Abstract Objective Recurrent deletions involving 17q12 are associated with a variety of clinical phenotypes, including congenital abnormalities of the kidney and urinary tract (CAKUT), maturity onset diabetes of the young, type 5, and neurodevelopmental disorders. Structural and/or functional renal disease is the most common phenotypic feature, although the prenatal renal phenotypes and the postnatal correlates have not been well characterized. Method We reviewed pre‐ and postnatal medical records of 26 cases with prenatally or postnatally identified 17q12/ HNF1B microdeletions (by chromosomal microarray or targeted gene sequencing), obtained through a multicenter collaboration. We specifically evaluated 17 of these cases (65%) with reported prenatal renal ultrasound findings. Results Heterogeneous prenatal renal phenotypes were noted, most commonly renal cysts (41%, n = 7/17) and echogenic kidneys (41%), although nonspecific dysplasia, enlarged kidneys, hydronephrosis, pelvic kidney with hydroureter, and lower urinary tract obstruction were also reported. Postnatally, most individuals developed renal cysts (73%, 11/15 live births), and there were no cases of end‐stage renal disease during childhood or the follow‐up period. Conclusion Our findings demonstrate that copy number variant analysis to assess for 17q12 microdeletion should be considered for a variety of prenatally detected renal anomalies. It is important to distinguish 17q12 microdeletion from other etiologies of CAKUT as the prognosis for renal function and presence of associated findings are distinct and may influence pregnancy and postnatal management.

HNF1B

Renal dysplasia

Etiology

10.1002/pd.6424

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NFIA Haploinsufficiency Is Associated with a CNS Malformation Syndrome and Urinary Tract Defects

PLoS Genetics (2007)

Lu W Fabiola Quintero‐Rivera Yanli Fan Fowzan S. Alkuraya Diana Donovan

Complex central nervous system (CNS) malformations frequently coexist with other developmental abnormalities, but whether the associated defects share a common genetic basis is often unclear. We describe five individuals who share phenotypically related CNS malformations and in some cases urinary tract defects, and also haploinsufficiency for the NFIA transcription factor gene due to chromosomal translocation or deletion. Two individuals have balanced translocations that disrupt NFIA. A third individual and two half-siblings in an unrelated family have interstitial microdeletions that include NFIA. All five individuals exhibit similar CNS malformations consisting of a thin, hypoplastic, or absent corpus callosum, and hydrocephalus or ventriculomegaly. The majority of these individuals also exhibit Chiari type I malformation, tethered spinal cord, and urinary tract defects that include vesicoureteral reflux. Other genes are also broken or deleted in all five individuals, and may contribute to the phenotype. However, the only common genetic defect is NFIA haploinsufficiency. In addition, previous analyses of Nfia−/− knockout mice indicate that Nfia deficiency also results in hydrocephalus and agenesis of the corpus callosum. Further investigation of the mouse Nfia+/− and Nfia−/− phenotypes now reveals that, at reduced penetrance, Nfia is also required in a dosage-sensitive manner for ureteral and renal development. Nfia is expressed in the developing ureter and metanephric mesenchyme, and Nfia+/− and Nfia−/− mice exhibit abnormalities of the ureteropelvic and ureterovesical junctions, as well as bifid and megaureter. Collectively, the mouse Nfia mutant phenotype and the common features among these five human cases indicate that NFIA haploinsufficiency contributes to a novel human CNS malformation syndrome that can also include ureteral and renal defects.

Haploinsufficiency

10.1371/journal.pgen.0030080

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NFIA-Related Disorder

T. Niroshini Senaratne Fabiola Quintero‐Rivera

Clinical characteristics For the purposes of this chapter, NFIA-related disorder is defined as heterozygous inactivation or disruption of only NFIA without involvement of adjacent or surrounding genes. NFIA-related disorder comprises central nervous system abnormalities (most commonly abnormalities of the corpus callosum) with or without urinary tract defects, such as unilateral or bilateral vesicoureteral reflux and hydronephrosis. Additional features include macrocephaly, seizures, developmental delay and/or cognitive impairment, nonspecific dysmorphic features, ventriculomegaly, and hypotonia, which can exacerbate motor delay and feeding issues in infancy. Rarer features may include strabismus, cutis marmorata, or craniosynostosis of the metopic, lambdoid, or sagittal suture. Diagnosis/testing The diagnosis of NFIA-related disorder is established in a proband by detection of one of the following: a heterozygous intragenic NFIA pathogenic variant; a heterozygous deletion of the 1p31.3 region that includes part or all of NFIA with surrounding genes intact; or a chromosome translocation/other rearrangement with a 1p31.3 breakpoint that disrupts NFIA. Management Treatment of manifestations: Standard treatment of seizure disorder, tethered spinal cord, recurrent urinary tract infections, hydronephrosis, strabismus, craniosynostosis, and developmental delays. Surveillance: Affected individuals should be followed by the appropriate specialists (e.g., neurologist, urologist, and/or clinical geneticist) as needed based on their particular features. Genetic counseling NFIA-related disorder is inherited in an autosomal dominant manner. Each child of an individual with NFIA-related disorder has a 50% chance of inheriting the causative genetic alteration. The proportion of NFIA-related disorder caused by de novo variants is approximately 75%-80%. Prenatal diagnosis for a pregnancy at increased risk is possible if the causative genetic alteration in an affected family member is known.

