Further delineation of the KAT6B molecular and phenotypic spectrum

KAT6B sequence variants have been identified previously in both patients with the Say-Barber-Biesecker type of blepharophimosis mental retardation syndromes (SBBS) and in the more severe genitopatellar syndrome (GPS). We report on the findings in a previously unreported group of 57 individuals with suggestive features of SBBS or GPS. Likely causative variants have been identified in 34/57 patients and were commonly located in the terminal exons of KAT6B. Of those where parental samples could be tested, all occurred de novo. Thirty out of thirty-four had truncating variants, one had a missense variant and the remaining three had the same synonymous change predicted to affect splicing. Variants in GPS tended to occur more proximally to those in SBBS patients, and genotype/phenotype analysis demonstrated significant clinical overlap between SBBS and GPS. The de novo synonymous change seen in three patients with features of SBBS occurred more proximally in exon 16. Statistical analysis of clinical features demonstrated that KAT6B variant-positive patients were more likely to display hypotonia, feeding difficulties, long thumbs/great toes and dental, thyroid and patella abnormalities than KAT6B variant-negative patients. The few reported patients with KAT6B haploinsufficiency had a much milder phenotype, though with some features overlapping those of SBBS. We report the findings in a previously unreported patient with a deletion of the KAT6B gene to further delineate the haploinsufficiency phenotype. The molecular mechanisms giving rise to the SBBS and GPS phenotypes are discussed.     

Novel truncating variants expand the phenotypic spectrum of KAT6B‐related disorders

Say–Barber–Biesecker–Young–Simpson syndrome (SBBYSS) and Genitopatellar syndrome (GTPTS) are very rare conditions caused by KAT6B truncating variants. Because of both syndromes often share common features the associated phenotypes are usually grouped under the term “KAT6B‐related disorders.” However, particular signs of each syndrome have been reported and their appearance seems to be dependent on where the KAT6B variant is located. Thus, whereas truncating variants associated with SBBYSS have their highest density in the distal part of exon 18, those resulting in GTPTS are distributed between the end of exon 17 and beginning of exon 18. Here, we reported two de novo heterozygous KAT6B truncating variants. The first variant (c.5802delA; p.A1935Pfs*16), identified in a boy with SSBYSS phenotype, resulting in the most distal KAT6B truncating variant reported up‐to‐date in the scientific literature. The second variant (c.3152delG; p.S1051Tfs*63), located in a region hitherto defined as specific of SBBYSS, seems to cause an overlapping SBBYSS/GTPTS phenotype. The clinical and genetic characterization of these patients could contribute to the understanding of the KAT6B‐related disorders.     

A novel homozygous synonymous variant further expands the phenotypic spectrum of POLR3A-related pathologies

Pathogenic biallelic variants in POL3RA have been associated with different disorders characterized by progressive neurological deterioration. These include the 4H leukodystrophy syndrome (hypomyelination, hypogonadotropic hypogonadism, and hypodontia) and adolescent-onset progressive spastic ataxia, as well as Wiedemann–Rautenstrauch syndrome (WRS), a recognizable neonatal progeroid syndrome. The phenotypic differences between these disorders are thought to occur mainly due to different functional effects of underlying POLR3A variants. Here we present the detailed clinical course of a 37-year-old woman in whom we identified a homozygous synonymous POLR3A variant c.3336G>A resulting in leaky splicing r.[3336ins192, =, 3243_3336del94]. She presented at birth with intrauterine growth retardation, lipodystrophy, muscular hypotonia, and several WRS-like facial features, albeit without sparse hair and prominent scalp veins. She had no signs of developmental delay or intellectual disability. Over the years, above characteristic facial features, she showed severe postnatal growth retardation, global lipodystrophy, joint contractures, thoracic hypoplasia, scoliosis, anodontia, spastic quadriplegia, bilateral hearing loss, aphonia, hypogonadotropic hypogonadism, and cerebellar peduncles hyperintensities in brain imaging. These manifestations partially overlap the clinical features of the previously reported POLR3A-associated disorders, mostly mimicking the WRS. Thus, our study expands the POLR3A-mediated phenotypic spectrum and suggests existence of a phenotypic continuum underlying biallelic POLR3A variants.     

