Publications by authors named "Yuri A Zarate"

72 Publications

CDK19-related disorder results from both loss-of-function and gain-of-function de novo missense variants.

Genet Med 2021 Jan 25. Epub 2021 Jan 25.

Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.

Purpose: To expand the recent description of a new neurodevelopmental syndrome related to alterations in CDK19.

Methods: Individuals were identified through international collaboration. Functional studies included autophosphorylation assays for CDK19 Gly28Arg and Tyr32His variants and in vivo zebrafish assays of the CDK19 and CDK19.

Results: We describe 11 unrelated individuals (age range: 9 months to 14 years) with de novo missense variants mapped to the kinase domain of CDK19, including two recurrent changes at residues Tyr32 and Gly28. In vitro autophosphorylation and substrate phosphorylation assays revealed that kinase activity of protein was lower for p.Gly28Arg and higher for p.Tyr32His substitutions compared with that of the wild-type protein. Injection of CDK19 messenger RNA (mRNA) with either the Tyr32His or the Gly28Arg variants using in vivo zebrafish model significantly increased fraction of embryos with morphological abnormalities. Overall, the phenotype of the now 14 individuals with CDK19-related disorder includes universal developmental delay and facial dysmorphism, hypotonia (79%), seizures (64%), ophthalmologic anomalies (64%), and autism/autistic traits (56%).

Conclusion: CDK19 de novo missense variants are responsible for a novel neurodevelopmental disorder. Both kinase assay and zebrafish experiments showed that the pathogenetic mechanism may be more diverse than previously thought.
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http://dx.doi.org/10.1038/s41436-020-01091-9DOI Listing
January 2021

A dyadic approach to the delineation of diagnostic entities in clinical genomics.

Am J Hum Genet 2021 01;108(1):8-15

Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA.

The delineation of disease entities is complex, yet recent advances in the molecular characterization of diseases provide opportunities to designate diseases in a biologically valid manner. Here, we have formalized an approach to the delineation of Mendelian genetic disorders that encompasses two distinct but inter-related concepts: (1) the gene that is mutated and (2) the phenotypic descriptor, preferably a recognizably distinct phenotype. We assert that only by a combinatorial or dyadic approach taking both of these attributes into account can a unitary, distinct genetic disorder be designated. We propose that all Mendelian disorders should be designated as "GENE-related phenotype descriptor" (e.g., "CFTR-related cystic fibrosis"). This approach to delineating and naming disorders reconciles the complexity of gene-to-phenotype relationships in a simple and clear manner yet communicates the complexity and nuance of these relationships.
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http://dx.doi.org/10.1016/j.ajhg.2020.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820621PMC
January 2021

Growth, development, and phenotypic spectrum of individuals with deletions of 2q33.1 involving SATB2.

Clin Genet 2020 Dec 31. Epub 2020 Dec 31.

Department of Cardiology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.

SATB2-Associated syndrome (SAS) is an autosomal dominant, multisystemic, neurodevelopmental disorder due to alterations in SATB2 at 2q33.1. A limited number of individuals with 2q33.1 contiguous deletions encompassing SATB2 (ΔSAS) have been described in the literature. We describe 17 additional individuals with ΔSAS, review the phenotype of 33 previously published individuals with 2q33.1 deletions (n = 50, mean age = 8.5 ± 7.8 years), and provide a comprehensive comparison to individuals with other molecular mechanisms that result in SAS (non-ΔSAS). Individuals in the ΔSAS group were often underweight for age (20/41 = 49%) with a progressive decline in weight (95% CI = -2.3 to -1.1, p < 0.0001) and height (95% CI = -2.3 to -1.0, p < 0.0001) Z-score means from birth to last available measurement. ΔSAS individuals were often noted to have a broad spectrum of facial dysmorphism. A composite image of ΔSAS individuals generated by automated image analysis was distinct as compared to matched controls and non-ΔSAS individuals. We also present additional genotype-phenotype correlations for individuals in the ΔSAS group such as an increased risk for aortic root/ascending aorta dilation and primary pulmonary hypertension for those individuals with contiguous gene deletions that include COL3A1/COL5A2 and BMPR2, respectively. Based on these findings, we provide additional care recommendations for individuals with ΔSAS variants.
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http://dx.doi.org/10.1111/cge.13912DOI Listing
December 2020

Introduction to the special issue on Clinical Genetics in Latin America.

Am J Med Genet C Semin Med Genet 2020 12 22;184(4):873-875. Epub 2020 Dec 22.

Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.

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http://dx.doi.org/10.1002/ajmg.c.31875DOI Listing
December 2020

De novo variants in SNAP25 cause an early-onset developmental and epileptic encephalopathy.

Genet Med 2020 Dec 10. Epub 2020 Dec 10.

Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.

Purpose: This study aims to provide a comprehensive description of the phenotypic and genotypic spectrum of SNAP25 developmental and epileptic encephalopathy (SNAP25-DEE) by reviewing newly identified and previously reported individuals.

Methods: Individuals harboring heterozygous missense or loss-of-function variants in SNAP25 were assembled through collaboration with international colleagues, matchmaking platforms, and literature review. For each individual, detailed phenotyping, classification, and structural modeling of the identified variant were performed.

