Characterization of 14 novel deletions underlying Rubinstein-Taybi syndrome: an update of the CREBBP deletion repertoire

Rubinstein-Taybi syndrome (RSTS) is a rare, clinically heterogeneous disorder characterized by cognitive impairment and several multiple congenital anomalies. The syndrome is caused by almost private point mutations in the CREBBP (~55% of cases) and EP300 (~8%) genes. The CREBBP mutational spectrum is variegated and characterized by point mutations (30-50 %) and deletions (~10%). The latter are diverse in size and genomic position and remove either the whole CREBBP gene and its flanking regions or only an intragenic portion. Here, we report 14 novel CREBBP deletions ranging from single exons to the whole gene and flanking regions which were identified by applying complementary cytomolecular techniques: fluorescence in situ hybridization, multiplex ligation-dependent probe amplification and array comparative genome hybridization, to a large cohort of RSTS patients. Deletions involving CREBBP account for 23% of our detected CREBBP mutations, making an important contribution to the mutational spectrum. Genotype-phenotype correlations revealed that patients with CREBBP deletions extending beyond this gene did not always have a more severe phenotype than patients harboring CREBBP point mutations, suggesting that neighboring genes play only a limited role in the etiopathogenesis of CREBBP-centerd contiguous gene syndrome. Accordingly, the extent of the deletion is not predictive of the severity of the clinical phenotype.

Molecular analysis, pathogenic mechanisms, and readthrough therapy on a large cohort of Kabuki syndrome patients

Kabuki syndrome (KS) is a multiple congenital anomalies syndrome characterized by characteristic facial features and varying degrees of mental retardation, caused by mutations in KMT2D/MLL2 and KDM6A/UTX genes. In this study, we performed a mutational screening on 303 Kabuki patients by direct sequencing, MLPA, and quantitative PCR identifying 133 KMT2D, 62 never described before, and four KDM6A mutations, three of them are novel. We found that a number of KMT2D truncating mutations result in mRNA degradation through the nonsense-mediated mRNA decay, contributing to protein haploinsufficiency. Furthermore, we demonstrated that the reduction of KMT2D protein level in patients’ lymphoblastoid and skin fibroblast cell lines carrying KMT2D-truncating mutations affects the expression levels of known KMT2D target genes. Finally, we hypothesized that the KS patients may benefit from a readthrough therapy to restore physiological levels of KMT2D and KDM6A proteins. To assess this, we performed a proof-of-principle study on 14 KMT2D and two KDM6A nonsense mutations using specific compounds that mediate translational readthrough and thereby stimulate the re-expression of full-length functional proteins. Our experimental data showed that both KMT2D and KDM6A nonsense mutations displayed high levels of readthrough in response to gentamicin treatment, paving the way to further studies aimed at eventually treating some Kabuki patients with readthrough inducers.

Microduplications in 22q11.2 and 8q22.1 associated with mild mental retardation and generalized overgrowth

The 22q11.2 microduplication is a genomic disorder, characterized from a variable phenotype ranging from different defects to normality. The most common microduplication of 22q11.2 is 3 Mb in size, but there are also cases reported with atypical duplications between 0.8 Mb and 6Mb. Here, we describe a case of a child with macrocephaly, overgrowth with advanced bone age, attention deficits, evidence of mild mental retardation and dysmorphic features. An array-CGH analysis detected a 252 Kb duplication at the 22q11.2 region inherited from mother and 142 Kb duplication at 8q22.1 region inherited from father. Both parents show mild dysmorphic features. The duplicated genes in chromosomes 22q and 8q are TOP3B and PGCP, respectively. We describe for the first time a patient carrying the smaller atypical 22q11.2 duplication who also presents with mild mental retardation and generalized overgrowth. This patient has an additional duplication in 8q22.1 which may act as a genomic modifier of its clinical phenotype.

Pure 16q21q22.1 deletion in a complex rearrangement possibly caused by a chromothripsis event

BACKGROUND

Partial monosomies of chromosome 16q are rare and overlapping effects from complex chromosomal rearrangements often hamper genotype-phenotype correlations for such imbalances. Here, we report the clinical features of an isolated partial monosomy 16q21q22.1 in a boy with a complex de novo rearrangement possibly resulting from a chromothripsis event.

