Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly often accompanied by other structural anomalies and/or neurobehavioral manifestations. Rare de novo protein-coding variants and copy-number variations contribute to CDH in the population. However, most individuals with CDH remain genetically undiagnosed. Here, we perform integrated de novo and common-variant analyses using 1,469 CDH individuals, including 1,064 child-parent trios and 6,133 ancestry-matched, unaffected controls for the genome-wide association study. We identify candidate CDH variants in 15 genes, including eight novel genes, through deleterious de novo variants. We further identify two genomic loci contributing to CDH risk through common variants with similar effect sizes among Europeans and Latinx. Both loci are in putative transcriptional regulatory regions of developmental patterning genes. Estimated heritability in common variants is ∼19%. Strikingly, there is no significant difference in estimated polygenic risk scores between isolated and complex CDH or between individuals harboring deleterious de novo variants and individuals without these variants. The data support a polygenic model as part of the CDH genetic architecture.

LMNB1 (OMIM# 150340), encodes lamin B1, a component of the nuclear lamina that assembles into a network during mitosis. Duplications that include the LMNB1 gene have been reported to cause an autosomal dominant adult-onset leukodystrophy. This disease encompasses progressive neurologic symptoms including autonomic dysfunction (bladder and bowel dysfunction, impaired thermoregulation, etc.), pyramidal signs (hypertonia, clonus, and spastic weakness), cerebellar signs (ataxia, tremors, and dysmetria), and occasionally late-onset dementia and psychiatric issues. These findings have been found to manifest starting in the fourth or fifth decade of life. LMNB1 duplications causing leukodystrophy have been reported to be fully penetrant. In this case, we expand the phenotype of this variant with a three generation family carrying a duplication in LMNB1 identified after the proband had workup for microcephaly. The female proband was born after an uncomplicated pregnancy and vaginal delivery at 39 2/7 weeks gestation. Birth weight was 2.870 kg (21st percentile), birth length was 42.3 cm (32nd percentile) and birth head circumference (HC) was 31.5 cm (2nd percentile). Microcephaly was initially attributed to cranial molding. She does not have additional siblings and parents are healthy. Maternal ancestry is Assyrian and paternal ancestry is English and German. Parents have no known consanguinity. At 2.5 months old, she was referred for genetic evaluation as part of workup for congenital microcephaly. She had infectious disease workup and an ophthalmologic exam that were both unremarkable. At that visit weight was 4.87 kg (25th percentile), length 53.7 cm (2nd percentile), and HC 35.5 cm (<1st centile, 50% for 1 week of age). Physical exam was notable for microcephaly without anterior forehead sloping and mild temporal narrowing. Maternal HC was 54 cm (40th percentile) and paternal HC was 57 cm (75th percentile). She was also later found to have a mild transaminitis and mild diffuse echogenicity on an abdominal ultrasound, but these findings have since self-resolved. At her 6 month follow up, her weight was 7.05 kg (30th percentile), length 61.5 cm (3rd percentile) and HC was 39 cm (<1st percentile, 50% for 2.5 months). Exam was otherwise unchanged. Chromosome microarray was obtained and identified a 3.169 Mb duplication at 5q23.2q23.3. Chromosome microarray results were as follows: arr[GRCh37] 5q23.2q23.3(124708550_127877362)x3. This 3.169 Mb duplication at 5q23.2q23.3 included 12 genes, four of which are associated with clinical disorders (LMNB1, FBN2, ALDH7A1, MEGF10). Heterozygous duplications of LMNB1 have been associated with autosomal dominant leukodystrophy. Missense de novo variants of LMNB1 have been associated with microcephaly. Heterozygous variants in FBN2 are associated with congenital contractural arachnodactyly and early onset macular degeneration; gross duplications of this gene have not been associated with disease. Biallelic variants in ALDH7A1 are associated with pyridoxine dependent epilepsy. Biallelic variants of MEGF10 are associated with early onset myopathy, areflexia, respiratory distress and dysphagia. Parental testing was completed and the duplication was found to be maternally inherited. Mother was healthy and asymptomatic at 38 years old. Maternal grandmother was subsequently tested and also identified to have the duplication. Maternal grandmother had a history of hypertension, hypercholesterolemia, and cleft lip that was repaired. Aside from late-onset dementia, she did not have any neurologic concerns or reported autonomic symptoms at 74 years of age. Brain MRI showed age-related global brain parenchymal volume loss otherwise no acute intracranial abnormality and no evidence of leukodystrophy. Maternal grandmother's head circumference was on the smaller side at 52.5 cm (5th percentile). Microcephaly panel subsequently completed on the proband was negative. This LMNB1 variant reported in our microcephalic proband, her clinically unaffected mother and maternal grandmother expands the clinical phenotype of LMNB1 duplications. Previous literature has only reported duplications as fully penetrant. While the mother may still develop symptoms, the maternal grandmother's lack of significant autonomic findings or leukodystrophy in her mid-70's reflects that not all individuals with a LMNB1 duplication will show classic symptoms. Previous studies have also reported microcephaly to be associated with de novo missense variants. As the cause of microcephaly was not otherwise identified in our proband, is it possible microcephaly may be linked to duplications in LMNB1 as well with varying range of severity.