Results: The cohort comprises 23 individuals with pathogenic or likely pathogenic de novo variants in SNAP25. Intellectual disability and early-onset epilepsy were identified as the core symptoms of SNAP25-DEE, with recurrent findings of movement disorders, cerebral visual impairment, and brain atrophy. Structural modeling for all variants predicted possible functional defects concerning SNAP25 or impaired interaction with other components of the SNARE complex.

Conclusion: We provide a comprehensive description of SNAP25-DEE with intellectual disability and early-onset epilepsy mostly occurring before the age of two years. These core symptoms and additional recurrent phenotypes show an overlap to genes encoding other components or associated proteins of the SNARE complex such as STX1B, STXBP1, or VAMP2. Thus, these findings advance the concept of a group of neurodevelopmental disorders that may be termed "SNAREopathies."
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http://dx.doi.org/10.1038/s41436-020-01020-wDOI Listing
December 2020

NEXMIF encephalopathy: an X-linked disorder with male and female phenotypic patterns.

Genet Med 2021 Feb 4;23(2):363-373. Epub 2020 Nov 4.

Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.

Purpose: Pathogenic variants in the X-linked gene NEXMIF (previously KIAA2022) are associated with intellectual disability (ID), autism spectrum disorder, and epilepsy. We aimed to delineate the female and male phenotypic spectrum of NEXMIF encephalopathy.

Methods: Through an international collaboration, we analyzed the phenotypes and genotypes of 87 patients with NEXMIF encephalopathy.

Results: Sixty-three females and 24 males (46 new patients) with NEXMIF encephalopathy were studied, with 30 novel variants. Phenotypic features included developmental delay/ID in 86/87 (99%), seizures in 71/86 (83%) and multiple comorbidities. Generalized seizures predominated including myoclonic seizures and absence seizures (both 46/70, 66%), absence with eyelid myoclonia (17/70, 24%), and atonic seizures (30/70, 43%). Males had more severe developmental impairment; females had epilepsy more frequently, and varied from unaffected to severely affected. All NEXMIF pathogenic variants led to a premature stop codon or were deleterious structural variants. Most arose de novo, although X-linked segregation occurred for both sexes. Somatic mosaicism occurred in two males and a family with suspected parental mosaicism.

Conclusion: NEXMIF encephalopathy is an X-linked, generalized developmental and epileptic encephalopathy characterized by myoclonic-atonic epilepsy overlapping with eyelid myoclonia with absence. Some patients have developmental encephalopathy without epilepsy. Males have more severe developmental impairment. NEXMIF encephalopathy arises due to loss-of-function variants.
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http://dx.doi.org/10.1038/s41436-020-00988-9DOI Listing
February 2021

JARID2 haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome.

Genet Med 2021 Feb 20;23(2):374-383. Epub 2020 Oct 20.

Department of Pediatrics, University of Montreal, Montreal, QC, Canada.

Purpose: JARID2, located on chromosome 6p22.3, is a regulator of histone methyltransferase complexes that is expressed in human neurons. So far, 13 individuals sharing clinical features including intellectual disability (ID) were reported with de novo heterozygous deletions in 6p22-p24 encompassing the full length JARID2 gene (OMIM 601594). However, all published individuals to date have a deletion of at least one other adjoining gene, making it difficult to determine if JARID2 is the critical gene responsible for the shared features. We aim to confirm JARID2 as a human disease gene and further elucidate the associated clinical phenotype.

Methods: Chromosome microarray analysis, exome sequencing, and an online matching platform (GeneMatcher) were used to identify individuals with single-nucleotide variants or deletions involving JARID2.

Results: We report 16 individuals in 15 families with a deletion or single-nucleotide variant in JARID2. Several of these variants are likely to result in haploinsufficiency due to nonsense-mediated messenger RNA (mRNA) decay. All individuals have developmental delay and/or ID and share some overlapping clinical characteristics such as facial features with those who have larger deletions involving JARID2.

Conclusion: We report that JARID2 haploinsufficiency leads to a clinically distinct neurodevelopmental syndrome, thus establishing gene-disease validity for the purpose of diagnostic reporting.
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http://dx.doi.org/10.1038/s41436-020-00992-zDOI Listing
February 2021

Managing Sleep and Behavioral Problems in a Preschooler with -Associated Syndrome.

Case Rep Genet 2020 12;2020:8868458. Epub 2020 Jul 12.

Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

-associated syndrome is an autosomal dominant, multisystemic disorder with associated sleep and behavioral abnormalities. Evidence is limited on appropriate management strategies in this population. We describe the medical management of a four-year-old child with poor sleep and significant behavioral problems. After failing initial treatment with melatonin, we initiated treatment clonidine along with high doses of trazodone for sleep. Daytime treatment with quetiapine was added to successfully manage behavioral issues. We present the challenges associated with treatment strategies in children with this syndrome.
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http://dx.doi.org/10.1155/2020/8868458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374225PMC
July 2020

Activating variants in PDGFRB result in a spectrum of disorders responsive to imatinib monotherapy.

Am J Med Genet A 2020 07 5;182(7):1576-1591. Epub 2020 Jun 5.

Division of Genetic Medicine, University of Washington, Seattle, Washington, USA.

