{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T15:00:43Z","timestamp":1784905243450,"version":"3.55.0"},"reference-count":32,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100015550","name":"Italian Ministry of Health","doi-asserted-by":"publisher","award":["Ricerca Corrente L3_20\/24"],"award-info":[{"award-number":["Ricerca Corrente L3_20\/24"]}],"id":[{"id":"10.13039\/501100015550","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Pathogenic variants in the PPP1R12A gene have been associated with a malformation syndrome involving the brain and the genitourinary systems (GUBS, MIM #618820). To date, neither hearing loss (HL) nor inner ear malformations have been reported in affected individuals, and these features are therefore not currently regarded as part of the PPP1R12A-related phenotype. Moreover, functional evidence supporting the pathogenicity of several reported variants remains limited. Methods: We investigated a 12.5-year-old patient presenting with profound bilateral sensorineural hearing loss associated with inner ear malformations, genitourinary and central nervous system abnormalities. The patient underwent comprehensive clinical, audiological and radiological assessments, followed by genetic testing via trio-based whole-exome sequencing (WES). The molecular consequences of the identified variant were evaluated through minigene splicing assay and RT\u2013PCR analysis on RNA extracted from peripheral blood cells. Results: WES identified a novel heterozygous splicing variant (c.792+3A&gt;C) in the PPP1R12A gene (NM_002480.3). Functional studies demonstrated that this variant causes complete skipping of exon 5, resulting in a frameshift and the introduction of a premature termination codon. RT\u2013PCR analysis confirmed the presence of the alternatively spliced transcript lacking exon 5. In addition, an extensive review of the literature indicated that no clear genotype\u2013phenotype correlation has yet been established for PPP1R12A-related disorders and, whereas the majority of previously reported patients share brain and genitourinary malformations our patient additionally presented with profound bilateral sensorineural HL and inner ear malformations. Conclusions: Our findings suggest that PPP1R12A-related disorders may exhibit a broader phenotypic variability than previously recognized and we further propose that HL and inner ear malformations may represent novel features associated with this clinical spectrum. Moreover, our study underscores the importance of functional studies for accurately defining the molecular consequences of novel variants and establishing appropriate clinical correlations.<\/jats:p>","DOI":"10.3390\/genes17080856","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T13:53:26Z","timestamp":1784901206000},"page":"856","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phenotypic Expansion of PPP1R12A-Related Syndrome: A Novel Splicing Variant Associated with Hearing Loss and Inner Ear Malformations"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0851-1473","authenticated-orcid":false,"given":"Giulia","family":"Pianigiani","sequence":"first","affiliation":[{"name":"Institute for Maternal and Child Health\u2014IRCCS \u201cBurlo Garofolo\u201d, Via dell\u2019Istria 65\/1, 34137 Trieste, Italy"},{"name":"Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lara Emily","family":"Rosso","sequence":"additional","affiliation":[{"name":"Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6290-445X","authenticated-orcid":false,"given":"Anna","family":"Morgan","sequence":"additional","affiliation":[{"name":"Institute for Maternal and Child Health\u2014IRCCS \u201cBurlo Garofolo\u201d, Via dell\u2019Istria 65\/1, 34137 Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7432-4708","authenticated-orcid":false,"given":"Beatrice","family":"Spedicati","sequence":"additional","affiliation":[{"name":"Institute for Maternal and Child Health\u2014IRCCS \u201cBurlo Garofolo\u201d, Via dell\u2019Istria 65\/1, 34137 Trieste, Italy"},{"name":"Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0434-4172","authenticated-orcid":false,"given":"Manuela","family":"Napoli","sequence":"additional","affiliation":[{"name":"Neuroradiology Unit, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy"},{"name":"Radiology Unit, Salus Hospital, GVM Care & Research, Via Ulderico Levi 7, 42123 Reggio Emilia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5033-7854","authenticated-orcid":false,"given":"Stefano Giuseppe","family":"Caraffi","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7586-6632","authenticated-orcid":false,"given":"Emanuele","family":"Coccia","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy"},{"name":"Department of Medical and Surgical Science (DIMEC), Alma