Trisomy 16 is the most common autosomal trisomy found in spontaneous abortions with mosaic versions seen in survivors. However, surviving children have multiple congenital defects and are at risk of growth and developmental delay. We report an additional case of mosaic trisomy 16 diagnosed by amniocentesis and confirmed after birth. Our patient is the first documented case of living mosaic trisomy 16 with the malformation constellation of lung agenesis, left pulmonary artery agenesis, congenital heart defects, and ipsilateral radial ray and limb abnormalities, expanding the phenotype of this rare condition. Additionally, this individual's unique combination of lung and cardiac defects caused morbidities that were challenging to manage and complicated family counseling as well.

Background: KMT2B-related dystonia is a primarily childhood-onset movement disorder characterized by progressive dystonia, spasticity, and developmental delay. A minority of individuals possess an inherited KMT2B variant. Case Report: As a child, the proband experienced mild developmental delay and laryngeal dystonia which progressed to generalized dystonia. Patellar hyperreflexia, postural tremor, and everted gait were documented. Whole exome sequencing identified a heterozygous pathogenic KMT2B variant in the proband, proband’s sister, and proband’s mother who had milder presentations. Discussion: This novel KMT2B variant reflects intrafamilial variable expressivity in KMT2B-related dystonia. Further identification of variants will allow for better appreciation of the phenotypic spectrum.

Background and Objectives Purine-rich element-binding protein A (PURA) gene encodes Pur-alpha, a conserved protein essential for normal postnatal brain development. Recently, a PURA syndrome characterized by intellectual disability, hypotonia, epilepsy, and dysmorphic features was suggested. The aim of this study was to define and expand the phenotypic spectrum of PURA syndrome by collecting data, including EEG, from a large cohort of affected patients. Methods Data on unpublished and published cases were collected through the PURA Syndrome Foundation and the literature. Data on clinical, genetic, neuroimaging, and neurophysiologic features were obtained. Results A cohort of 142 patients was included. Characteristics of the PURA syndrome included neonatal hypotonia, feeding difficulties, and respiratory distress. Sixty percent of the patients developed epilepsy with myoclonic, generalized tonic-clonic, focal seizures, and/or epileptic spasms. EEG showed generalized, multifocal, or focal epileptic abnormalities. Lennox-Gastaut was the most common epilepsy syndrome. Drug refractoriness was common: 33.3% achieved seizure freedom. We found 97 pathogenic variants in PURA without any clear genotype-phenotype associations. Discussion The PURA syndrome presents with a developmental and epileptic encephalopathy with characteristics recognizable from neonatal age, which should prompt genetic screening. Sixty percent have drug-resistant epilepsy with focal or generalized seizures. We collected more than 90 pathogenic variants without observing overt genotype-phenotype associations.