More than 50 individuals with activating variants in the receptor tyrosine kinase PDGFRB have been reported, separated based on clinical features into solitary myofibromas, infantile myofibromatosis, Penttinen syndrome with premature aging and osteopenia, Kosaki overgrowth syndrome, and fusiform aneurysms. Despite their descriptions as distinct clinical entities, review of previous reports demonstrates substantial phenotypic overlap. We present a case series of 12 patients with activating variants in PDGFRB and review of the literature. We describe five patients with PDGFRB activating variants whose clinical features overlap multiple diagnostic entities. Seven additional patients from a large family had variable expressivity and late-onset disease, including adult onset features and two individuals with sudden death. Three patients were treated with imatinib and had robust and rapid response, including the first two reported infants with multicentric myofibromas treated with imatinib monotherapy and one with a recurrent p.Val665Ala (Penttinen) variant. Along with previously reported individuals, our cohort suggests infants and young children had few abnormal features, while older individuals had multiple additional features, several of which appeared to worsen with advancing age. Our analysis supports a diagnostic entity of a spectrum disorders due to activating variants in PDGFRB. Differences in reported phenotypes can be dramatic and correlate with advancing age, genotype, and to mosaicism in some individuals.
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http://dx.doi.org/10.1002/ajmg.a.61615DOI Listing
July 2020

Aortic Geometry in Patients with Duplication 7q11.23 Compared to Healthy Controls.

Pediatr Cardiol 2020 Aug 30;41(6):1199-1205. Epub 2020 May 30.

Lucile Packard Children's Hospital Stanford, 750 Welch Road, Suite 321, Palo Alto, CA, 94304, USA.

The aim of this study was to compare the size and geometry of the aorta in patients with 7q11.23 duplication (Dup7) to healthy controls. We retrospectively reviewed all echocardiograms in all patients with Dup7 evaluated at our institutions from June 2017 through September 2019. All standard aortic diameter measurements were made and recorded. Z-scores for the measurements were calculated. For comparison, a set of control echocardiograms was developed by randomly selecting 24 normal echocardiograms in age-matched patients who had undergone echocardiograms for an indication of either chest pain or syncope. In 58 echocardiograms from 21 Dup7 patients, all aortic measurements were increased compared to controls (p < 0.0001). Effacement of the sinotubular junction (STJ) of the aorta was present in all Dup7 patients. Our novel STJ-to-aortic annulus ratio of ≥ 1.15 had a 98.28% sensitivity (95% CI 90.76-99.96) and 100% specificity (95% CI 85.75-100) for distinguishing Dup7 from controls with a positive predictive value of 100% and a negative predictive value of 96.00% (95% CI 77.47-99.41). All patients in our study with Dup7 had echocardiographic evidence of aortopathy. Effacement of the STJ was present in all Dup7 patients. The STJ-to-annulus ratio is a better indicator of aortopathy in Dup7 than the aortic Z-score.
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http://dx.doi.org/10.1007/s00246-020-02375-2DOI Listing
August 2020

Epilepsy and Electroencephalographic Abnormalities in SATB2-Associated Syndrome.

Pediatr Neurol 2020 11 13;112:94-100. Epub 2020 Apr 13.

Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas. Electronic address:

Background: Seizures are an under-reported feature of the SATB2-associated syndrome phenotype. We describe the electroencephalographic findings and seizure semiology and treatment in a population of individuals with SATB2-associated syndrome.

Methods: We performed a retrospective review of 101 individuals with SATB2-associated syndrome who were reported to have had a previous electroencephalographic study to identify those who had at least one reported abnormal result. For completeness, a supplemental survey was distributed to the caregivers and input from the treating neurologist was obtained whenever possible.

Results: Forty-one subjects were identified as having at least one prior abnormal electroencephalography. Thirty-eight individuals (93%) had epileptiform discharges, 28 (74%) with central localization. Sleep stages were included as part of the electroencephalographies performed in 31 individuals (76%), and epileptiform activity was recorded during sleep in all instances (100%). Definite clinical seizures were diagnosed in 17 individuals (42%) with a mean age of onset of 3.2 years (four months to six years), and focal seizures were the most common type of seizure observed (42%). Six subjects with definite clinical seizures needed polytherapy (35%). Delayed myelination and/or abnormal white matter hyperintensities were seen on neuroimaging in 19 individuals (61%).

Conclusions: Epileptiform abnormalities are commonly seen in individuals with SATB2-associated syndrome. A baseline electroencephalography that preferably includes sleep stages is recommended during the initial evaluation of all individuals with SATB2-associated syndrome, regardless of clinical suspicion of epilepsy.
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http://dx.doi.org/10.1016/j.pediatrneurol.2020.04.006DOI Listing
November 2020

Further delineation of the clinical spectrum of KAT6B disorders and allelic series of pathogenic variants.

Genet Med 2020 Aug 19;22(8):1338-1347. Epub 2020 May 19.

Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, QC, Canada.

Purpose: Genitopatellar syndrome and Say-Barber-Biesecker-Young-Simpson syndrome are caused by variants in the KAT6B gene and are part of a broad clinical spectrum called KAT6B disorders, whose variable expressivity is increasingly being recognized.

Methods: We herein present the phenotypes of 32 previously unreported individuals with a molecularly confirmed diagnosis of a KAT6B disorder, report 24 new pathogenic KAT6B variants, and review phenotypic information available on all published individuals with this condition. We also suggest a classification of clinical subtypes within the KAT6B disorder spectrum.

