Impact of genetic and non-genetic factors on phenotypic diversity in NBAS-associated disease.

Biallelic pathogenic variants in neuroblastoma-amplified sequence (NBAS) cause a pleiotropic multisystem disorder. Three clinical subgroups have been defined correlating with the localisation of pathogenic variants in the NBAS gene: variants affecting the C-terminal region of NBAS result in SOPH syndrome (short stature, optic atrophy, Pelger-Huët anomaly), variants affecting the Sec 39 domain are associated with infantile liver failure syndrome type 2 (ILFS2) and variants affecting the ß-propeller domain give rise to a combined phenotype. However, there is still unexplained phenotypic diversity across the three subgroups, challenging the current concept of genotype-phenotype correlations in NBAS-associated disease. Therefore, besides examining the genetic influence, we aim to elucidate the potential impact of pre-symptomatic diagnosis, emergency management and other modifying variables on the clinical phenotype. We investigated genotype-phenotype correlations in individuals sharing the same genotypes (n = 30 individuals), and in those sharing the same missense variants with a loss-of-function variant in trans (n = 38 individuals). Effects of a pre-symptomatic diagnosis and emergency management on the severity of acute liver failure (ALF) episodes also were analysed, comparing liver function tests (ALAT, ASAT, INR) and mortality. A strong genotype-phenotype correlation was demonstrated in individuals sharing the same genotype; this was especially true for the ILFS2 subgroup. Genotype-phenotype correlation in patients sharing only one missense variant was still high, though at a lower level. Pre-symptomatic diagnosis in combination with an emergency management protocol leads to a trend of reduced severity of ALF. High genetic impact on clinical phenotype in NBAS-associated disease facilitates monitoring and management of affected patients sharing the same genotype. Pre-symptomatic diagnosis and an emergency management protocol do not prevent ALF but may reduce its clinical severity.

A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome.

In a patient diagnosed with both Kallmann syndrome (KS) and intellectual disability (ID), who carried an apparently balanced translocation t(7;12)(q22;q24)dn, array comparative genomic hybridization (aCGH) disclosed a cryptic heterozygous 4.7 Mb deletion del(12)(p11.21p11.23), unrelated to the translocation breakpoint. This novel discovery prompted us to consider the possibility that the combination of KS and neurological disorder in this patient could be attributed to gene(s) within this specific deletion at 12p11.21-12p11.23, rather than disrupted or dysregulated genes at the translocation breakpoints. To further support this hypothesis, we expanded our study by screening five candidate genes at both breakpoints of the chromosomal translocation in a cohort of 48 KS patients. However, no mutations were found, thus reinforcing our supposition. In order to delve deeper into the characterization of the 12p11.21-12p11.23 region, we enlisted six additional patients with small copy number variations (CNVs) and analyzed eight individuals carrying small CNVs in this region from the DECIPHER database. Our investigation utilized a combination of complementary approaches. Firstly, we conducted a comprehensive phenotypic-genotypic comparison of reported CNV cases. Additionally, we reviewed knockout animal models that exhibit phenotypic similarities to human conditions. Moreover, we analyzed reported variants in candidate genes and explored their association with corresponding phenotypes. Lastly, we examined the interacting genes associated with these phenotypes to gain further insights. As a result, we identified a dozen candidate genes: TSPAN11 as a potential KS candidate gene, TM7SF3, STK38L, ARNTL2, ERGIC2, TMTC1, DENND5B, and ETFBKMT as candidate genes for the neurodevelopmental disorder, and INTS13, REP15, PPFIBP1, and FAR2 as candidate genes for KS with ID. Notably, the high-level expression pattern of these genes in relevant human tissues further supported their candidacy. Based on our findings, we propose that dosage alterations of these candidate genes may contribute to sexual and/or cognitive impairments observed in patients with KS and/or ID. However, the confirmation of their causal roles necessitates further identification of point mutations in these candidate genes through next-generation sequencing.