Ventriculomegaly

Source

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Mutational landscape of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) involving the central nervous system

Leukemia & lymphoma/Leukemia and lymphoma (2025)

Anna Shestakova Nahideh Haghighi Ying Zhang Jana Tarabay Mark G. Evans

10.1080/10428194.2025.2452341

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Genomic Copy Number Aberrations and Copy Neutral Loss of Heterozygosity Evaluation in Myeloid Neoplasms: Evidence-Based Recommendations for Clinical Genetic Testing From the Myeloid Malignancies Working Group of the Cancer Genomics Consortium

Cancer Genetics (2017)

Jennelle C. Hodge Rashmi Kanagal‐Shamanna Xinjie Xu Christine R. Bryke Durga Prasad Dash

SNP array

10.1016/j.cancergen.2017.04.017

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Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group

Xinjie Xu Christine R. Bryke Madina Sukhanova Emma Huxley Durga Prasad Dash

Abstract Structural genomic abnormalities, including balanced chromosomal rearrangements, copy number gains and losses and copy-neutral loss-of-heterozygosity (CN-LOH) represent an important category of diagnostic, prognostic and therapeutic markers in acute myeloid leukemia (AML). Genome-wide evaluation for copy number abnormalities (CNAs) is at present performed by karyotype analysis which has low resolution and is unobtainable in a subset of cases. Furthermore, examination for possible CN-LOH in leukemia cells is at present not routinely performed in the clinical setting. Chromosomal microarray (CMA) analysis is a widely available assay for CNAs and CN-LOH in diagnostic laboratories, but there are currently no guidelines how to best incorporate this technology into clinical testing algorithms for neoplastic diseases including AML. The Cancer Genomics Consortium Working Group for Myeloid Neoplasms performed an extensive review of peer-reviewed publications focused on CMA analysis in AML. Here we summarize evidence regarding clinical utility of CMA analysis in AML extracted from published data, and provide recommendations for optimal utilization of CMA testing in the diagnostic workup. In addition, we provide a list of CNAs and CN-LOH regions which have documented clinical significance in diagnosis, prognosis and treatment decisions in AML.

Copy number analysis

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Pathogenic paternally inherited NLGN4X deletion in a female with autism spectrum disorder: Clinical, cytogenetic, and molecular characterization

American Journal of Medical Genetics Part A (2020)

Nathan Kopp Ina Amarillo Julian A. Martínez‐Agosto Fabiola Quintero‐Rivera

Abstract Neuroligin 4 X‐linked ( NLGN4X ) is an X‐linked postsynaptic scaffolding protein, with functional role in excitatory synapsis development and maintenance, that has been associated with neuropsychiatric disorders such as intellectual disability, autism spectrum disorders (ASD), anxiety, attention deficit hyperactivity disorder (ADHD), and Tourette's syndrome. Chromosomal microarray analysis identified a paternally inherited, 445 Kb deletion on Xp22.3 that includes the entire NLGN4X in a 2.5 year old female (46,XX) with congenital hypotonia, strabismus, ASD, and increased aggressive behavioral issues. Her family history is significant for a mother with learning disabilities, a father with anxiety, major depressive disorder, and substance abuse, as well as two maternal half‐brothers with developmental delays. X‐inactivation studies in the proband's blood showed random X‐inactivation despite the presence of an abnormal X chromosome. Furthermore, trio exome sequencing did not reveal any other deleterious variant that could explain her phenotype. Our report describes the first example of a paternally inherited NLGN4X microdeletion as the genetic etiology of ASD in a female proband, and the psychiatric phenotypes in the father. It also provides further evidence that NLGN4X is sensitive to dosage changes in females, and can contribute to a variety of psychiatric features within the same family.

Proband

10.1002/ajmg.a.62025

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Citations (9)