Results: We demonstrate that cerebral anomalies, optic nerve hypoplasia, neurobehavioral difficulties, and distal limb anomalies other than long thumbs and great toes, such as polydactyly, are more frequently observed than initially reported. Intestinal malrotation and its serious consequences can be present in affected individuals. Additionally, we identified four children with Pierre Robin sequence, four individuals who had increased nuchal translucency/cystic hygroma prenatally, and two fetuses with severe renal anomalies leading to renal failure. We also report an individual in which a pathogenic variant was inherited from a mildly affected parent.

Conclusion: Our work provides a comprehensive review and expansion of the genotypic and phenotypic spectrum of KAT6B disorders that will assist clinicians in the assessment, counseling, and management of affected individuals.
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http://dx.doi.org/10.1038/s41436-020-0811-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7737399PMC
August 2020

Phenotypic and molecular description of an individual with a disruptive variant in the SULF2 gene.

Clin Dysmorphol 2020 Jul;29(3):144-147

Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.

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http://dx.doi.org/10.1097/MCD.0000000000000309DOI Listing
July 2020

MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis.

Brain 2020 01;143(1):55-68

Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.

MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.
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http://dx.doi.org/10.1093/brain/awz379DOI Listing
January 2020

Genetic variants in DGAT1 cause diverse clinical presentations of malnutrition through a specific molecular mechanism.

Eur J Med Genet 2020 Apr 25;63(4):103817. Epub 2019 Nov 25.

Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA. Electronic address:

Background: DGAT1, a gene encoding a protein involved in lipid metabolism, has been recently implicated in causing a rare nutritional and digestive disease presenting as Congenital Diarrheal Disorder (CDD). Genetic causes of malnutrition can be classified as metabolic disorders, caused by loss of a specific enzyme's function. However, disease driven by genetic variants in lipid metabolism genes is not well understood, and additional information is needed to better understand these effects.

Methods: We gathered a multi-institutional cohort of undiagnosed patients with a constellation of phenotypes presenting as malnutrition and metal ion dysregulation. Clinical Whole Exome Sequencing (WES) was performed on four patients and their unaffected parents. We prioritized genetic variants based on multiple criteria including population allele frequency and presumed inheritance pattern, and identified a candidate gene. Computational modeling was used to investigate if the altered amino acids are likely to result in a dysfunctional enzyme.

Results: We identified a multi-institutional cohort of patients presenting with malnutrition-like symptoms and likely pathogenic genomic variants within DGAT1. Multiple approaches were used to profile the effect these variants have on protein structure and function. Laboratory and nutritional intervention studies showed rapid and robust patient responses.

Conclusions: This report adds on to the database for existing mutations known within DGAT1, a gene recently implicated with CDD, and also expands its clinical spectrum. Identification of these DGAT1 mutations by WES has allowed for changes in the patients' nutritional rehabilitation, reversed growth failure and enabled them to be weaned off of total parenteral nutrition (TPN).
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http://dx.doi.org/10.1016/j.ejmg.2019.103817DOI Listing
April 2020

Using facial analysis technology in a typical genetic clinic: experience from 30 individuals from a single institution.

J Hum Genet 2019 12 24;64(12):1243-1245. Epub 2019 Sep 24.

Division of Medical Genetics, A. I. du Pont Hospital for Children/Nemours, Wilmington, DE, USA.

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http://dx.doi.org/10.1038/s10038-019-0673-6DOI Listing
December 2019

Redefining the Etiologic Landscape of Cerebellar Malformations.

Am J Hum Genet 2019 09 29;105(3):606-615. Epub 2019 Aug 29.

Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Department of Neurology, University of Washington, Seattle, WA 98105, USA. Electronic address:

Cerebellar malformations are diverse congenital anomalies frequently associated with developmental disability. Although genetic and prenatal non-genetic causes have been described, no systematic analysis has been performed. Here, we present a large-exome sequencing study of Dandy-Walker malformation (DWM) and cerebellar hypoplasia (CBLH). We performed exome sequencing in 282 individuals from 100 families with DWM or CBLH, and we established a molecular diagnosis in 36 of 100 families, with a significantly higher yield for CBLH (51%) than for DWM (16%). The 41 variants impact 27 neurodevelopmental-disorder-associated genes, thus demonstrating that CBLH and DWM are often features of monogenic neurodevelopmental disorders. Though only seven monogenic causes (19%) were identified in more than one individual, neuroimaging review of 131 additional individuals confirmed cerebellar abnormalities in 23 of 27 genetic disorders (85%). Prenatal risk factors were frequently found among individuals without a genetic diagnosis (30 of 64 individuals [47%]). Single-cell RNA sequencing of prenatal human cerebellar tissue revealed gene enrichment in neuronal and vascular cell types; this suggests that defective vasculogenesis may disrupt cerebellar development. Further, de novo gain-of-function variants in PDGFRB, a tyrosine kinase receptor essential for vascular progenitor signaling, were associated with CBLH, and this discovery links genetic and non-genetic etiologies. Our results suggest that genetic defects impact specific cerebellar cell types and implicate abnormal vascular development as a mechanism for cerebellar malformations. We also confirmed a major contribution for non-genetic prenatal factors in individuals with cerebellar abnormalities, substantially influencing diagnostic evaluation and counseling regarding recurrence risk and prognosis.
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http://dx.doi.org/10.1016/j.ajhg.2019.07.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731369PMC
September 2019

Behavioral phenotype and sleep problems in SATB2-associated syndrome.

Dev Med Child Neurol 2020 07 16;62(7):827-832. Epub 2019 Aug 16.

