Gary A. Bellus

Germline variants that disrupt components of the epigenetic machinery cause syndromic neurodevelopmental disorders. Using exome and genome sequencing, we identified de novo variants in KDM2A , a lysine demethylase crucial for embryonic development, in 18 individuals with developmental delays and/or intellectual disabilities. The severity ranged from learning disabilities to severe intellectual disability. Other core symptoms included feeding difficulties, growth issues such as intrauterine growth restriction, short stature and microcephaly as well as recurrent facial features like epicanthic folds, upslanted palpebral fissures, thin lips, and low-set ears. Expression of human disease-causing KDM2A variants in a Drosophila melanogaster model led to neural degeneration, motor defects, and reduced lifespan. Interestingly, pathogenic variants in KDM2A affected physiological attributes including subcellular distribution, expression and stability in human cells. Genetic epistasis experiments indicated that KDM2A variants likely exert their effects through a potential gain-of-function mechanism, as eliminating endogenous KDM2A in Drosophila did not produce noticeable neurodevelopmental phenotypes. Data from Enzymatic-Methylation sequencing supports the suggested gene-disease association by showing an aberrant methylome profiles in affected individuals’ peripheral blood. Combining our genetic, phenotypic and functional findings, we establish de novo variants in KDM2A as causative for a syndromic neurodevelopmental disorder.

While most individuals with a clinical diagnosis of Neurofibromatosis type 1 (NF1) have a detectable pathogenic variant in the NF1 gene, other conditions have phenotypic features overlapping with NF1. Without molecular confirmation, individuals may be misdiagnosed and have a different underlying condition. Namely, if a child has constitutional mismatch repair deficiency (CMMRD), early detection and prevention strategies for cancer risk would include surveillance recommendations not typically recommended for children with NF1. This study aimed to explore phenotypes of individuals with a clinical diagnosis of NF1 to identify subpopulations who may benefit from further genetic counseling or testing for an alternate diagnosis. Retrospective review of 240 medical records of children who attended a neurocutaneous clinic identified 135 children with a molecularly confirmed pathogenic variant in NF1 or autosomal dominant pattern of clinical NF1 (“controls”) and 102 children deemed “at-risk” for another condition like CMMRD. Clinical presentation, family history of NF1, personal history of cancer, and family history of cancer were compared. When comparing clinical presentation, family history, and cancer history, minimal statistical differences were found, indicating that the at-risk population appears clinically indistinguishable from those with a clear diagnosis of NF1. Given the lack of distinguishable features between the at-risk and control population, this study suggests that tiered genetic testing for all individuals being evaluated for NF1 may be beneficial for identifying patients who may be misdiagnosed with NF1 and subsequently mismanaged. This study suggests that at-risk population with a suspected NF1 diagnosis may benefit from further evaluation. Correct diagnosis of constitutional mismatch repair deficiency is crucial to diagnose cancer at an early stage or prevent cancer from occurring. Prevention relevance: This study suggests that at-risk population with a suspected NF1 diagnosis may benefit from further evaluation. Correct diagnosis of constitutional mismatch repair deficiency is crucial to diagnose cancer at an early stage or prevent cancer from occurring.

Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype–phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.

Neurofibromatosis type 1 (NF1) is one of the most frequent genetic disorders, affecting 1:3,000 worldwide. Identification of genotype–phenotype correlations is challenging because of the wide range clinical variability, the progressive nature of the disorder, and extreme diversity of the mutational spectrum. We report 136 individuals with a distinct phenotype carrying one of five different NF1 missense mutations affecting p.Arg1809. Patients presented with multiple café‐au‐lait macules (CALM) with or without freckling and Lisch nodules, but no externally visible plexiform neurofibromas or clear cutaneous neurofibromas were found. About 25% of the individuals had Noonan‐like features. Pulmonic stenosis and short stature were significantly more prevalent compared with classic cohorts (P < 0.0001). Developmental delays and/or learning disabilities were reported in over 50% of patients. Melanocytes cultured from a CALM in a segmental NF1‐patient showed two different somatic NF1 mutations, p.Arg1809Cys and a multi‐exon deletion, providing genetic evidence that p.Arg1809Cys is a loss‐of‐function mutation in the melanocytes and causes a pigmentary phenotype. Constitutional missense mutations at p.Arg1809 affect 1.23% of unrelated NF1 probands in the UAB cohort, therefore this specific NF1 genotype–phenotype correlation will affect counseling and management of a significant number of patients.

We report on a young girl with polysyndactyly, coarctation of the aorta, and tongue hamartomas. These features are similar to those reported in individuals with variant forms of orofaciodigital syndrome known as congenital heart defects, hamartomas of the tongue and polysyndactly (CHDHTP: OMIM 217085) [Örstavik et al., 1992] and orocardiodigital syndrome [Digilio et al., 1996]. Whole exome sequencing revealed that she is a compound heterozygote for a frame shift mutation and a likely pathogenic sequence variant in WDPCP, a gene that regulates planar cell polarity and ciliogenesis. Results of genotyping in her parents and unaffected siblings were consistent with autosomal recessive inheritance of the mutation and the WDPCP variant. These results suggest that disruption of planar cell polarity and ciliogenesis may result in this unusual form of orofaciodigital syndrome.

We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers. Hum Mutat 33:165–179, 2012.

Chiari malformations are multifactorial and heterogeneous entities, characterized by abnormalities in the posterior fossa. They have been identified in association with various genetic syndromes in recent years. Two previous studies have noted an association of Chiari malformations with Rubinstein–Taybi syndrome (RTS). In this clinical report, we highlight identical twins with RTS caused by a mutation in CREBBP that presented with slightly different Chiari malformations in association with an extensive multiloculated syrinx and scoliosis. RTS has been found to be associated with craniocervical abnormalities in literature review, and this clinical report demonstrates the prudent consideration of the physician who cares for patients impacted by RTS to effectively screen via symptomatology and physical examination for Chiari pathology or other craniocervical abnormalities.

Legius syndrome, is a recently identified autosomal dominant disorder caused by loss of function mutations in the SPRED1 gene, with individuals mainly presenting with multiple café‐au‐lait macules (CALM), freckling and macrocephaly. So far, only SPRED1 point mutations have been identified as the cause of this syndrome. To determine if copy number changes (CNCs) are a cause of Legius syndrome, we have used a Multiplex Ligation‐dependent Probe Amplification (MLPA) assay covering all SPRED1 exons in a cohort of 510 NF1‐negative patients presenting with multiple CALMs with or without freckling, but no other NF1 diagnostic signs. Four different deletions were identified by MLPA and confirmed by quantitative PCR, reverse transcriptase PCR and/or array CGH: a deletion of exon 1 and the SPRED1 promoter region in a proband and two first‐degree relatives; a deletion of the entire SPRED1 gene in a sporadic patient; a deletion of exon 2‐6 in a proband and her father; and an ∼6.6 Mb deletion on chromosome 15 that spans SPRED1 in a sporadic patient. Deletions account for ∼10% of the 40 detected SPRED1 mutations in this cohort of 510 individuals. These results indicate the need for dosage analysis to complement sequencing‐based SPRED1 mutation analyses.