science approach with life scientist friendly interfaces","volume":"11","author":"Venselaar","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2025012806260079300_ref21","doi-asserted-by":"publisher","first-page":"13758","DOI":"10.1038\/s41598-019-50334-6","article-title":"The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2","volume":"9","author":"Vakkilainen","year":"2019","journal-title":"Sci Rep"},{"key":"2025012806260079300_ref22","volume-title":"FastQC A Quality Control Tool for High Throughput Sequence Data","author":"Simon","year":"2020"},{"issue":"1","key":"2025012806260079300_ref23","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2012","journal-title":"Bioinformatics"},{"issue":"5","key":"2025012806260079300_ref24","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"Schneider","year":"2017","journal-title":"Genome Res"},{"issue":"9","key":"2025012806260079300_ref25","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for the ENCODE project","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res"},{"issue":"16","key":"2025012806260079300_ref26","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"16","key":"2025012806260079300_ref27","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","article-title":"RSeQC: quality control of RNA-seq experiments","volume":"28","author":"Wang","year":"2012","journal-title":"Bioinformatics"},{"key":"2025012806260079300_ref28","volume-title":"Picard Toolkit","author":"Broad Institute"},{"issue":"19","key":"2025012806260079300_ref29","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"issue":"3","key":"2025012806260079300_ref30","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","article-title":"Predicting splicing from primary sequence with deep learning","volume":"176","author":"Jaganathan","year":"2019","journal-title":"Cell"},{"issue":"1","key":"2025012806260079300_ref31","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/0022-2836(91)90380-O","article-title":"Prediction of human mRNA donor and acceptor sites from the DNA sequence","volume":"220","author":"Brunak","year":"1991","journal-title":"J Mol Biol"},{"issue":"17","key":"2025012806260079300_ref32","doi-asserted-by":"publisher","first-page":"3439","DOI":"10.1093\/nar\/24.17.3439","article-title":"Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information","volume":"24","author":"Hebsgaard","year":"1996","journal-title":"Nucleic Acids Res"},{"issue":"2-3","key":"2025012806260079300_ref33","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1089\/1066527041410418","article-title":"Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals","volume":"11","author":"Gene","year":"2004","journal-title":"J Comput Biol"},{"issue":"12","key":"2025012806260079300_ref34","doi-asserted-by":"publisher","first-page":"2308","DOI":"10.1002\/humu.24491","article-title":"SPiP: splicing prediction pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing","volume":"43","author":"Leman","year":"2022","journal-title":"Hum Mutat"},{"issue":"20","key":"2025012806260079300_ref35","doi-asserted-by":"publisher","first-page":"3166","DOI":"10.1093\/bioinformatics\/btx401","article-title":"BPP: a sequence-based algorithm for branch point prediction","volume":"33","author":"Zhang","year":"2017","journal-title":"Bioinformatics"},{"issue":"1","key":"2025012806260079300_ref36","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"issue":"19","key":"2025012806260079300_ref37","doi-asserted-by":"publisher","first-page":"5981","DOI":"10.1158\/1078-0432.ccr-17-0725","article-title":"A first-time-in-human study of GSK2636771, a phosphoinositide 3 kinase beta-selective inhibitor, in patients with advanced solid tumors","volume":"23","author":"Mateo","year":"2017","journal-title":"Clin Cancer Res"},{"issue":"3","key":"2025012806260079300_ref38","doi-asserted-by":"publisher","first-page":"p17","DOI":"10.1159\/000319318","article-title":"Novel PHEX gene mutation associated with X linked hypophosphatemic rickets","volume":"116","author":"Chandran","year":"2010","journal-title":"Nephron Physiol"},{"issue":"6","key":"2025012806260079300_ref39","doi-asserted-by":"publisher","first-page":"1400","DOI":"10.1002\/ajmg.a.61558","article-title":"Limitations of exome sequencing in detecting rare and undiagnosed diseases","volume":"182","author":"Burdick","year":"2020","journal-title":"Am J Med Genet A"},{"issue":"2","key":"2025012806260079300_ref40","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1002\/jbmr.4454","article-title":"Molecular diagnoses of X-linked and other genetic hypophosphatemias: results from a sponsored genetic testing program","volume":"37","author":"Rush","year":"2022","journal-title":"J Bone Miner Res"},{"key":"2025012806260079300_ref41","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/B978-0-12-816222-4.00004-6","volume-title":"Genetics and Genomics of Eye Disease","author":"Au","year":"2020"}],"container-title":["JBMR Plus"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jbmrplus\/advance-article-pdf\/doi\/10.1093\/jbmrpl\/ziae169\/61267556\/ziae169.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jbmrplus\/article-pdf\/9\/2\/ziae169\/61267556\/ziae169.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jbmrplus\/article-pdf\/9\/2\/ziae169\/61267556\/ziae169.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,28]],"date-time":"2025-01-28T06:26:23Z","timestamp":1738045583000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jbmrplus\/article\/doi\/10.1093\/jbmrpl\/ziae169\/7931661"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,23]]},"references-count":41,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/jbmrpl\/ziae169","relation":{},"ISSN":["2473-4039"],"issn-type":[{"value":"2473-4039","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,2]]},"published":{"date-parts":[[2024,12,23]]},"article-number":"ziae169"}}