Partial monosomy of chromosome 1p36.3: Characterization of the critical region and delineation of a syndrome

We describe 5 patients ranging in age from 3 to 47 years, with karyotypic abnormalities resulting in monosomy for portion of 1p36.3, microcephaly, mental retardation, prominent forehead, deep-set eyes, depressed nasal bridge, flat midface, relative prognathism, and abnormal ears. Four patients have small hands and feet. All exhibited selfabusive behavior. Additional findings in some of the patients include brain anomalies, optic atrophy, hearing loss and skeletal deformities. The breakpoints within chromosome 1 were designated at 1p36.31 (3 cases), 1p36.32 (1 case) and 1p36.33 (1 case), Thus, the smallest region of deletion overlap is 1p36.33→1pter. Detection of the abnormal 1 relied on high resolution G-band analysis. Fluorescence in situ hybridization (FISH) utilizing a DNA probe (Oncor D1Z2) containing the repetitive sequences in distal 1p36, confirmed a deletion of one 1 homologue in all 5 cases. The abnormal 1 resulted from a de novo deletion in only one patient. The remaining patients were either confirmed (3 cases) or suspected (1 case) to have unbalanced translocations. Despite the additional genetic imbalance present in these four cases, monosomy of 1p36.33 appears to be responsible for a specific clinical phenotype. Characterization of this phenotype should assist in the clinical diagnosis of this chromosome abnormality. © 1995 Wiley-Liss, Inc.     

The level of 6-phosphogluconate dehydrogenase (6-PGD) activity in a patient with a 1p terminal deletion suggests that the gene locus is not distal to sub-band p36.3 on chromosome 1

A rare case of chromosome 1p deletion is reported in a mentally retarded male infant with a derived chromosome: 45,XY,-1,-13,tdic(1;13)(1qter----1p36.2::13p11.2----++ +13qter). Parental chromosomes were normal. Since the patient's 6-PGD specific activity was in the normal range, it is probable that he retained both 6-PGD alleles. Consequently, if a dosage affect exists, then the locus for 6-PGD must be proximal to 1p36.3.     

一例类似Prader-Willi综合征表型患者的染色体1p36.3隐匿缺失检测

目的 对1例具有类似Prader-Willi综合征(Prader-Will-like syndrome,PWS)表型患者进行核型分析,确诊其病因.方法 应用高分辨染色体显带技术分析核型及甲基化PCR技术分析15号染色体的遗传印迹区,应用多重连接依赖性探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术筛查患者染色体亚端粒区的异常,经荧光原位杂交(fluorescence in situ hybridization,FISH)验证并结合实时定量PCR进一步确定患者染色体的缺失区域.结果 高分辨染色体检测未发现患者核型异常,甲基化PCR未发现患者的15号染色体遗传印迹基因异常,MLPA分析显示患者存在1p亚端粒区缺失,该结果得到1p亚端粒区探针的FISH证实.进一步选择1p36区域的3个BAC探针进行FISH分析,结合实时定量PCR技术,显示缺失区域位于1p36.3区的4.2 Mb范围内,家系分析显示患者为新发生的染色体异常.确诊为1p36缺失综合征.结论 对类似PWS表型的患者,应进一步做细胞分子学诊断,以明确其发病原因.     

Microdeletions of chromosome 7p21, including TWIST1, associated with significant microcephaly, facial dysmorphism, and short stature

Saethre-Chotzen syndrome due to TWIST1 mutations is characterized by coronal synostosis, facial dysmorphism and additional variable anomalies. Small deletions comprising the whole TWIST1 account for a small proportion of patients with Saethre-Chotzen syndrome. Here we describe 3 patients with facial dysmorphism, marked microcephaly, short stature (2/3 patients), and overlapping 7p21 microdeletions. Molecular karyotyping identified small deletions of chromosome 7p21 including TWIST1 with a size of 526 kb, 9.2 Mb, and 11.7 Mb, respectively. The clinical manifestations of these patients do not resemble the typical phenotype of Saethre-Chotzen syndrome. In the two patients with larger microdeletions, severe mental retardation and significant short stature are present. Facial dysmorphism of patient 3 includes also signs of blepharophimosis-ptosis-epicanthus inversus syndrome.     