Mater Studiorum University of Bologna, Via Massarenti 9, 40138 Bologna, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeria","family":"Polizzi","sequence":"additional","affiliation":[{"name":"Department of Audiology, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Livia","family":"Garavelli","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4507-6589","authenticated-orcid":false,"given":"Giorgia","family":"Girotto","sequence":"additional","affiliation":[{"name":"Institute for Maternal and Child Health\u2014IRCCS \u201cBurlo Garofolo\u201d, Via dell\u2019Istria 65\/1, 34137 Trieste, Italy"},{"name":"Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, 34149 Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"key":"ref_1","unstructured":"Adam, M.P., Feldman, J., Mirzaa, G.M., Pagon, R.A., Wallace, S.E., Bean, L.J.H., Gripp, K.W., and Amemiya, A. (1993). PPP1R12A-Related Urogenital and\/or Brain Malformation Syndrome. GeneReviews\u00ae, University of Washington, Seattle. Updated 7 March 2024."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1126\/science.273.5272.245","article-title":"Regulation of Myosin Phosphatase by Rho and Rho-Associated Kinase (Rho-Kinase)","volume":"273","author":"Kimura","year":"1996","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.bbamcr.2018.07.023","article-title":"Myosin Phosphatase: Unexpected Functions of a Long-Known Enzyme","volume":"1866","author":"Kiss","year":"2019","journal-title":"Biochim. Biophys. Acta Mol. Cell Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.4103\/1673-5374.369101","article-title":"The Role of Rho GTPase Family in Cochlear Hair Cells and Hearing","volume":"18","author":"Dai","year":"2023","journal-title":"Neural Regen. Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40246-018-0161-7","article-title":"Computational Analysis of MRNA Expression Profiling in the Inner Ear Reveals Candidate Transcription Factors Associated with Proliferation, Differentiation, and Deafness","volume":"12","author":"Perl","year":"2018","journal-title":"Hum. Genom."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Liu, H., Chen, L., Giffen, K.P., Stringham, S.T., Li, Y., Judge, P.D., Beisel, K.W., and He, D.Z.Z. (2018). Cell-Specific Transcriptome Analysis Shows That Adult Pillar and Deiters\u2019 Cells Express Genes Encoding Machinery for Specializations of Cochlear Hair Cells. Front. Mol. Neurosci., 11.","DOI":"10.3389\/fnmol.2018.00356"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"112623","DOI":"10.1016\/j.celrep.2023.112623","article-title":"A Single-Cell Level Comparison of Human Inner Ear Organoids with the Human Cochlea and Vestibular Organs","volume":"42","author":"Steinhart","year":"2023","journal-title":"Cell Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.ajhg.2019.12.004","article-title":"Loss-of-Function Variants in PPP1R12A: From Isolated Sex Reversal to Holoprosencephaly Spectrum and Urogenital Malformations","volume":"106","author":"Hughes","year":"2020","journal-title":"Am. J. Hum. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2952","DOI":"10.1093\/humrep\/deac239","article-title":"Persistent M\u00fcllerian Duct Syndrome Associated with Genetic Defects in the Regulatory Subunit of Myosin Phosphatase","volume":"37","author":"Picard","year":"2022","journal-title":"Hum. Reprod."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e2223","DOI":"10.1002\/mgg3.2223","article-title":"Clinical Report and Genetic Analysis of a Neonate with Genitourinary and\/or Brain Malformation Syndrome Caused by a Non-Coding Sequence Variant of PPP1R12A","volume":"11","author":"Diao","year":"2023","journal-title":"Mol. Genet. Genomic Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1007\/s00439-022-02509-x","article-title":"Targeting de Novo Loss-of-Function Variants in Constrained Disease Genes Improves Diagnostic Rates in the 100,000 Genomes Project","volume":"142","author":"Seaby","year":"2023","journal-title":"Hum. Genet."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Tong, L., Wang, X., Wang, H., Yang, R., Li, X., and Yin, X. (2024). Functional Analysis of a Novel Nonsense PPP1R12A Variant in a Chinese Family with Infantile Epilepsy. BMC Med. Genomics, 17.","DOI":"10.1186\/s12920-024-02009-z"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e63876","DOI":"10.1002\/ajmg.a.63876","article-title":"Loss-of-Function Variant in PPP1R12A-Related Urogenital and\/or Brain Malformation Syndrome: Expanded Phenotype of Sex Reversal","volume":"197","year":"2025","journal-title":"Am. J. Med. Genet. A"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.21037\/tp-2025-166","article-title":"PPP1R12A Mutation Leads to Different Genders of Twinning: A Case Report and Literature Review","volume":"14","author":"Tian","year":"2025","journal-title":"Transl. Pediatr."