Vertical transmission of a large calvarial ossification defect due to heterozygous variants of ALX4 and TWIST1.

ALX4 is a homeobox gene expressed in the mesenchyme of developing bone and is known to play an important role in the regulation of osteogenesis. Enlarged parietal foramina (EPF) is a phenotype of delayed intramembranous ossification of calvarial bones due to variants of ALX4. The contrasting phenotype of premature ossification of sutures is observed with heterozygous loss-of-function variants of TWIST1, which is an important regulator of osteoblast differentiation. Here, we describe an individual with a large cranium defect, with dominant transmission from the mother, both carrying disease causing heterozygous variants in ALX4 and TWIST1. The distinct phenotype of absent superior and posterior calvarium in the child and his mother was in sharp contrast to the other affected maternal relatives with a recognizable ALX4-related EPF phenotype. This report demonstrates comorbid disorders of Saethre-Chotzen syndrome and EPF in a mother and her child, resulting in severe skull defects reminiscent of calvarial abnormalities observed with bilallelic ALX4 variants. To our knowledge this is the first instance of ALX4 and TWIST1 variants acting synergistically to cause a unique phenotype influencing skull ossification.

Severe SOPH syndrome due to a novel NBAS mutation in a 27-year-old woman-Review of this pleiotropic, autosomal recessive disorder: Mystery solved after two decades.

Autosomal recessive SOPH syndrome was first described in the Yakuts population of Asia by Maksimova et al. in 2010. It arises from biallelic pathogenic variants in the NBAS gene and is characterized by severe postnatal growth retardation, senile facial appearance, small hands and feet, optic atrophy with loss of visual acuity and color vision, and normal intelligence (OMIM #614800). The presence of Pelger-Hüet anomaly in this disorder led to its name as an acronym for Short stature, Optic nerve atrophy, and Pelger-Hüet anomaly. Recent publications have further contributed to the characterization of this syndrome through additional phenotype-genotype correlations. We review the clinical features described in these publications and report on a 27-year-old woman with dwarfism with osteolysis and multiple skeletal problems, minor anomalies, immunodeficiency, diabetes mellitus, and multiple secondary medical problems. Her condition was considered an unknown autosomal recessive disorder for many years until exome sequencing provided the diagnosis by revealing a founder disease-causing variant that was compound heterozygous with a novel pathogenic variant in NBAS. Based on the major clinical features of this individual and others reported earlier, a revision of the acronym is warranted to facilitate clinical recognition.

Gorlin-like phenotype in a patient with a PTCH2 variant of uncertain significance.

Gorlin syndrome, also known as Nevoid Basal-Cell Carcinoma Syndrome (NBCCS), is an autosomal dominant tumor predisposition syndrome that presents early in life with characteristic congenital malformations and tumors. This syndrome most commonly results from germline mutations of the PTCH1 tumor suppressor gene, which shows high penetrance and great intra and interfamilial phenotypic variability, as well as the SUFU tumor suppressor gene. Recently, the PTCH2 gene has also been implicated as a cause of Gorlin syndrome. Notably, these patients displayed milder phenotypes of Gorlin syndrome when considered against PTCH1 and SUFU-related disease. We report a patient with a novel PTCH2 mutation inherited from his father. The proband displays several minor diagnostic features of Gorlin syndrome, supporting the pathogenic role of this gene. Features in the proband include macrocephaly, a wide face, prominent forehead, hypertelorism/telecanthus, large eyes, cleft lip and palate, thin vertical palmar creases, penoscrotal inversion, and a hyperpigmented spot on his penis. His father displays macrocephaly, several nevi on his back and shoulders, and a single palmar pit on his left hand, raising suspicion for Gorlin syndrome. Whole exome sequence (trio) found that the proband and father are heterozygous for NM_003738.4:c.3347C>T;p.(Pro1116Leu) in exon 21 of PTCH2, found also in his mildly affected brother. This semi-conservative amino acid substitution has been reported in the literature, but its significance is unclear. Notably, the proband, brother, and father do not meet clinical criteria for Gorlin syndrome. However, the clinical findings described in this family support the association between PTCH2 mutations and Gorlin-like phenotypes.