Expanding the genotypic and phenotypic spectrum of severe serine biosynthesis disorders

Serine biosynthesis disorders comprise a spectrum of very rare autosomal recessive inborn errors of metabolism with wide phenotypic variability. Neu–Laxova syndrome represents the most severe expression and is characterized by multiple congenital anomalies and pre‐ or perinatal lethality. Here, we present the mutation spectrum and a detailed phenotypic analysis in 15 unrelated families with severe types of serine biosynthesis disorders. We identified likely disease‐causing variants in the PHGDH and PSAT1 genes, several of which have not been reported previously. Phenotype analysis and a comprehensive review of the literature corroborates the evidence that serine biosynthesis disorders represent a continuum with varying degrees of phenotypic expression and suggest that even gradual differences at the severe end of the spectrum may be correlated with particular genotypes. We postulate that the individual residual enzyme activity of mutant proteins is the major determinant of the phenotypic variability, but further functional studies are needed to explore effects at the enzyme protein level.     

Wolfram syndrome: identification of a phenotypic and genotypic variant from Jordan

Wolfram syndrome is an autosomal recessive disorder with probable locus heterogeneity. Only insulin-dependent diabetes mellitus and progressive optic-nerve atrophy are necessary to make the diagnosis, but associated findings include diabetes insipidus, sensorineural hearing loss, ataxia, peripheral neuropathy, urinary-tract atony, and psychiatric illnesses. We performed clinical and molecular studies on four consanguineous families with 16 affected individuals. We point out a new phenotypic variant with absent diabetes insipidus, presence of peptic ulcer disease and bleeding tendency secondary to a platelet aggregation defect. The same phenotypic variant turned out to be a genotypic variant with linkage to a second Wolfram syndrome locus (WFS2) on chromosome 4q22-24.     

GATA6 mutations: Characterization of two novel patients and a comprehensive overview of the GATA6 genotypic and phenotypic spectrum

The first human mutations in GATA6 were described in a cohort of patients with persistent truncus arteriosus, and the phenotypic spectrum has expanded since then. This study underscores the broad phenotypic spectrum by presenting two patients with de novo GATA6 mutations, both exhibiting complex cardiac defects, pancreatic, and other abnormalities. Furthermore, we provided a detailed overview of all published human genetic variation in/near GATA6 published to date and the associated phenotypes (n = 78). We conclude that the most common phenotypes associated with a mutation in GATA6 were structural cardiac and pancreatic abnormalities, with a penetrance of 87 and 60%, respectively. Other common malformations were gallbladder agenesis, congenital diaphragmatic hernia, and neurocognitive abnormalities, mostly developmental delay. Fifty‐eight percent of the mutations were de novo, and these patients more often had an anomaly of intracardiac connections, an anomaly of the great arteries, and hypothyroidism, compared with those with inherited mutations. Functional studies mostly support loss‐of‐function as the pathophysiological mechanism. In conclusion, GATA6 mutations give a wide range of phenotypic defects, most frequently malformations of the heart and pancreas. This highlights the importance of detailed clinical evaluation of identified carriers to evaluate their full phenotypic spectrum.     

Novel biallelic variants expand the SLC5A6-related phenotypic spectrum

The sodium (Na⁺):multivitamin transporter (SMVT), encoded by SLC5A6, belongs to the sodium:solute symporter family and is required for the Na⁺-dependent uptake of biotin (vitamin B7), pantothenic acid (vitamin B5), the vitamin-like substance α-lipoic acid, and iodide. Compound heterozygous SLC5A6 variants have been reported in individuals with variable multisystemic disorder, including failure to thrive, developmental delay, seizures, cerebral palsy, brain atrophy, gastrointestinal problems, immunodeficiency, and/or osteopenia. We expand the phenotypic spectrum associated with biallelic SLC5A6 variants affecting function by reporting five individuals from three families with motor neuropathies. We identified the homozygous variant c.1285 A > G [p.(Ser429Gly)] in three affected siblings and a simplex patient and the maternally inherited c.280 C > T [p.(Arg94*)] variant and the paternally inherited c.485 A > G [p.(Tyr162Cys)] variant in the simplex patient of the third family. Both missense variants were predicted to affect function by in silico tools. 3D homology modeling of the human SMVT revealed 13 transmembrane helices (TMs) and Tyr162 and Ser429 to be located at the cytoplasmic facing region of TM4 and within TM11, respectively. The SLC5A6 missense variants p.(Tyr162Cys) and p.(Ser429Gly) did not affect plasma membrane localization of the ectopically expressed multivitamin transporter suggesting reduced but not abolished function, such as lower catalytic activity. Targeted therapeutic intervention yielded clinical improvement in four of the five patients. Early molecular diagnosis by exome sequencing is essential for timely replacement therapy in affected individuals.Subject terms: Peripheral neuropathies, Genetics research     