Department of Child and Adolescent Psychiatry, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

Aim: To determine the nature and frequency of behavioral phenotypes and sleep disturbances in individuals with SATB2-associated syndrome (SAS).

Method: The Strengths and Difficulties Questionnaire (SDQ) and an age-appropriate sleep questionnaire were distributed to the parents of individuals with SAS. All scores were compared to available normative data.

Results: Thirty-one individuals completed the assessment (18 females, 13 males; mean age 7y 4mo [SD 4y 1mo], range 2-16y). Individuals with SAS had significantly higher Total Difficulty scores than the normative sample (14.9 [SD 5.8] vs 7.1 [SD 5.7], p<0.001). A high frequency of emotional problems (22.6% vs 8%, p=0.01), peer problems (48.4% vs 10%, p<0.001), hyperactivity (48.4% vs 9%, p<0.001), and low prosocial behaviors (45.2% vs 9%, p<0.001) contribute to the behavioral profile in SAS. Concurrent sleeping difficulties were also frequently identified. Ten individuals in the 5 to 15 years age range had at least one sleep disorder (mean Sleep Disturbance Scale for Children total score 40.9 [SD 8.4] vs 35.1 [SD 7.7], p<0.001).

Interpretation: With previous limited available objective neurobehavioral data on the SAS population, we reported evidence of high-risk for a broad spectrum of burdensome behavioral phenotype and concurrent sleeping difficulties, the latter being particularly prevalent during early childhood. Routine assessment and treatment for behavioral issues and sleep problems is recommended.

What This Paper Adds: Emotional and peer problems, hyperactivity, and low prosocial behavior are common in SATB2-associated syndrome. The Strength and Difficulties Questionnaire Total Difficulty scores are atypical in nearly half of individuals. Behavioral difficulties are perceived as burdensome to over half of the parents. Nearly half of individuals have at least one sleep disorder. Sleep-wake transition disorders were most common.
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http://dx.doi.org/10.1111/dmcn.14330DOI Listing
July 2020

HIST1H1E heterozygous protein-truncating variants cause a recognizable syndrome with intellectual disability and distinctive facial gestalt: A study to clarify the HIST1H1E syndrome phenotype in 30 individuals.

Am J Med Genet A 2019 10 9;179(10):2049-2055. Epub 2019 Aug 9.

Institute of Cancer Research, London, UK.

Histone Gene Cluster 1 Member E, HIST1H1E, encodes Histone H1.4, is one of a family of epigenetic regulator genes, acts as a linker histone protein, and is responsible for higher order chromatin structure. HIST1H1E syndrome (also known as Rahman syndrome, OMIM #617537) is a recently described intellectual disability (ID) syndrome. Since the initial description of five unrelated individuals with three different heterozygous protein-truncating variants (PTVs) in the HIST1H1E gene in 2017, we have recruited 30 patients, all with HIST1H1E PTVs that result in the same shift in frame and that cluster to a 94-base pair region in the HIST1H1E carboxy terminal domain. The identification of 30 patients with HIST1H1E variants has allowed the clarification of the HIST1H1E syndrome phenotype. Major findings include an ID and a recognizable facial appearance. ID was reported in all patients and is most frequently of moderate severity. The facial gestalt consists of a high frontal hairline and full lower cheeks in early childhood and, in later childhood and adulthood, affected individuals have a strikingly high frontal hairline, frontal bossing, and deep-set eyes. Other associated clinical features include hypothyroidism, abnormal dentition, behavioral issues, cryptorchidism, skeletal anomalies, and cardiac anomalies. Brain magnetic resonance imaging (MRI) is frequently abnormal with a slender corpus callosum a frequent finding.
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http://dx.doi.org/10.1002/ajmg.a.61321DOI Listing
October 2019

Speech, language, and feeding phenotypes of SATB2-associated syndrome.

Clin Genet 2019 12 12;96(6):485-492. Epub 2019 Aug 12.

Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas.

SATB2-associated syndrome (SAS) is a recently identified disorder characterized by neurodevelopmental deficits and craniofacial anomalies. Assessments of speech, language, and feeding-related issues were conducted among 61 individuals with SAS (median age = 86 months, range = 26 months to 29 years of age). Individuals with SAS were mostly non-verbal communicators (72.1%) with severe deficits in both language comprehension and expression. The majority of individuals had receptive vocabulary skills of a child younger than 3 years of age. Based on parent report, the average spoken lexicon was 28.6 (SD = 84.6, n = 55) with a range of 0 to 500 (median = 5 words). All of the individuals with SAS with enough verbal ability either showed signs of childhood apraxia of speech or already had a diagnosis (n = 40) and 73.3% exhibited problems with reliable communication with unfamiliar partners. Hypernasal resonance (17.8%) due to velopharyngeal insufficiency secondary to a history of cleft palate and/or apraxic palatal movement (60.0% of hypernasal patients with no history of cleft palate), problems with chewing (68.2%), overstuffing the mouth with solids (64.9%), pharyngeal phase dysphagia (60.8%), and sialorrhea (63.3%) were common in this population. Mutation type was not predictive of receptive or expressive language abilities. We developed language and communication treatment recommendations based on these findings.
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http://dx.doi.org/10.1111/cge.13619DOI Listing
December 2019

Satb2 regulates proliferation and nuclear integrity of pre-osteoblasts.