Trisomy 9 mosaic syndrome (T9M) is a rare condition characterized by multiorgan system involvement including craniofacial dysmorphisms, cardiac, genitourinary (GU), skeletal, and central nervous system (CNS) abnormalities. Although more than 100 cases have been reported in the literature, a comprehensive review has not been performed nor have clinical guidelines been established. Therefore, we describe the clinical features of 16 additional patients, review features of previously reported individuals, and suggest clinical guidelines. Our findings expand the clinical phenotype of T9M, including novel features of amblyopia, astigmatism, corectopia of pupil, posterior embryotoxon, and diaphragmatic eventration. Most patients had prenatal and perinatal issues, particularly from respiratory, growth, and feeding standpoints. Although small birth parameters were common, long-term growth trends varied widely. An association with advanced parental ages was also identified. The spectrum of growth and development was wide, ranging from nonverbal patients to those able to participate in educational programs with age-appropriate peers. The severity of clinical outcomes was unrelated to blood lymphocyte mosaicism levels. Microarray analysis had a higher diagnostic rate compared to standard karyotype analysis and should be utilized if this diagnosis is suspected. Future longitudinal studies will be key to monitor long-term outcomes of individuals with T9M and determine best practices for clinical management.

BACKGROUND AND OBJECTIVES:Purine-rich element-binding protein A (PURA) gene encodes Pur-α, a conserved protein essential for normal postnatal brain development. Recently, a PURA syndrome characterized by intellectual disability, hypotonia, epilepsy, and dysmorphic features was suggested. The aim of this study was to define and expand the phenotypic spectrum of PURA syndrome by collecting data, including EEG, from a large cohort of affected patients.METHODS:Data on unpublished and published cases were collected through the PURA Syndrome Foundation and the literature. Data on clinical, genetic, neuroimaging, and neurophysiologic features were obtained.RESULTS:A cohort of 142 patients was included. Characteristics of the PURA syndrome included neonatal hypotonia, feeding difficulties, and respiratory distress. Sixty percent of the patients developed epilepsy with myoclonic, generalized tonic-clonic, focal seizures, and/or epileptic spasms. EEG showed generalized, multifocal, or focal epileptic abnormalities. Lennox-Gastaut was the most common epilepsy syndrome. Drug refractoriness was common: 33.3% achieved seizure freedom. We found 97 pathogenic variants in PURA without any clear genotype-phenotype associations.DISCUSSION:The PURA syndrome presents with a developmental and epileptic encephalopathy with characteristics recognizable from neonatal age, which should prompt genetic screening. Sixty percent have drug-resistant epilepsy with focal or generalized seizures. We collected more than 90 pathogenic variants without observing overt genotype-phenotype associations.

Preimplantation genetic testing for monogenic disorders (PGT-M) was originally developed to identify embryos affected with serious childhood-onset disorders, but its use has recently broadened. Guidance on the use of PGT-M in the United States (U.S.) is currently limited, with no formal laws or guidelines established on its use. The goals of this study were to determine for which types of conditions U.S. laboratories currently do not offer PGT-M, to explore ethical considerations U.S. laboratory genetic counselors (GCs) take into consideration when deciding to accept or reject a PGT-M request, and to explore whether U.S. laboratory GCs believe PGT-M should be offered for conditions with reduced penetrance or for variants of uncertain significance (VUS). Qualitative analysis of semi-structured interviews with nine genetic counselors, from five different PGT-M laboratories, was conducted. Participants were required to be GCs working at a PGT-M laboratory in the U.S. and either actively counsel patients on PGT-M or determine a patient's eligibility for PGT-M. Two participants reported their separate laboratories have no limitations for allowable PGT-M testing, while the other seven participants representing three other laboratories reported having limitations. The main ethical consideration GCs reported considering when deciding to accept or reject a PGT-M request was patient autonomy, with a focus on the patient understanding risks of the testing. All participants reported believing PGT-M should be allowable for conditions with reduced penetrance and VUS, with all participants stating their respective laboratories allow for this currently. However, all participants reported a lack of sufficient guidelines and that having guidelines from a professional organization would be beneficial to their practice. In conclusion, lack of current guidelines in the United States has created discrepancies between PGT-M laboratories. PGT-M laboratory GCs support the use of PGT-M for conditions with reduced penetrance and VUS with informed consent. The need for guidelines is supported.