De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay.

Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10(-11)) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases.

RAF1 variants causing biventricular hypertrophic cardiomyopathy in two preterm infants: further phenotypic delineation and review of literature.

Noonan syndrome (NS) is an autosomal dominant disorder characterized by distinctive facial features, short neck, short stature, congenital heart defects, pectus deformities, and variable developmental delays. NS is genetically heterogeneous as pathogenic variants in several genes involved in the Ras/mitogen-activated protein kinase pathway have been associated with a NS phenotype. Overall, 50% of patients harbor pathogenic variants in PTPN11, whereas 3-17% of patients have variants in RAF1. We present two premature neonates with progressive biventricular hypertrophy found to have RAF1 variants in the CR2 domain. Molecular testing in patient 1 revealed a missense variant of a highly conserved residue c.782 C>G (p.P261R). This variant has been reported once with fatal outcome. Patient 2 also had a missense variant in a highly conserved neighboring residue c.770 C>T (p.S257L). This variant has been previously reported, most recently associated with the development of pulmonary arterial hypertension. Both our patients had prenatal findings of polyhydramnios, short long bones, hydrops fetalis, and cardiac anomalies with progressive biventricular hypertrophic cardiomyopathy. Both patients had a lethal outcome. Our findings further support the pathogenicity and lethality of p.P261R, and the need to monitor for pulmonary arterial hypertension in p.S257L. In addition, the second patient was presented with progressive hydrocephalus due to aqueductal stenosis. This could be related to the NS phenotype. More cases with this association are needed to confirm this finding.

Evaluación diagnóstica del paciente dismórfico / Diagnostic evaluation of the dysmorphic patient

Dismorfología se refiere al estudio de los pacientes con malformaciones congénitas. En este concepto se incluyen también pacientes con otras alteraciones morfológicas que lo hacen aparecer diferente. En este artículo revisamos los diferentes tipos de alteraciones que el médico debe reconocer, tanto cualitativas, como malformaciones, deformaciones, disrupciones y displasias, como cuantitativas enfatizando la importancia de diferenciar si éstas constituyen variación normal, racial o familiar, o son indicadores de una afección genética. Delinearemos la forma de estudiar al paciente y los problemas más frecuentes que dificultan establecer el diagnóstico. Si la malformación es aislada, de causa poligénica/multifactorial, es habitualmente el médico tratante quien establece el diagnóstico y otorga asesoramiento genético. En caso de anomalías múltiples, en que hay que determinar su etiología específica, lo recomendable es referir el paciente a un genetista clínico. Sólo así se podrá dar asesoramiento genético responsable ayudando al paciente a lograr su máximo potencial genético y a la familia a tener hijos normales.

Dysmorphology refers to the study of patients with congenital malformations. However, dysmorphology not only includes the study of birth defects but also the study of patients with other anomalies making him/her look different. In this article we review qualitative abnormalities, such us malformations, deformations, disruptions and displasias as well as quantitative variations which may represent normal, racial or familial, variation or be part of a genetic disorder. We review the study of the patient and frequent diagnostic problems. If the congenital anomaly is isolated, non-syndromic, of polygenic/multifactorial etiology, it is the responsibility of the primary physician to establish the diagnosis and provide genetic counseling. However, in cases of multiple anomalies when the physician should establish the specific etiology, the recommendation is to refer the patient to a clinical geneticist. The main goal of the evaluation is to determine the etiology of the abnormalities. Only then can the physician provide responsible genetic counseling, helping the patient to achieve his/her maximum genetic potential and allow the family to have normal children.

Identification of large NF1 duplications reciprocal to NAHR-mediated type-1 NF1 deletions.