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"102679","DOI":"10.1016\/j.epsc.2023.102679","article-title":"Anorectal Malformation in a 46, XY Patient with a de Novo Stop-Loss Variant in PPP1R12A and Associated Difference in Sexual Development: A Case Report","volume":"95","author":"Harris","year":"2023","journal-title":"J. Pediatr. Surg. Case Rep."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e64217","DOI":"10.1002\/ajmg.a.64217","article-title":"Intestinal Atresia in PPP1R12A-Related Urogenital and Brain Malformation Syndrome","volume":"197","author":"Gomes","year":"2025","journal-title":"Am. J. Med. Genet. A"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1177\/15500594251346337","article-title":"Hypersynchronous EEG Patterns in a Patient with Holoprosencephaly","volume":"56","author":"Pandya","year":"2025","journal-title":"Clin. EEG Neurosci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.ajhg.2025.01.021","article-title":"Pathogenic de Novo Variants in PPP2R5C Cause a Neurodevelopmental Disorder within the Houge-Janssens Syndrome Spectrum","volume":"112","author":"Verbinnen","year":"2025","journal-title":"Am. J. Hum. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"148945","DOI":"10.1016\/j.gene.2024.148945","article-title":"PPP2R5E: New Gene Potentially Involved in Specific Learning Disorders and Myopathy","volume":"933","author":"Musumeci","year":"2025","journal-title":"Gene"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Spedicati, B., Santin, A., Nardone, G.G., Rubinato, E., Lenarduzzi, S., Graziano, C., Garavelli, L., Miccoli, S., Bigoni, S., and Morgan, A. (2023). The Enigmatic Genetic Landscape of Hereditary Hearing Loss: A Multistep Diagnostic Strategy in the Italian Population. Biomedicines, 11.","DOI":"10.3390\/biomedicines11030703"},{"key":"ref_21","doi-asserted-by":"crossref","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."},{"key":"ref_22","doi-asserted-by":"crossref","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":"Yeo","year":"2004","journal-title":"J. Comput. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"13534","DOI":"10.1093\/nar\/gku1206","article-title":"In Silico Prediction of Splice-Altering Single Nucleotide Variants in the Human Genome","volume":"42","author":"Jian","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","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"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1001\/jamaoto.2025.2866","article-title":"Reevaluation of Enlarged Vestibular Aqueduct","volume":"151","author":"Huang","year":"2025","journal-title":"JAMA Otolaryngol.\u2013Head Neck Surg."},{"key":"ref_26","doi-asserted-by":"crossref","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."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/nrm4063","article-title":"Nonsense-Mediated MRNA Decay: An Intricate Machinery That Shapes Transcriptomes","volume":"16","author":"Jensen","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/s41580-019-0126-2","article-title":"Quality and Quantity Control of Gene Expression by Nonsense-Mediated MRNA Decay","volume":"20","author":"Kurosaki","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2247764","DOI":"10.1155\/crpe\/2247764","article-title":"PPP1R12A Mutation Presenting with Congenital Jejunal Atresia and Short Stature: A Pediatric Endocrinology Case Report","volume":"2026","author":"Saul","year":"2026","journal-title":"Case Rep. Pediatr."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.ydbio.2014.08.022","article-title":"Junctionally Restricted RhoA Activity Is Necessary for Apical Constriction during Phase 2 Inner Ear Placode Invagination","volume":"394","author":"Sai","year":"2014","journal-title":"Dev. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"905","DOI":"10.3892\/ijmm.2014.1634","article-title":"Myosin Light Chain Kinase Regulates Hearing in Mice by Influencing the F-Actin Cytoskeleton of Outer Hair Cells and Cochleae","volume":"33","author":"Yang","year":"2014","journal-title":"Int. J. Mol. Med."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1007\/s11248-005-3453-3","article-title":"The Targeted Disruption of the MYPT1 Gene Results in Embryonic Lethality","volume":"14","author":"Okamoto","year":"2005","journal-title":"Transgenic Res."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/8\/856\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T14:01:21Z","timestamp":1784901681000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/8\/856"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,24]]},"references-count":32,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["genes17080856"],"URL":"https:\/\/doi.org\/10.3390\/genes17080856","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,24]]}}}