We report the first case of a 294 kb loss, notable for including the entirety of GPD1L, on chromosome 3p22.3-p24 in a 3-year-old girl with multiple congenital anomalies including absent left foot, single umbilical artery, bilateral vesico-ureteral reflux, rectovaginal fistula, and imperforate anus. Although GPD1L mutations have been associated with cardiac arrhythmias, including Brugada syndrome and sudden unexpected infant death syndrome, full deletions in the GPD1L gene have not been reported neither the patient nor her mother, who was later identified to carry the variant, have any signs or symptoms of Brugada syndrome. This may indicate these individuals have findings that have not yet been identified, full gene deletions of GDP1L are not necessarily disease causing, or there is incomplete penetrance of this gene or cardiac manifestations can occur at a later age.

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.

Purpose Hearing loss (HL) is the most common sensory disorder in children. Prompt molecular diagnosis may guide screening and management, especially in syndromic cases when HL is the single presenting feature. Exome sequencing (ES) is an appealing diagnostic tool for HL as the genetic causes are highly heterogeneous. Methods ES was performed on a prospective cohort of 43 probands with HL. Sequence data were analyzed for primary and secondary findings. Capture and coverage analysis was performed for genes and variants associated with HL. Results The diagnostic rate using ES was 37.2%, compared with 15.8% for the clinical HL panel. Secondary findings were discovered in three patients. For 247 genes associated with HL, 94.7% of the exons were targeted for capture and 81.7% of these exons were covered at 20× or greater. Further analysis of 454 randomly selected HL-associated variants showed that 89% were targeted for capture and 75% were covered at a read depth of at least 20×. Conclusion ES has an improved yield compared with clinical testing and may capture diagnoses not initially considered due to subtle clinical phenotypes. Technical challenges were identified, including inadequate capture and coverage of HL genes. Additional considerations of ES include secondary findings, cost, and turnaround time.

Lysosomal storage diseases (LSDs) are a heterogeneous group of genetic disorders caused by defects in lysosomal function that lead to multiorgan system damage. Due to wide clinical variability within even a single disorder, making a diagnosis can be difficult and identification may be delayed. Enzyme replacement therapy (ERT) was first approved as a treatment for the LSD Gaucher disease in 1991. ERT development for other LSDs followed, and ERT is currently approved for eight LSDs in the United States. ERT may help slow progression and improve clinical symptoms, but it cannot affect neurologic features due to its inability to cross the blood-brain barrier. Additional therapies for LSDs that have been investigated include stem cell transplants, gene therapy, small molecule approaches, and genome editing. Although newer approaches seem promising, there is no "cure" for any LSDs, and management remains focused on early diagnosis and treatment. [Pediatr Ann. 2018;47(5):e191-e197.].

Introduction: Sudden cardiac arrest/death (SCA/D) is an uncommon, but tragic occurrence in youth. Causes include inherited structural, functional, and electrical cardiac abnormalities, with more th...