Approximately 5% of all patients with neurofibromatosis type-1 (NF1) exhibit large deletions of the NF1 gene region. To date, only nine unrelated cases of large NF1 duplications have been reported, with none of the affected patients exhibiting multiple café au lait spots (CALS), Lisch nodules, freckling, or neurofibromas, the hallmark signs of NF1. Here, we have characterized two novel NF1 duplications, one sporadic and one familial. Both index patients with NF1 duplications exhibited learning disabilities and atypical CALS. Additionally, patient R609021 had Lisch nodules, whereas patient R653070 exhibited two inguinal freckles. The mother and sister of patient R609021 also harbored the NF1 duplication and exhibited cognitive dysfunction but no CALS. The breakpoints of the nine NF1 duplications reported previously have not been identified and hence their underlying generative mechanisms have remained unclear. In this study, we performed high-resolution breakpoint analysis that indicated that the two duplications studied were mediated by nonallelic homologous recombination (NAHR) and that the duplication breakpoints were located within the NAHR hotspot paralogous recombination site 2 (PRS2), which also harbors the type-1 NF1 deletion breakpoints. Hence, our study indicates for the first time that NF1 duplications are reciprocal to type-1 NF1 deletions and originate from the same NAHR events.

Congenital glaucoma and neurofibromatosis in a monozygotic twin: case report and review of the literature.

We describe a dramatic case of an identical twin presenting at birth with unilateral congenital glaucoma. Because of the suspicion of neurofibromatosis 1 a magnetic resonance image of the neural axis was obtained, which revealed a plexiform neurofibroma with spinal cord impingement. Diagnosis of neurofibromatosis 1 was confirmed by 3 months of age with the emergence of café-au-lait spots. This case was compared with all 19 reports published in the English literature of neurofibromatosis 1 associated with congenital glaucoma. Initial presentation, family history, characteristics ofthe clinical syndrome, and outcome of glaucoma in infants with neurofibromatosis 1 and congenital glaucoma were reviewed. A plexiform neurofibroma of the ipsilateral eyelid was present in eight patients and ipsilateral facial hypertrophy occurred in three patients. Café-au-lait spots appeared between the ages of 5 weeks and 8 years; none of the patients were reported to have café-au-lait spots at birth. Newborns with unilateral congenital glaucoma should raise high suspicion for neurofibromatosis 1 and its associated findings, which might need immediate intervention.

EXIT procedure: a case report.

The EXIT (Ex-Utero Intrapartum Treatment) procedure is an extremely valuable tool in providing time to secure the airway in infants with large fetal neck masses and abnormalities of the upper airway which impede resuscitation. The fetus is partially delivered while maintaining utero-placental-fetal circulation. We report the use of this technique in a case of huge cystic hygromas of the neck and chest due to a nuchal bleb-lethal dysplasia. Although severe pulmonary hypoplasia precluded an optimal outcome, this report shows that this procedure is technically feasible. We believe this to be the first case performed and reported in Louisiana.

Provisional new syndrome of MR/MCA with evolving phenotype.

We report on a 10-year-old patient with a provisionally new syndrome of MR/MCA with an evolving phenotype. Major findings at birth included short umbilical cord; striking hypotonia and cutis laxa with increased OFC; facial abnormalities with epicanthal folds, telecanthus, mild hypertelorism, wide flat nasal bridge, hypoplastic nose with upturned nostrils, and low-set dysplastic ears; asymmetric deformed chest with prominent sternum and winged scapulae; wider thumbs and halluces; left cryptorchidism and unusual perianal creases. Chromosomal and metabolic studies were normal. With aging, the phenotype has changed significantly: cutis laxa disappeared, the perianal creases and hypotonia are much milder, the initial apparent macrocephaly turned out to be true microcephaly, broad thumbs are less evident, but skeletal anomalies are more striking. Unsuccessful extensive diagnostic searches since birth and presentation in meetings suggest the presence of a private syndrome.