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

PurposeGenitopatellar 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.MethodsWe 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.ResultsWe 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.ConclusionOur 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.     

Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations

Background

Noonan syndrome, cardio‐facio‐cutaneous syndrome (CFC) and Costello syndrome constitute a group of developmental disorders with an overlapping pattern of congenital anomalies. Each of these conditions can be caused by germline mutations in key components of the highly conserved Ras‐MAPK pathway, possibly reflecting a similar pathogenesis underlying the three disorders. Germline mutations in KRAS have recently been identified in a small number of patients with Noonan syndrome and CFC.

Methods and results

260 patients were screened for KRAS mutations by direct sequencing. Overall, we detected KRAS mutations in 12 patients, including three known and eight novel sequence alterations. All mutations are predicted to cause single amino acid substitutions. Remarkably, our cohort of individuals with KRAS mutations showed a high clinical variability, ranging from Noonan syndrome to CFC, and also included two patients who met the clinical criteria of Costello syndrome.

Conclusion

Our findings reinforce the picture of a clustered distribution of disease associated KRAS germline alterations. We further defined the phenotypic spectrum associated with KRAS missense mutations and provided the first evidence of clinical differences in patients with KRAS mutations compared with Noonan syndrome affected individuals with heterozygous PTPN11 mutations and CFC patients carrying a BRAF, MEK1 or MEK1 alteration, respectively. We speculate that the observed phenotypic variability may be related, at least in part, to specific genotypes and possibly reflects the central role of K‐Ras in a number of different signalling pathways.Noonan syndrome (OMIM 163950), cardio‐facio‐cutaneous syndrome (CFC; OMIM 115150) and Costello syndrome (OMIM 218040) are distinct entities that share a common pattern of congenital anomalies, including typical heart defects, overlapping craniofacial dysmorphisms, short stature and a variable degree of mental retardation. Discrimination between the three conditions is based mainly on distinct clinical features such as dry hyperkeratotic skin and hair abnormalities in patients with CFC,¹ and redundant and loose skin with deep palmar and plantar creases as well as a coarse facial appearance in those with Costello syndrome.² In addition, mental development is more severely impaired in CFC and Costello syndrome whereas Noonan syndrome is usually associated with minor cognitive deficits or even normal intelligence.³ While patients with Noonan syndrome and CFC have no or only a slightly increased risk of tumour development, the incidence of tumours in Costello syndrome has been estimated to be 7–21%.⁴ Although various attempts have been undertaken to develop standardised diagnostic criteria for these entities,^5,6 considerable overlap exists and in some instances a patient''s phenotype cannot be clearly assigned to one of these conditions.Missense mutations in PTPN11 were first identified in patients with Noonan syndrome⁷ and subsequently have been shown to account for almost 50% of cases.^8,9PTPN11 encodes the protein tyrosine phosphatase SHP‐2 which relays growth signals from activated tyrosine kinase receptors to other signalling molecules, particularly Ras (reviewed by Neel et al¹⁰). Noonan syndrome causing PTPN11 mutations have been thought to result in gain‐of‐function of SHP‐2 and cause deregulation of Ras dependent signalling cascades.¹¹ Heterozygous germline mutations in KRAS were reported to occur in a minority of patients with Noonan syndrome¹² and CFC,^12,13 shortly after mutations in HRAS had been detected in the majority of individuals with Costello syndrome.¹⁴ Moreover, mutations in BRAF, MEK1 and MEK2, encoding proteins involved in Ras downstream signalling, were shown to cause CFC syndrome.^13,15 Taken together, the current data suggest that germline missense mutations in the aforementioned genes culminate in deregulated Ras‐MAPK signalling that most likely represents the common pathogenetic basis of this group of developmental disorders.^16,17Ras isoforms encoded by the three genes KRAS, HRAS and NRAS represent highly conserved signal transduction molecules. They act as molecular switches through cycling between an active GTP bound and an inactive GDP bound state,¹⁸ and in their active form they interact with a variety of downstream effector proteins.¹⁹RAS genes have long been known as proto‐oncogenes mutated in various types of human cancers (reviewed by Bos²⁰). The majority of these oncogenic RAS mutations affect amino acid residues G12, G13 and Q61 and cause Ras to accumulate in the active GTP bound state by impairing intrinsic GTPase activity and conferring resistance to GTPase activating proteins (GAPs).²⁰ Germline HRAS mutations associated with Costello syndrome almost exclusively affect codons 12 and 13 and are identical to somatic alterations identified in cancer,¹⁴ hence explaining the high risk of tumour development in Costello syndrome. In contrast, KRAS mutations described to date in patients with Noonan syndrome/CFC are distinct from those found in malignancies. Similar to the concept of activating PTPN11 mutations in Noonan syndrome and malignancies,¹¹KRAS mutations associated with Noonan syndrome or CFC might give rise to mutant proteins with a relatively mild gain‐of‐function which are tolerated in the germline as well as during embryonic development. Specifically, KRAS mutations identified in Noonan syndrome patients include V14I and T58I whereas P34R and G60R were found in CFC patients.^12,13 Mutations in KRAS exon 6, causing amino acid alterations in the C terminal portion of isoform B, such as D153V and V152G, were found to be associated with a severe Noonan syndrome or CFC phenotype.^12,13,21 It has been proposed that all mutations lead to stabilisation of K‐Ras in the active conformation, most likely by different gain‐of‐function mechanisms.^12,21Here we report the results of KRAS mutation screening in a large cohort of patients with Noonan syndrome and related disorders.     