The introduction of diagnostic clinical genome and exome sequencing (CGES) is changing the scope of practice for clinical geneticists. Many large institutions are making a significant investment in infrastructure and technology, allowing clinicians to access CGES, especially as health-care coverage begins to extend to clinically indicated genomic sequencing-based tests. Translating and realizing the comprehensive clinical benefits of genomic medicine remain a key challenge for the current and future care of patients. With the increasing application of CGES, it is necessary for geneticists and other health-care providers to understand its benefits and limitations in order to interpret the clinical relevance of genomic variants identified in the context of health and disease. New, collaborative working relationships with specialists across diverse disciplines (e.g., clinicians, laboratorians, bioinformaticians) will undoubtedly be key attributes of the future practice of clinical genetics and may serve as an example for other specialties in medicine. These new skills and relationships will also inform the development of the future model of clinical genetics training curricula. To address the evolving role of the clinical geneticist in the rapidly changing climate of genomic medicine, two Clinical Genetics Think Tank meetings were held that brought together physicians, laboratorians, scientists, genetic counselors, trainees, and patients with experience in clinical genetics, genetic diagnostics, and genetics education. This article provides recommendations that will guide the integration of genomics into clinical practice.Genet Med 18 11, 1075-1084.

Background: Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural and electrical abnormalities prior to symptomatic events and allow appropriate surveillance and treatment. This study investigated the diagnostic utility of exome sequencing (ES) by evaluating the capture and coverage of genes related to SCA/D.Methods: Samples from 102 individuals (13 with known molecular etiologies for SCA/D, 30 individuals without known molecular etiologies for SCA/D and 59 with other conditions) were analyzed following exome capture and sequencing at an average read depth of 100X. Reads were mapped to human genome GRCh37 using Novoalign, and post-processing and analysis was done using Picard and GATK. A total of 103 genes (2,190 exons) related to SCA/D were used as a primary filter. An additional 100 random variants within the targeted genes associated with SCA/D were also selected and evaluated for depth of sequencing and coverage. Although the primary objective was to evaluate the adequacy of depth of sequencing and coverage of targeted SCA/D genes and not for primary diagnosis, all patients who had SCA/D (known or unknown molecular etiologies) were evaluated with the project's variant analysis pipeline to determine if the molecular etiologies could be successfully identified.Results: The majority of exons (97.6 %) were captured and fully covered on average at minimum of 20x sequencing depth. The proportion of unique genomic positions reported within poorly covered exons remained small (4 %). Exonic regions with less coverage reflect the need to enrich these areas to improve coverage. Despite limitations in coverage, we identified 100 % of cases with a prior known molecular etiology for SCA/D, and analysis of an additional 30 individuals with SCA/D but no known molecular etiology revealed a diagnostic answer in 5/30 (17 %). We also demonstrated 95 % of 100 randomly selected reported variants within our targeted genes would have been picked up on ES based on our coverage analysis.Conclusions: ES is a helpful clinical diagnostic tool for SCA/D given its potential to successfully identify a molecular diagnosis, but clinicians should be aware of limitations of available platforms from technical and diagnostic perspectives.