Molecular and clinical characterization of a patient with duplication of 1p36.3 and metopic synostosis

Chromosome 1p duplications are rare. There have been only 11 reported cases of isolated 1p duplication, all of which were proximal, interstitial duplications. We present a patient with a terminal duplication of 1p (1p36.3). To our knowledge, this is the first such reported case. Our patient presented with metopic synostosis, rectal stenosis, atrial septal defect, and mildly delayed gross motor development. Molecular characterization using microsatellite marker analysis and fluorescence in situ hybridization (FISH) revealed an area of duplication between p58 and D1S2893, approximately 13 cM in size. We compare our patient's clinical findings with the clinical phenotype found in patients with the corresponding deletion of 1p36.3 and discuss the role of gene dosage in other deletion/duplication syndromes.     

Reciprocal translocation t(1;15)(p36.2;p11.2): Confirmation of a suggestive cytogenetic diagnosis by in situ hybridization and clinical case report on resulting monosomy (1p)

A newborn girl with generalized muscular hypotonia and minor anomalies was referred for chromosome analysis. Cytogenetic investigation showed a satellite and an Ag-positive NOR on the distal short arm of one chromosome 1, thus indicating an unbalanced translocation involving the short arm of an acrocentric chromosome. The phenotypically normal mother had the same satellited chromosome 1 with Ag-positive NOR. One chromosome 15 was the only acrocentric chromosome in her karyotype lacking recognizable satellites and an Ag-positive NOR. Thus a balanced reciprocal translocation between the short arms of chromosomes 1 and 15 in the mother was suggested. The cytogenetic diagnosis was confirmed by nonradioactive in situ hybridization with the most distal DNA probe on chromosome 1, the probe p1-79, localized at chromosome band 1p36.3. The probe was biotinylated by nick-translation, and detection was done by FITC labelled avidin binding. Hybridization signals were observed on both the mother's normal chromosome 1 and the derivative chromosome 15 but not on her derivative chromosome 1. Consequently, the index patient has an unbalanced karyotype with monosomy (1p36.3). Comparing their clinical reports shows that patients with similar terminal deletions of 1p share several manifestations. © 1992 Wiley-Liss, Inc.     

Bi-allelic PAGR1 variants are associated with microcephaly and a severe neurodevelopmental disorder: Genetic evidence from two families

Exome and genome sequencing were used to identify the genetic etiology of a severe neurodevelopmental disorder in two unrelated Ashkenazi Jewish families with three affected individuals. The clinical findings included a prenatal presentation of microcephaly, polyhydramnios and clenched hands while postnatal findings included microcephaly, severe developmental delay, dysmorphism, neurologic deficits, and death in infancy. A shared rare homozygous, missense variant (c.274A > G; p.Ser92Gly, NM_024516.4) was identified in PAGR1, a gene currently not associated with a Mendelian disease. PAGR1 encodes a component of the histone methyltransferase MLL2/MLL3 complex and may function in the DNA damage response pathway. Complete knockout of the murine Pagr1a is embryonic-lethal. Given the available evidence, PAGR1 is a strong candidate gene for a novel autosomal recessive severe syndromic neurodevelopmental disorder.     

Biallelic PRMT7 pathogenic variants are associated with a recognizable syndromic neurodevelopmental disorder with short stature,obesity, and craniofacial and digital abnormalities

PurposeProtein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyzes the methylation of arginine residues on several protein substrates. Biallelic pathogenic PRMT7 variants have previously been associated with a syndromic neurodevelopmental disorder characterized by short stature, brachydactyly, intellectual developmental disability, and seizures. To our knowledge, no comprehensive study describes the detailed clinical characteristics of this syndrome. Thus, we aim to delineate the phenotypic spectrum of PRMT7-related disorder.MethodsWe assembled a cohort of 51 affected individuals from 39 different families, gathering clinical information from 36 newly described affected individuals and reviewing data of 15 individuals from the literature.ResultsThe main clinical characteristics of the PRMT7-related syndrome are short stature, mild to severe developmental delay/intellectual disability, hypotonia, brachydactyly, and distinct facial morphology, including bifrontal narrowing, prominent supraorbital ridges, sparse eyebrows, short nose with full/broad nasal tip, thin upper lip, full and everted lower lip, and a prominent or squared-off jaw. Additional variable findings include seizures, obesity, nonspecific magnetic resonance imaging abnormalities, eye abnormalities (i.e., strabismus or nystagmus), and hearing loss.ConclusionThis study further delineates and expands the molecular, phenotypic spectrum and natural history of PRMT7-related syndrome characterized by a neurodevelopmental disorder with skeletal, growth, and endocrine abnormalities.     