Bone 2019 10 17;127:488-498. Epub 2019 Jul 17.

Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States of America. Electronic address:

Special AT-rich sequence binding protein 2 (Satb2) is a matrix attachment region (MAR) binding protein. Satb2 impacts skeletal development by regulating gene transcription required for osteogenic differentiation. Although its role as a high-order transcription factor is well supported, other roles for Satb2 in skeletal development remain unclear. In particular, the impact of dosage sensitivity (heterozygous mutations) and variance on phenotypic severity is still not well understood. To further investigate molecular and cellular mechanisms of Satb2-mediated skeletal defects, we used the CRISPR/Cas9 system to generate Satb2 mutations in MC3T3-E1 cells. Our data suggest that, in addition to its role in differentiation, Satb2 regulates progenitor proliferation. We also find that mutations in Satb2 cause chromatin defects including nuclear blebbing and donut-shaped nuclei. These defects may contribute to a slight increase in apoptosis in mutant cells, but apoptosis is insufficient to explain the proliferation defects. Satb2 expression exhibits population-level variation and is most highly expressed from late G1 to late G2. Based on these data, we hypothesize that Satb2 may regulate proliferation through two separate mechanisms. First, Satb2 may regulate the expression of genes necessary for cell cycle progression in pre-osteoblasts. Second, similar to other MAR-binding proteins, Satb2 may participate in DNA replication. We also hypothesize that variation in the severity or penetrance of Satb2-mediated proliferation defects is due to stochastic variation in Satb2 binding to DNA, which may be buffered in some genetic backgrounds. Further elucidation of the role of Satb2 in proliferation has potential impacts on our understanding of both skeletal defects and cancer.
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http://dx.doi.org/10.1016/j.bone.2019.07.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708767PMC
October 2019

Nuclear radiation and prevalence of structural birth defects among infants born to women from the Marshall Islands.

Birth Defects Res 2019 10 16;111(16):1192-1204. Epub 2019 Jul 16.

Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Arkansas Center for Birth Defects Research and Prevention, Little Rock, Arkansas.

Background: With their unique history of exposure to extensive nuclear testing between 1946 and 1958, descendants of Marshall Island residents may have underappreciated genetic abnormalities, increasing their risk of birth defects.

Methods: We conducted a retrospective cohort study of resident women with at least one singleton live birth between 1997 and 2013 in northwest Arkansas using state birth certificate data linked to data from the Arkansas Reproductive Health Monitoring System, a statewide birth defects registry. We calculated unadjusted and adjusted prevalence ratios (PR) and 95% confidence intervals (CI) from modified Poisson regression analyses for non-Hispanic (NH) whites, NH-blacks, Hispanics and Marshallese, using NH-whites as the reference group.

Results: Of the 91,662 singleton births during the study period, 2,488 were to Marshallese women. Due to the relatively small number of Marshallese births, we could not calculate prevalence estimates for some defects. Marshallese infants had higher rates of congenital cataracts (PR = 9.3; 95% CI: 3.1, 27.9). Although the number of defects was low, Marshallese infants also had higher rates of truncus arteriosus (PR = 44.0; 95% CI: 2.2, 896.1).

Conclusions: Marshallese infants may have increased risk of specific birth defects, but estimates are unstable because of small sample size so results are inconclusive. Larger population-based studies would allow for further investigation of this potential risk among Marshallese infants.
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http://dx.doi.org/10.1002/bdr2.1551DOI Listing
October 2019

Frequency and age at occurrence of clinical manifestations of disease in patients with hypophosphatasia: a systematic literature review.

Orphanet J Rare Dis 2019 04 25;14(1):85. Epub 2019 Apr 25.

Department of Endocrinology, Hospital Infantil Universitario Niño Jesús, IIS La Princesa, Madrid, Spain.

Background: Hypophosphatasia (HPP) is a rare, inherited, metabolic disease caused by tissue-nonspecific alkaline phosphatase deficiency, characterized by bone mineralization defects and systemic complications. Understanding of the clinical course and burden of HPP is limited by its rarity. This systematic literature review and synthesis of case report data aimed to determine the frequency and timing of clinical HPP manifestations and events.

Methods: Case reports and series of patients with HPP who had been followed longitudinally for ≥1 year were identified. Demographics and clinical data of interest, identified through consultation with clinical experts in HPP, were extracted. Occurrences of clinical manifestations/events of interest were categorized, classified by age at first reported occurrence of HPP manifestations and visualized over time. Clinical manifestations/events considered to contribute to the clinical burden of HPP were identified. Kaplan-Meier curves were used to estimate the median (range) age at first occurrence of the most frequently reported manifestations/events.

Results: From the 283 studies that met the inclusion criteria, 265 patients with HPP with ≥1 year of longitudinal follow-up were identified (median [interquartile range] age 4 [0-34] years; 45% male). The types of clinical manifestations/events of interest experienced by individuals with ≥1 such manifestation/event (n = 261) often differed between older and younger patients. Most (94%) of the 265 patients experienced ≥1 manifestation/event deemed to contribute to the clinical burden of HPP; premature tooth loss (53.5%), fractures (35.8%), pain (33.6%), and gross motor/ambulation difficulties (30.9%) were most frequently reported. The median (range) age at first reported occurrence of respiratory symptoms, cranial abnormalities, and premature tooth loss ranged from 0.3 to 10 years, whereas the median age at first reported occurrence of fractures, pain, gross motor/ambulation difficulties, and surgery ranged from 33 to 70 years.