RESULTS

The patient presented with low birth weight, microcephaly, developmental delay, facial dysmorphisms, short stature, dysmorphic ears and cardiopathy. Standard and molecular cytogenetics showed a complex rearrangement characterised by a pericentromeric inversion in one of chromosomes 12 and an inverted insertional translocation of the 12q14q21.1 region, from the rearranged chromosome 12, into the q21q22.1 tract of a chromosome 16. Array-CGH analysis unravelled a partial 16q21q22.1 monosomy, localised in the rearranged chromosome 16.

CONCLUSIONS

The comparison of the present case to other 16q21q22 monosomies contributed to narrow down the critical region for cardiac anomalies in the 16q22 deletion syndrome. However, more cases, well characterised both for phenotypic signs and genomic details, are needed to further restrict candidate regions for phenotypic signs in 16q deletions. The present case also provided evidence that a very complex rearrangement, possibly caused by a chromothripsis event, might be hidden behind a classical phenotype that is specific for a syndrome.

20 novel point mutations and one large deletion in EXT1 and EXT2 genes: report of diagnostic screening in a large Italian cohort of patients affected by hereditary multiple exostosis

BACKGROUND

Hereditary multiple exostosis represents the most frequent bone tumor disease in humans. It consists of cartilage deformities affecting the juxta-ephyseal region of long bones. Usually benign, exostosis could degenerate in malignant chondrosarcoma form in less than 5% of the cases. Being caused by mutations in the predicted tumor suppressor genes, EXT1 (chr 8q23-q24) and EXT2 (chr 11p11-p12) genes, HMEs are usually inherited with an autosomal dominant pattern, although "de novo" cases are not infrequent.

AIM

Here we present our genetic diagnostic report on the largest Southern Italy cohort of HME patients consisting of 90 subjects recruited over the last 5years.

RESULTS

Molecular screening performed by direct sequencing of both EXT1 and EXT2 genes, by MLPA and Array CGH analyses led to the identification of 66 mutations (56 different occurrences) and one large EXT2 deletion out of 90 patients (74.4%). The total of 21 mutations (20 different occurrences, 33.3%) and the EXT2 gene deletion were novel. In agreement with literature data, EXT1 gene mutations were scattered along all the protein sequence, while EXT2 lesions fell in the first part of the protein. Conservation, damaging prediction and 3-D modeling, in-silico, analyses, performed on three novel missense variants, confirmed that at least in two cases the novel aminoacidic changes could alter the structure stability causing a strong protein misfolding.

CONCLUSIONS

Here we present 20 novel EXT1/EXT2 mutations and one large EXT2 deletion identified in the largest Southern Italy cohort of patients affected by hereditary multiple exostosis.

Clinical significance of rare copy number variations in epilepsy: a case-control survey using microarray-based comparative genomic hybridization

OBJECTIVE

To perform an extensive search for genomic rearrangements by microarray-based comparative genomic hybridization in patients with epilepsy.

DESIGN

Prospective cohort study.

SETTING

Epilepsy centers in Italy.

PATIENTS

Two hundred seventy-nine patients with unexplained epilepsy, 265 individuals with nonsyndromic mental retardation but no epilepsy, and 246 healthy control subjects were screened by microarray-based comparative genomic hybridization.

MAIN OUTCOME MEASURES

Identification of copy number variations (CNVs) and gene enrichment.

RESULTS

Rare CNVs occurred in 26 patients (9.3%) and 16 healthy control subjects (6.5%) (P = .26). The CNVs identified in patients were larger (P = .03) and showed higher gene content (P = .02) than those in control subjects. The CNVs larger than 1 megabase (P = .002) and including more than 10 genes (P = .005) occurred more frequently in patients than in control subjects. Nine patients (34.6%) among those harboring rare CNVs showed rearrangements associated with emerging microdeletion or microduplication syndromes. Mental retardation and neuropsychiatric features were associated with rare CNVs (P = .004), whereas epilepsy type was not. The CNV rate in patients with epilepsy and mental retardation or neuropsychiatric features is not different from that observed in patients with mental retardation only. Moreover, significant enrichment of genes involved in ion transport was observed within CNVs identified in patients with epilepsy.