Autosomal recessive primary microcephaly (MCPH) is a rare phenotype characterized by a occipitofrontal circumference (OFC) at birth measuring less than at least three standard deviations (SD) below the mean [Verloes et al.; Pagnamenta et al., 2012]. Individuals have reduced brain size, varied intellectual deficit without major cortical architecture abnormalities, absence of other organ malformations, and typically normal facial appearance aside from a sloping forehead that may accompany small cranial size [Issa et al., 2013a; Mahmood et al., 2011; Hassan et al., 2007; Woods et al., 2005; Issa et al., 2013b], which may help distinguish MCPH from other syndromic disorders associated with microcephaly. This disorder is genetically heterogeneous [Hassan et al., 2007] with at least 12 associated genes to date [Kaindl, 2014]. Initially, phenotypes were thought to be indistinguishable regardless of the causative gene, but later studies have suggested particular clinical features associated with different types of MCPH [Mahmood et al., 2011]. Mutations in the Cyclin-dependent protein kinase 5 regulatory subunit-associated protein 2 (CDK5RAP2) gene at the MCPH3 locus is one of the less common causes of MCPH, with only six families reported in the literature. CDK5RAP2 is thought to play a key role in cohesion and condensation of chromosomes during mitosis as the protein product localizes at the spindle poles [Issa et al., 2013b; 2013a; Bond et al., 2005; Mahmood et al., 2011; Kesavapany et al., 2004; Hassan et al., 2007; Megraw et al., 2011]. It is required for spindle check point regulation [Zhang et al., 2009] and is thought to potentially affect neuronal mitosis by disrupting the microtubules that are required for mitotic spindle assembly [Hassan et al., 2007; Mahmood et al., 2011]. CDK5RAP2 has also been shown to be expressed highly in the central nervous system in mouse and human studies [Issa et al., 2013a; Mahmood et al., 2011]. Previously reported individuals with mutations in CDK5RAP2 have a wide range of neurologic deficits (Supplementary Table I). This is the seventh report of an individual with MCPH who was found to have compound heterozygote mutations in CDK5RAP2, one novel and one previously reported. Informed consent was obtained from the patient's mother to participate in this report and allow publication of patient photographs and clinical information. The patient is a male who presented at six months of age due to failure to thrive requiring nasogastric tube feeding. There were no significant prenatal complications. He was born via spontaneous vaginal delivery at 40 weeks gestation to an 18-year-old G1P1 Honduran mother and a 24-year-old Guatemalan father. Family history was unremarkable, and parents were non-consanguineous. Birth weight was 3.2 kg (−0.3 SD), birth length was 47 cm (−1.5 SD), and birth occipito-frontal circumference (OFC) was 30.5 cm (−3.1 SD). Since birth the patient had poor growth, with OFC being disproportionately small (Supplemental Online Fig. 1A–D). A cranial MRI done at 4.5 months was limited due to patient motion, but grossly there were no major structural abnormalities. At six months old the patient's physical exam was notable for severe microcephaly with OFC at 35.5 cm (−6.4 SD), posterior plagiocephaly, sloping forehead, and upslanted palpebral fissures consistent with ethnicity (Fig. 1A). Development was appropriate for age; he was able to sit unsupported, pull to stand, reach for objects, recognize strangers, and babble. Cranial MRI done at six months showed severe microcephaly, small frontal lobes, abnormal corpus callosum with foreshortening, absent rostrum and blunted appearance of the splenium (Fig. 1C). Follow up exam at 13 months of age showed his OFC was 37.5 cm (−6.8 SD), and his development was appropriate for a 13 month old. He walked independently at ten months and was able to self-feed (though he continued to require nasogastric feedings for seven months due to poor weight gain), wave bye-bye, follow 1-step commands, and say 5–6 words. By 21 months his OFC was 39 cm (−6.6 SD). His motor skills were appropriate for age, but his vocabulary had not progressed. Evaluation through early intervention services identified expressive speech delay requiring speech therapy. Evaluation by a developmental pediatrician was recommended to the family but was not completed. A heart murmur noted at 21 months of age was evaluated by cardiology as benign, and echocardiogram and electrocardiogram were normal. Sequence analysis of CDK5RAP2 showed two predicted truncating nonsense mutations: 1) NM_018249.5: c.4441C>T (p.Arg1481*) in exon 30 predicting protein truncation by 412 amino acids, first reported by Issa et al., [2013b] and 2) NM_018249.5: c.5227C>T (p.Gln1743*) in exon 34 predicting protein truncation by 150 amino acids, which has not been reported previously (Fig. 2A–B). Additional testing included a single nucleotide polymorphism (SNP) array (Ilumina HumanOmni1-Quad BeadChip), which did not identify pathogenic deletions or duplications. High density