Post-transplant lymphoproliferative disorders: a morphologic, phenotypic and genotypic spectrum of disease

The post-transplant lymphoproliferative disorders represent a spectrum of life-threatening, generally Epstein-Barr virus-associated lymphoid proliferations which occur in the setting of exogenous immunosuppression following organ transplantation. Histopathological, phenotypic, genotypic and Epstein-Barr virus studies have revealed a broad range of abnormalities. At one end of the spectrum, they are polymorphic polyclonal proliferations with many features of a florid viral infection and, at the other end, they are monomorphic and monoclonal which would fulfill the criteria for a conventional non-Hodgkin's lymphoma, usually of B-cell type. Some patients have both polyclonal and monoclonal lesions and some have two or more monoclonal populations. Finally, because of the varied appearances, different classification schemes have been developed with reported prognostic implications.     

APC mutation and phenotypic spectrum of Singapore familial adenomatous polyposis patients

Familial adenomatous polyposis (FAP) is a familial form of colon cancer caused by mutation of the adenomatous polyposis coli (APC) gene. Although the APC gene has been extensively studied in the Caucasian population, it has not been previously described in the Chinese population. In the present study, we investigated APC mutation and phenotypic spectrum in the Singapore FAP families who are predominantly Chinese. The protein truncation test (PTT) was used to screen the entire APC gene for germline mutations in 28 unrelated families. Fifteen different mutations were identified in 22 families. Eight mutations were 1-11 basepair deletions or insertions; three involved deletions of whole exons and four were nonsense mutations. Nine of the mutations, including two complex rearrangements, are novel. Eight families including three de novo cases have the same (AAAGA) deletion at codon 1309, indicating that like the Western families, codon 1309 is also the mutation 'hot spot' for Singapore FAP families. In contrast, we did not find any mutation in codon 1061, the second hot spot for the Western population. Congenital hypertrophy of the retinal pigment epithelium (CHRPE) is consistently associated with the prescribed domain (codons 463 to 1387) and is the only phenotype with no intra-family variation. Other than CHRPE, differences in the type and frequency of extracolonic manifestations within the FAP families suggest the influence of modifying genes and environmental factors.     