Type I bipolar disorder associated with a fragile site on chromosome 1

The objective of this paper is to study the association between chromosomal fragile sites and type I bipolar disorder. This case-control study compares bipolar patients with normal controls. Ten cases of type I bipolar disorder diagnosed according to DSM-III-R criteria and the Composite International Diagnostic Interview (CIDI) were selected from the Escola Paulista affective disorders outpatient clinic and 10 healthy controls (CIDI negative for psychiatric diagnoses) matched for sex and age were drawn from the otorhinolaryngologic outpatient clinic of the same hospital. The cytogenetic analysis was carried out with blood lymphocytes, which were cultured in a folic acid--free medium. A total of 100 mitoses per subject were blindly analyzed to the psychiatric diagnostic assignment, and fragile sites were identified according to a minimum expected frequency of events per band in conformity with a Poisson distribution. A higher frequency of chromosomal lesions for cases than controls was found for the following bands: 1q32, 5q31, and 11q23, the 1q32 being considered a fragile site. Although no evident neuropsychiatric etiological component has been mapped to the 1q32 region so far, this finding may lead to further investigation of a possible linkage between genetic markers of this region and bipolar disorder. © 1995 Wiley-Liss, Inc.     

Significance of the small subtelomeric area of chromosome 1 (1p36.3) in the progression of malignant melanoma: FISH deletion screening with YAC DNA probes

The short arm of chromosome 1 (1p), especially the subtelomeric region of 1p36, is a common site for abnormalities in malignant melanoma of the skin. In a recent study nodular melanomas displayed deletions of 1p36 in an augmented percentage of cases. To evaluate the dimension of these deletions and to study their significance for the progression of malignant melanoma we analyzed seven melanoma cell lines, 32 primary tumors, and 32 metastatic tumors by fluorescence in situ hybridization with the DNA probe D1Z2 in 1p36.3 and eight YAC DNA probes hybridizing to 1p36, 1p32, 1p31, and 1p21. All cell lines, 91% of the metastatic tumors and 63% of nodular melanomas showed a deletion of 1p36.3. In the YAC hybridization experiments, the most frequent deletions were found in 1p36 in all cell lines, in 13% of nodular melanoma, and in 44% of metastatic tumors. Deletions in 1p36 were mostly confined to a rather small area near the locus D1Z2. The frequent occurrence of this deletion in melanomas with a high metastatic potential and the abundant accumulation of this deletion in metastasis point to genes located on 1p36, which might be of significance for the metastatic capability of malignant melanoma. Received: 8 February 1999 / Accepted: 15 April 1999     

An interstitial deletion of 7.1 Mb in chromosome band 6p22.3 associated with developmental delay and dysmorphic features including heart defects, short neck, and eye abnormalities

Seven cases with an interstitial deletion of the short arm of chromosome 6 involving the 6p22 region have previously been reported. The clinical phenotype of these cases includes developmental delay, brain-, heart-, and kidney defects, eye abnormalities, short neck, craniofacial malformations, hypotonia, as well as clinodactyly or syndactyly. Here, we report a patient with a 7.1 Mb interstitial deletion of chromosome band 6p22.3, detected by genome-wide screening array CGH. The patient is a 4-year-old girl with developmental delay and dysmorphic features including eye abnormalities, short neck, and a ventricular septum defect. The deleted region at 6p22.3 in our patient overlaps with six out of the seven previously reported cases with a 6p22–24 interstitial deletion. This enabled us to further narrow down the critical region for the 6p22 deletion phenotype to 2.2 Mb. Twelve genes are mapped to the overlapping deleted region, among them the gene encoding the ataxin-1 protein, the ATXN1 gene. Mice with homozygous deletions in ATXN1 are phenotypically normal but show cognitive delay. Haploinsufficiency of ATXN1 may therefore contribute to the learning difficulties observed in the patients harboring a 6p22 deletion.     