array Comparative Genomic Hybridization (array-CGH) assay (custom Agilent 4 × 180) of the following genes also did not show evidence of deletions or duplications: ASPM, ARFGEF2, CDK5RAP2, CEP63, CEP152, CENPJ, MED17, MCPH1, NDE1, PNKP, STIL, SLC25A19, and WDR62. The phenotypic spectrum of patients with MCPH is broad, and aside from the presence of congenital microcephaly and absence of other organ malformations, clinical findings may vary [Verloes et al., 2009; Mahmood et al., 2011]. CDK5RAP2 is one of the more rare causes of MCPH with six mutations across six families reported prior in the literature. Supplementary Table I outlines all known reported patients and clinical phenotypes in detail, and Fig. 2C shows the locations of mutations in CDK5RAP2 that have been described. The first patients were described in two consanguineous Northern Pakistani families [Bond et al., 2005]. All affected individuals had congenital microcephaly and varying degrees of intellectual deficit. A third Northern Pakistani consanguineous family with similar phenotype was reported by [Hassan et al., 2007], and the nonsense mutation reported (c.246T>A, p.Y82*) was also described by [Bond et al., 2005]. Additional patients have since been reported in a consanguineous Somali family identified by [Pagnamenta et al., 2012], a Caucasian/Cherokee female [Tan et al., 2014], and two Italian brothers [Issa et al., 2013b] as well as the individual described here. The range of growth restriction has varied among the reported families. Every affected individual has congenital microcephaly by definition, but birth weight ranges from low [Pagnamenta et al., 2012; Bond et al., 2005] to normal. The child reported here had normal birth weight (38th centile, Supplemental Online Fig. 1B), but by three months weight gain was so poor he required nasogastric feedings. However, Family 2 reported by Bond et al., 2005 had normal growth after birth. Reported length/height has also varied from low [Tan et al., 2014; Pagnamenta et al., 2012; Issa et al., 2013b] to normal. The child reported here started with lower birth length (10th centile, Supplemental Online Fig. 1C) but eventually also fell off the growth curve by 6 months. Conversely, Patient 1 reported by Issa et al., [2013b] was below 10th centile in length at 3 months, but this improved to average stature by 9 years of age. Findings suggest accurate longitudinal growth predictions are difficult to make in patients with MCPH caused by CDK5RAP2 mutations. From a development standpoint most affected individuals are reported to have normal gross motor skills, but all have some degree of cognitive delay and varied ages at presentation. Patient VI:7 reported by Bond et al., [2005] had worsened cognitive functioning as a teenager than as a child. The individual reported here met early cognitive and motor developmental milestones, but by 21 months was diagnosed with mild speech delay. Intelligence testing performed on a number of reported patients with MCPH caused by CDK5RAP2 mutations (Supplementary Table I) further supports the spectrum of developmental delay that can be seen. Caution must be taken when counseling families regarding outcomes given this variability. In summary, we present the first patient of Hispanic descent with MCPH with compound heterozygote mutations in CDK5RAP2, including a novel pathogenic nonsense mutation. This patient highlights the clinical relevance of CDK5RAP2 and demonstrates the variability present in patients with CDK5RAP2 mutations from both a growth and development standpoint, which should be taken into consideration during prognostic discussions with affected patients and their families. The authors acknowledge the patient and his family for their agreement to participate in this report. 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Pallister-Hall syndrome is a complex malformation syndrome characterized by a wide range of anomalies including hypothalamic hamartoma, polydactyly, bifid epiglottis, and genitourinary abnormalities. It is usually caused by truncating frameshift/nonsense and splicing mutations in the middle third of GLI3. The clinical course ranges from mild to lethal in the neonatal period. We present the first patient with Pallister-Hall syndrome reported with total colonic aganglionosis, a rare form of Hirschsprung disease with poor long-term outcome. The patient also had an imperforate anus, which is the third individual with Pallister-Hall syndrome reported with both Hirschsprung disease and an imperforate anus. Molecular testing via amniocentesis showed an apparently de novo novel nonsense mutation c.2641 C>T (p.Gln881*). His overall medical course was difficult and was complicated by respiratory failure and pan-hypopituitarism. Invasive care was ultimately withdrawn, and the patient expired at three months of age. This patient's phenotype was complex with unusual gastrointestinal features ultimately leading to a unfavorable prognosis and outcome, highlighting the range of clinical severity in patients with Pallister-Hall syndrome.