Genome-wide sequencing expands the phenotypic spectrum of EP300 variants

Many disease genes are defined by their role in causing specific clinically recognizable syndromes. Heterozygous loss of function of the gene EP300 is responsible for a minority of cases of Rubinstein-Taybi syndrome (RSTS). With the application of whole-exome sequencing and whole-genome sequencing, there is the potential to discover new genotype-phenotype correlations. The purpose of this case series is to describe three unrelated females without classic manifestations of RSTS who were unexpectedly found on genome-wide sequencing to have likely pathogenic variants in EP300. These individuals expand our knowledge of the disease spectrum by virtue of their very rare or novel clinical features. Results are placed within the context of all prior published EP300 cases not ascertained by targeted testing, which are disproportionately female compared with a cohort identified because of a clinical suspicion of RSTS (p = 0.01). There are implications for diagnosis, management, and genetic counselling of individuals with EP300-related disease.     

Novel PRNP sequence variant associated with familial encephalopathy

Human transmissible spongiform encephalopathies (TSEs) are a group of chronic progressive neurodegenerative disorders that may be hereditary, infectious, or sporadic. Hereditary TSEs are associated with mutations in the PRNP gene on chromosome 20p12-pter. We report on a family in which seven patients developed limb and truncal ataxia, dysarthria, myoclonic jerks, and cognitive decline. The age of onset in the 30s, 40s, or 50s, prolonged disease duration, cerebellar atrophy on imaging, and the presence of synchronic periodic discharges on electroencephalogram suggested a familial encephalopathy resembling Gerstmann-Str?ussler-Scheinker disease. A novel H187R mutation has been identified in affected, but not in unaffected, family members or unrelated controls suggesting a pathogenic role for this mutation. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:653-656, 1999. Published 1999 Wiley-Liss, Inc.     

A homozygous frameshift variant expands the clinical spectrum of SAMD9 gene defects

SAMD9, a ubiquitously expressed protein, is involved in several mechanisms, including endosome fusion, growth suppression and modulation of innate immune responses to stress and viral infections. While biallelic mutations in SAMD9 are linked to normophosphatemic familial tumoral calcinosis, heterozygous gain-of-function mutations in the same gene are responsible for MIRAGE, a multisystemic syndrome characterized by m yelodysplasia, i nfection, r estriction of growth, a drenal hypoplasia, g enital phenotypes, and e nteropathy. A two-and-a-half-year-old girl, from a consanguineous Lebanese family, was included in this study. She presents with pre- and post-natal growth retardation, recurrent fevers, persistent diarrhea, elevated CRP and intermittent hypoglycemia. Whole genome sequencing revealed a homozygous frameshift variant in SAMD9 (NM_017654.4: c.480_481del; p.Val162Ilefs*5) in the proband. Sanger sequencing confirms its segregation with the disease in the family, and immunoblotting showed that the detected variant abolishes SAMD9 expression in the patient. Our findings expand the clinical spectrum linked to SAMD9 and highlight the importance of investigating further cases with mutations in this gene, as this will pave the way towards the understanding of the pathways driving these diseases.     

Richieri‐Costa‐Pereira syndrome: Expanding its phenotypic and genotypic spectrum

Richieri‐Costa‐Pereira syndrome is a rare autosomal recessive acrofacial dysostosis that has been mainly described in Brazilian individuals. The cardinal features include Robin sequence, cleft mandible, laryngeal anomalies and limb defects. A biallelic expansion of a complex repeated motif in the 5′ untranslated region of EIF4A3 has been shown to cause this syndrome, commonly with 15 or 16 repeats. The only patient with mild clinical findings harbored a 14‐repeat expansion in 1 allele and a point mutation in the other allele. This proband is described here in more details, as well as is his affected sister, and 5 new individuals with Richieri‐Costa‐Pereira syndrome, including a patient from England, of African ancestry. This study has expanded the phenotype in this syndrome by the observation of microcephaly, better characterization of skeletal abnormalities, less severe phenotype with only mild facial dysmorphisms and limb anomalies, as well as the absence of cleft mandible, which is a hallmark of the syndrome. Although the most frequent mutation in this study was the recurrent 16‐repeat expansion in EIF4A3, there was an overrepresentation of the 14‐repeat expansion, with mild phenotypic expression, thus suggesting that the number of these motifs could play a role in phenotypic delineation.