De novo triplication at 1p36.23p36.22 further refines the dosage sensitive region of overlap in Setleis syndrome (focal facial dermal dysplasia type III)

Setleis syndrome (SS), or focal facial dermal dysplasia type III (FFDD3, MIM #227260), is an autosomal recessive condition caused by biallelic loss-of-function variants in TWIST2. It is characterized by bitemporal atrophic skin lesions and distinctive facial features. Individuals with de novo or inherited duplication or triplication of the chromosomal region 1p36.22p36.21 have also been reported to have the SS phenotype with additional neurodevelopmental challenges (rarely seen in individuals with TWIST2 mutations) and variable expressivity and penetrance. Triplication of this region is also associated with more severe manifestations compared to a duplication. We report a 2-year-old female patient with features of SS associated with a de novo 3.603 Mb triplication at 1p36.23p36.22 identified on postnatal microarray analysis. Her triplication shares a 281.263 kb overlap with gains at 1p36.22, reported by previous groups, delineating the shortest region of overlap (SRO) to date. This SRO involves 10 RefSeq and 4 OMIM morbid map genes and highlights the candidate dosage-sensitive element(s) underlying the cardinal features of SS phenotype in individuals with gains at 1p36.     

9 Mb deletion including chromosome band 3q24 associated with unsuspicious facial gestalt, persistent ductus omphaloentericus, mild mental retardation and tic

9 Mb deletion including chromosome band 3q24 associated with unsuspicious facial gestalt, persistent ductus omphaloentericus, mild mental retardation and tic.     

Direct duplication of chromosome 1, dir dup(1)(p21.2 → p32) in a Bedouin boy with multiple congenital anomalies

Here we describe a Bedouin boy with a de novo duplication of 1p and multiple congenital anomalies. He had microcephaly, convergent squint, anteverted nostrils, malformed ears, micrognathia, hypoplasia of the terminal phalanges, clinodactyly of 5th fingers, simian creases, left inguinal hernia, cryptorchidism, and severe postnatal growth retardation. Our clinical findings are compared with those of previous reports of duplication involving chromosome 1p.     

Heterozygous de novo variants in CSNK1G1 are associated with syndromic developmental delay and autism spectrum disorder

The gamma-1 isoform of casein kinase 1, the protein encoded by CSNK1G1, is involved in the growth and morphogenesis of cells. This protein is expressed ubiquitously among many tissue types, including the brain, where it regulates the phosphorylation of N-methyl-D-aspartate receptors and plays a role in synaptic transmission. One prior individual with a de novo variant in CSNK1G presenting with severe developmental delay and early-onset epilepsy has been reported. Here we report an updated clinical history of this previously published case, as well as four additional individuals with de novo variants in CSNK1G1 identified via microarray-based comparative genomic hybridization, exome, or genome sequencing. All individuals (n = 5) had developmental delay. At least three individuals had diagnoses of autism spectrum disorder. All participants were noted to have dysmorphic facial features, although the reported findings varied widely and therefore may not clearly be recognizable. None of the participants had additional major malformations. Taken together, our data suggest that CSNK1G1 may be a cause of syndromic developmental delay and possibly autism spectrum disorder.     

Pathogenicity analysis and splicing rescue of a classical splice site variant (c.1343+1G>T) of CNOT1 gene associated with neurodevelopmental disorders

Mutations in the CNOT1 gene lead to an incurable rare neurological disorder mainly manifested as a clinical spectrum of intellectual disability, developmental delay, seizures, and behavioral problems. In this study, we investigated a classical splice site variant of CNOT1 (c.1343+1G>T) associated with neurodevelopmental disorders, which was a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. To link CNOT1 dysfunction with the neurodevelopmental phenotype observed in a patient, in vitro minigene assay was used to verify the effect of CNOT1 gene splice site variant c.1343+1G>T on mRNA splicing. We also explored the impact of transient transfection introducing modified U1 snRNA on correcting the splicing variant. Through minigene expression in mammalian cells, we demonstrated that the variant induced complete exon 12 skipping, which explained the patient's clinical condition and provided additional genetic diagnosis evidence for the clinical significance of the variant. Moreover, we confirmed that the aberrant splice pattern could be partially corrected by the modified U1 snRNA at the mRNA level, which provided strong evidence for the therapeutic potential of modified U1 snRNA in neutralizing the hazardous effect of incorrect splicing patterns.