Conclusions: HPP is associated with a high clinical burden of disease, regardless of age at first reported occurrence of HPP manifestations. Over an individual's lifetime, the types of manifestations/events experienced can change and multiple HPP-related clinical manifestations/events can accumulate. These observations may reflect evolution and progression of the disease.
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http://dx.doi.org/10.1186/s13023-019-1062-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485115PMC
April 2019

Mutation update for the SATB2 gene.

Hum Mutat 2019 08 18;40(8):1013-1029. Epub 2019 Jun 18.

Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts.

SATB2-associated syndrome (SAS) is an autosomal dominant neurodevelopmental disorder caused by alterations in the SATB2 gene. Here we present a review of published pathogenic variants in the SATB2 gene to date and report 38 novel alterations found in 57 additional previously unreported individuals. Overall, we present a compilation of 120 unique variants identified in 155 unrelated families ranging from single nucleotide coding variants to genomic rearrangements distributed throughout the entire coding region of SATB2. Single nucleotide variants predicted to result in the occurrence of a premature stop codon were the most commonly seen (51/120 = 42.5%) followed by missense variants (31/120 = 25.8%). We review the rather limited functional characterization of pathogenic variants and discuss current understanding of the consequences of the different molecular alterations. We present an expansive phenotypic review along with novel genotype-phenotype correlations. Lastly, we discuss current knowledge of animal models and present future prospects. This review should help provide better guidance for the care of individuals diagnosed with SAS.
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http://dx.doi.org/10.1002/humu.23771DOI Listing
August 2019

Constitutive activation of the PI3K-AKT pathway and cardiovascular abnormalities in an individual with Kosaki overgrowth syndrome.

Am J Med Genet A 2019 06 2;179(6):1047-1052. Epub 2019 Apr 2.

Division of Cardiology, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.

Kosaki overgrowth syndrome is a recently described syndrome characterized by distinctive facial features, brain white matter lesions, and developmental delay. Germline activating heterozygous PDGFRB mutations have been reported in this condition. Systemic connective tissue-type findings have been described in some individuals. We describe a 19-year-old Caucasian female with a history of hydrocephalus, Dandy-Walker malformation, cervical spine arachnoid cyst, progressive scoliosis, and overgrowth. Her physical exam included distinctive craniofacial dysmorphism, as well as soft and hyperextensible skin. Cardiovascular imaging during adolescence revealed saccular aneurysms in both coronary artery systems and subtle tortuosity of the cervical vertebral arteries. Exome sequencing trio analysis identified a de novo previously reported pathogenic variant in PDGFRB, c.1696T>C (p.[Trp566Arg]). Further functional studies included platelet-derived growth factor cellular metabolic pathway activity that confirmed the variant causes a constitutive activation of the PI3K-AKT pathway. This is the first report to characterize the activating nature of this PDGFRB variant. We also highlight the connective tissue findings seen in Kosaki overgrowth syndrome and recommend baseline echocardiographic evaluation in all individuals with this condition with particular emphasis on coronary arteries.
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http://dx.doi.org/10.1002/ajmg.a.61145DOI Listing
June 2019

Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability.

Authors:
Benjamin Cogné Sophie Ehresmann Eliane Beauregard-Lacroix Justine Rousseau Thomas Besnard Thomas Garcia Slavé Petrovski Shiri Avni Kirsty McWalter Patrick R Blackburn Stephan J Sanders Kévin Uguen Jacqueline Harris Julie S Cohen Moira Blyth Anna Lehman Jonathan Berg Mindy H Li Usha Kini Shelagh Joss Charlotte von der Lippe Christopher T Gordon Jennifer B Humberson Laurie Robak Daryl A Scott Vernon R Sutton Cara M Skraban Jennifer J Johnston Annapurna Poduri Magnus Nordenskjöld Vandana Shashi Erica H Gerkes Ernie M H F Bongers Christian Gilissen Yuri A Zarate Malin Kvarnung Kevin P Lally Peggy A Kulch Brina Daniels Andres Hernandez-Garcia Nicholas Stong Julie McGaughran Kyle Retterer Kristian Tveten Jennifer Sullivan Madeleine R Geisheker Asbjorg Stray-Pedersen Jennifer M Tarpinian Eric W Klee Julie C Sapp Jacob Zyskind Øystein L Holla Emma Bedoukian Francesca Filippini Anne Guimier Arnaud Picard Øyvind L Busk Jaya Punetha Rolph Pfundt Anna Lindstrand Ann Nordgren Fayth Kalb Megha Desai Ashley Harmon Ebanks Shalini N Jhangiani Tammie Dewan Zeynep H Coban Akdemir Aida Telegrafi Elaine H Zackai Amber Begtrup Xiaofei Song Annick Toutain Ingrid M Wentzensen Sylvie Odent Dominique Bonneau Xénia Latypova Wallid Deb Sylvia Redon Frédéric Bilan Marine Legendre Caitlin Troyer Kerri Whitlock Oana Caluseriu Marine I Murphree Pavel N Pichurin Katherine Agre Ralitza Gavrilova Tuula Rinne Meredith Park Catherine Shain Erin L Heinzen Rui Xiao Jeanne Amiel Stanislas Lyonnet Bertrand Isidor Leslie G Biesecker Dan Lowenstein Jennifer E Posey Anne-Sophie Denommé-Pichon Claude Férec Xiang-Jiao Yang Jill A Rosenfeld Brigitte Gilbert-Dussardier Séverine Audebert-Bellanger Richard Redon Holly A F Stessman Christoffer Nellaker Yaping Yang James R Lupski David B Goldstein Evan E Eichler Francois Bolduc Stéphane Bézieau Sébastien Küry Philippe M Campeau

Am J Hum Genet 2019 03 28;104(3):530-541. Epub 2019 Feb 28.

Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T1J4, Canada. Electronic address:

Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.
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http://dx.doi.org/10.1016/j.ajhg.2019.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407527PMC
March 2019

Widening phenotypic spectrum of GABBR2 mutation.

Acta Neurol Belg 2019 Sep 1;119(3):493-496. Epub 2019 Feb 1.

Section of Genetics and Metabolism, Department of Pediatrics, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

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http://dx.doi.org/10.1007/s13760-019-01088-5DOI Listing
September 2019

SATB2-associated syndrome (SAS) and associated dental findings.

Spec Care Dentist 2019 Mar 16;39(2):220-224. Epub 2019 Jan 16.

Arkansas Children's Hospital, Little Rock, Arkansas, USA.

Objective: Identify, diagnose, and document oral clinical and radiographic evidence associated with the genetic condition known as special AT-rich sequence-binding protein 2 (SATB2)-associated syndrome. Through identifying and publishing these common dental and behavioral findings, we hope to educate oral and medical healthcare providers to identify this condition in an attempt to develop meaningful comprehensive care to this patient population.

Methods: A total of 37 patients (19 female), ranging from ages 2 to 20 were evaluated at Arkansas Children's Hospital in Little Rock, Arkansas. Patient geographic distribution included: the United States, Canada, Portugal, Spain, and the Netherlands. Patients were clinically and radiographically examined for oral findings. Panoramic radiographs were obtained when patient's behavior allowed. Patient's parents or guardians were also interviewed concerning dental, medical, and behavioral histories.

Results: Clinical findings included delayed tooth eruption, bruxism, sialorrhea, larger than normal teeth with an increased propensity for maxillary anterior tooth trauma due to unsteady ambulation. Radiographic findings included delayed permanent root formation, significantly delayed or missing second bicuspids, malformed teeth, and taurodontism. Medical and behavioral issues included: insomnia, hyperphagia, cognitive delays, and an extremely high pain threshold.

Conclusion: Patients with SATB2-associated syndrome have shown to have a consistent and unique set of dental findings both clinically and radiographically. A thorough health and dental history along with the aforementioned results of the study may facilitate a diagnosis of this syndrome. Due to the complexity of the patient's dental needs and behavior, a health practitioner with special needs care experience on a comprehensive craniofacial team would be optimal.
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http://dx.doi.org/10.1111/scd.12340DOI Listing
March 2019

Dental radiographic findings in 18 individuals with SATB2-associated syndrome.

Clin Oral Investig 2018 Nov 12;22(8):2947-2951. Epub 2018 Oct 12.

Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

Objective: To characterize the radiographic dental phenotype of individuals with SATB2-associated syndrome (SAS).

Materials And Methods: Participants were evaluated by a multidisciplinary team during a concurrent clinic conducted during the 1st international SAS family meeting held in 2017 at a single institution. Whenever possible, panoramic and/or periapical radiographs were obtained in clinic or previously obtained and provided by the caregiver.

Results: Of the 37 individuals evaluated, 18 (12 males, median age 8.5 years) underwent radiographic examination. Dental radiographs revealed anomalies in all individuals starting at 2 years of age. The most consistent finding was delayed development of the mandibular second bicuspids (83%) with other common radiographic findings including delayed development of the roots of the permanent teeth (78%), severely rotated (56%) or malformed teeth (44%), and taurodontism (44%).

Conclusions: Dental anomalies are fully penetrant and can be documented radiographically in all individuals with SAS.

Clinical Relevance: Dental radiographic findings of delayed second premolar development and delayed development of permanent root formation, especially concurrent with findings of taurodontism and malformed teeth, support a clinical suspicion for SAS and should help differentiate SAS from other neurodevelopmental syndromes.
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http://dx.doi.org/10.1007/s00784-018-2702-9DOI Listing
November 2018

Combined Tongue-Palate Fusion With Alveolar Bands in a Patient With Pierre Robin Sequence and Van der Woude Syndrome.

Cleft Palate Craniofac J 2019 01 30;56(1):123-126. Epub 2018 Apr 30.

3 Department of Otolaryngology, Head and Neck Surgery, The University of Arkansas for Medical Sciences, Little Rock, AR, USA.

This report describes the presentation of a newborn male with circumferential tongue-palate fusion associated with cleft palate and alveolar bands. After intraoral adhesions lysis, the patient was diagnosed with Pierre Robin sequence. A family history of cleft lip and palate was noted, and interferon regulatory factor 6 ( IRF6) sequencing revealed a heterozygous variant, confirming the diagnosis of van der Woude syndrome. The disruption of IRF6 resulted in abnormal orofacial development including micrognathia and intraoral adhesions as well as tongue-palate fusion, then resulting in glossoptosis with airway obstruction and cleft palate.
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http://dx.doi.org/10.1177/1055665618773192DOI Listing
January 2019