CONCLUSIONS

Patients with epilepsy show a significantly increased burden of large, rare, gene-rich CNVs, particularly when associated with mental retardation and neuropsychiatric features. The limited overlap between CNVs observed in the epilepsy group and those observed in the group with mental retardation only as well as the involvement of specific (ion channel) genes indicate a specific association between the identified CNVs and epilepsy. Screening for CNVs should be performed for diagnostic purposes preferentially in patients with epilepsy and mental retardation or neuropsychiatric features.

Clinical phenotype and molecular characterization of 6q terminal deletion syndrome: Five new cases

Mental retardation, facial dysmorphisms, seizures, and brain abnormalities are features of 6q terminal deletions. We have ascertained five patients with 6q subtelomere deletions (four de novo, one as a result of an unbalanced translocation) and determined the size of the deletion ranging from 3 to 13 Mb. Our patients showed a recognizable phenotype including mental retardation, characteristic facial appearance, and a distinctive clinico-neuroradiological picture. Focal epilepsy with consistent electroencephalographic features and with certain brain anomalies on neuroimaging studies should suggest 6q terminal deletion. The awareness of the distinctive clinical picture will help in the diagnosis of this chromosomal abnormality.

Phenotypic and molecular characterisation of the Aarskog–Scott syndrome: a survey of the clinical variability in light of FGD1 mutation analysis in 46 patients

Faciogenital dysplasia or Aarskog-Scott syndrome (AAS) is a genetically heterogeneous developmental disorder. The X-linked form of AAS has been ascribed to mutations in the FGD1 gene. However, although AAS may be considered as a relatively frequent clinical diagnosis, mutations have been established in few patients. Genetic heterogeneity and the clinical overlap with a number of other syndromes might explain this discrepancy. In this study, we have conducted a single-strand conformation polymorphism (SSCP) analysis of the entire coding region of FGD1 in 46 AAS patients and identified eight novel mutations, including one insertion, four deletions and three missense mutations (19.56% detection rate). One mutation (528insC) was found in two independent families. The mutations are scattered all along the coding sequence. Phenotypically, all affected males present with the characteristic AAS phenotype. FGD1 mutations were not associated with severe mental retardation. However, neuropsychiatric disorders, mainly behavioural and learning problems in childhood, were observed in five out of 12 mutated individuals. The current study provides further evidence that mutations of FGD1 may cause AAS and expands the spectrum of disease-causing mutations. The importance of considering the neuropsychological phenotype of AAS patients is discussed.

A mutation in the pleckstrin homology (PH) domain of the FGD1 gene in an Italian family with faciogenital dysplasia (Aarskog-Scott syndrome)

Aarskog-Scott Syndrome (AAS) is an X-linked disorder characterised by short stature and multiple facial, limb and genital abnormalities. A gene, FGD1, altered in a patient with AAS phenotype, has been identified and found to encode a protein with homology to Rho/Rac guanine nucleotide exchange factors (Rho/Rac GEF). However, since this original report on identification of a mutated FGD1 gene in an AAS patient, no additional mutations in the FGD1 gene have been described. We analysed 13 independent patients with clinical diagnosis of AAS. One patient presented a mutation that results in a nucleotide change in exon 10 of the FGD1 gene (G2559>A) substituting a Gln for Arg in position 610. The mutation was found to segregate with the AAS phenotype in affected males and carrier females in the family of this patient. Interestingly, Arg-610 is located within one of the two pleckstrin homology (PH) domains of the FGD1 gene and it corresponds to a highly conserved residue which has been involved in InsP binding in PH domains of other proteins. The same residue is often mutated in the Bruton's tyrosine kinase (Btk) gene in patients with an X-linked agammaglobulinemia. The Arg610Gln mutation represents the first case of a mutation in the PH domain of the FGD1 gene and additional evidence that mutations in PH domains can be associated to human diseases.

Phenotypic variability in the chromosome 9 ring

The syndrome associated to the 9 ring is not commonly observed. The first remark was by Kistenmacher (1970) who examined a male. Later observation of other cases has allowed the syndrome to be described, so that it can be said to be characterized by constant signs, such as microcephaly, psychomotor retardation of varying entity and facial dysmorphism corresponding to that observed in 9 p monosomy. The variability of the phenotype has to be compared with the entity of the telomeric deletion, since the clinical outlook, especially the entity of retardation, could be less serious in case of small deletions.

Autosomal recessive familial exudative vitreoretinopathy: evidence for genetic heterogeneity

Two unrelated families with familial exudative vitreoretinopathy (FEVR) show apparent autosomal recessive inheritance rather than the previously reported autosomal dominant or X-linked recessive mode of inheritance. Compared with the other modes of inheritance, the inherited clinical features here include earlier onset (at birth) and a more severe progressive course.

Ring (13),t(2;6) associated with familial fragile (16)

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Abnormal B.A.E.P. in a family with Moebius syndrome: evidence for supranuclear lesion

A family with Moebius syndrome is presented. Neurological lesions in the affected members are various: complete VI and VII cranial nerves palsy associated with mental retardation in the proband; left convergent strabismus and mental retardation in a brother of the proband and only mental retardation in a sister of the proband. The brainstem auditory evoked potentials (B.A.E.P.), investigated in the proband and his affected sister, are abnormal. The presence of the anomaly after the 3rd wave is consistent with a disfunction of the auditory tract at a supranuclear level. The mental deficiency and the supranuclear site of the acoustic lesion are an indication for a more general involvement of C.N.S. than cranial nerve nuclei alone. Karyotype and dermatoglyphics of the three affected subjects were normal. The authors hypothesized the same disorganogenetic factor acting very early (4th-6th week of gestational age) on the metamerization process of limb buds mesoderm and brainstem gray matter.

Study of a form of pulverulent cataract in a large kindred

A large kindred (64 members in four generations), affected by a form of apparently congenital pulverulent cataract, was studied for linkage of its gene locus with that of the Fy blood group. No indication of linkage was found. The involvement of the cortex distinguishes this form from the zonular pulverulent cataract (total nuclear) of Nettleship and Ogilvie, the locus of which is probably linked with Fy. A correlation between morphological and genetic heterogeneity, based on the linkage with Fy, cannot be established because of the scarcity of published data.

Multiple skeletal familial abnormalities associated with balanced reciprocal translocation 2;8(q32;p13)

A father and three of his offspring had skeletal abnormalities consisting of a short forearm, cubitus valgus, fusion of first and second cervical vertebrae, and cleft of L5 and S1. All four had a reciprocal, apparently balanced, translocation 2;8(q32;p13). Normal sibs had normal chromosomes. We conclude that this may be a rare instance of an autosomal dominant condition associated with a balanced chromosome translocation.

[Severe mental retardation and slight dysmorphism in a child with a bisatellite extrachromosome: inversion duplication (15)?]

A de novo tetrasomy 15 has been reported, in a 6 years old child. The patient had severe mental retardation an minimal physical stigmata, consisting in slight skeletal and facial dismorphism. Cytogenetic analysis showed that extrachromosome, G-like long, was bisatellited and dicentric and was interpreted either as an inversion duplication 15 or as 15; G or D translocation.

[Aarskog's syndrome (facial-digital-genital syndrome). Study of a family (author's transl)]

A case of Aarskog syndrome in a 6-years old boy is reported. The patient showed clinical pictures typical of the syndrome: characteristic dysmorphic facies, palpebral ptosis, brachyfalangism, abnormality of the scrotum. Minimal stigmata and clinodactyly of 5th finger were present in a sister. Isolated bilateral clinodactyly was found in other 4 members of the family. The significance of this sign in the context of the syndrome has been discussed. Unusual dermatoglyphic patterns were present in the proband, mother and sister.

[XXXXY syndrome: clinical-radiological findings in one patient (author's transl)]

A case of XXXXY syndrome in a 15 year old male is reported. Clinical findings (mental retardation, muscular hypotonia, hypogonadism, characteristic facies), chromosome analyses as well as fingerprint ridge counts were typical of the syndrome. Several radiological abnormalities were found. It is noteworthy that features consistent with epiphysial dysplasia were present. In the patient's kindred a case of "cri du chat" syndrome and a 5:9 balanced translocation were discovered.

A and B postaxial polydactyly in two members of the same family

Two cases of previously unreported simultaneous presence of A and B postaxial polydactyly in two brothers out of 12 affected members of a kindred are reported. The findings are consistent with the hypothesis that in this family A and b types of postaxial polydactyly are caused by a single gene rather than by two different genes.

Primary protrusio acetabuli in four generations of an Italian family

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