Patient with del(12)(q12q13.12) manifesting abnormalities compatible with Noonan syndrome

ARID2, a rare cause of Coffin-Siris syndrome: A novel microdeletion at 12q12q13.11 causing severe short stature and literature review

Coffin-Siris syndrome (CSS) 6 is caused by heterozygous pathogenic variants in the AT-rich interaction domain 2 (ARID2) gene on 12q12. Currently, only 26 cases with both detailed clinical and genetic information have been documented in the literature. Microdeletions of the entire ARID2 gene are rare. In this study, we report a 5-year-7-month-old Chinese female who underwent whole-exome sequencing to discover that she had a de novo 1.563 Mb heterozygous copy number loss at 12q12q13.11, involving an entire deletion of ARID2. The female had severe short stature with obvious dysmorphic facial features, global developmental delay and hypoplastic fingers and toes. Her growth hormone level was normal, with reduced IGF-1 and increased CA19-9 levels. After a review of the 27 patients with ARID2 deficiency, a significant positive correlation was observed between age and height standard deviation score (SDS) (r = 0.71, p = 0.0002), suggesting a possibility of growth catch-up. This study expands the genetic and phenotypic spectrum of CCS6 and provides a decision-making reference for growth hormone therapy.

Association between ARID2 and RAS-MAPK pathway in intellectual disability and short stature

BACKGROUND

ARID2 belongs to the Switch/sucrose non-fermenting complex, in which the genetic defects have been found in patients with dysmorphism, short stature and intellectual disability (ID). As the phenotypes of patients with ARID2 mutations partially overlap with those of RASopathy, this study evaluated the biochemical association between ARID2 and RAS-MAPK pathway.

METHODS

The phenotypes of 22 patients with either an ARID2 heterozygous mutation or haploinsufficiency were reviewed. Comprehensive molecular analyses were performed using somatic and induced pluripotent stem cells (iPSCs) of a patient with ARID2 haploinsufficiency as well as using the mouse model of Arid2 haploinsufficiency by CRISPR/Cas9 gene editing.

RESULTS

The phenotypic characteristics of ARID2 deficiency include RASopathy, Coffin-Lowy syndrome or Coffin-Siris syndrome or undefined syndromic ID. Transient ARID2 knockout HeLa cells using an shRNA increased ERK1 and ERK2 phosphorylation. Impaired neuronal differentiation with enhanced RAS-MAPK activity was observed in patient-iPSCs. In addition, Arid2 haploinsufficient mice exhibited reduced body size and learning/memory deficit. ARID2 haploinsufficiency was associated with reduced IFITM1 expression, which interacts with caveolin-1 (CAV-1) and inhibits ERK activation.

DISCUSSION

ARID2 haploinsufficiency is associated with enhanced RAS-MAPK activity, leading to reduced IFITM1 and CAV-1 expression, thereby increasing ERK activity. This altered interaction might lead to abnormal neuronal development and a short stature.

Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31

We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning.

Deletion at 12q12 increases the risk of developmental delay and intellectual disability

Single-nucleotide polymorphism (SNP) arrays have been widely used to identify novel genomic imbalances. Many of these genomic imbalances have been confirmed to interact with developmental delays, intellectual disabilities (IDs), and congenital defects. Here, we identify a Chinese girl with a 3.18-Mb deletion at 12q12 (human genome build 19: 43,418,911-46,601,627) who showed postnatal growth delay, low-set ears, small hands and feet, widely spaced nipples, and blue sclerae. Deletions at 12q12 are extremely rare chromosomal imbalances; only four cases involving a deletion of this type have previously been reported. In these five sporadic cases, all of the patients exhibited developmental issues accompanied by different degrees of ID. A review of DECIPHER patient data revealed an additional six cases involving genomic deletion at 12q12. Many of the patients in these cases exhibited developmental delay and ID. When these patients were included, 91% and 73% of individuals with a deletion in this chromosomal region presented with developmental retardation and ID, respectively. Database searches indicated that this copy number variant (CNV) has not been found in normal humans. Therefore, we suggest that a CNV in this region is a risk factor for developmental retardation and ID.

Haploinsufficiency of ANO6, NELL2 and DBX2 in a boy with intellectual disability and growth delay

We report on a 10-year-old-boy presenting with moderate intellectual disability (ID), impaired motor skills, hypotonia, growth delay, minor anomalies, misaligned teeth, pectus excavatum, small hands and feet, widely spaced nipples, and a 1.13 Mb de novo deletion on HSA12q12 (chr12:44,830,147-45,964,945 bp, hg19), deleting ANO6, NELL2, and DBX2 and the pseudogenes PLEKHA8P1 and RACGAP1P. We suggest DBX2 and NELL2 as disease-causing genes and their haploinsufficiency to be involved in the psychomotor delay in the patient. DBX2 encodes a homeobox protein, highly expressed during neuronal development and regulating differentiation of interneurons in brain and spinal cord. NELL2 is expressed in most of the central and peripheral nervous system, with highest expression in hippocampus and cerebellum, maximizing during neuronal differentiation. The deletion in our patient is the smallest in HSA12q12 reported to date, and it is included in the deletion carried by four previously reported patients. The clinical presentation of these patients points to the recurrence of the following manifestation, possibly delineating a 12q12 deletion syndrome phenotype: moderate to severe developmental/intellectual delay, hypotonia, postnatal growth retardation, skeletal and dental anomalies, minor facial anomalies including strabismus, down slanting palpebral fissures, and large/low-set ears.

12q21.2q22 deletion: a new patient

Interstitial deletions of long arm of chromosome 12 are rare, and the interstitial deletion 12q21.1q22 has been reported to the best of our knowledge in only four patients. Comparing the patients reported, a characteristic phenotypic pattern (facial features like prominent forehead, short and upturned nose, low set ears, and ectodermal abnormalities) can be identified. It has been suggested to be considered a deletion syndrome [Klein et al., (2005); Am J Med Genet 138:349-354]. We report on a 34-month-old girl, who was referred to our clinic at 6 months of age, presenting at birth with axial hypotonia, enlarged anterior fontanel, ventriculomegaly, dysmorphic facies (prominent forehead, sparse hair and eyebrows, short palpebral fissures), failure to thrive and development delay. Her cytogenetic study showed an interstitial deletion of the long arm of chromosome 12: 46,XX,del(12)(q21.1q22) redefined by array comparative genomic hybridization. We compare and review our patient with the four previously reported cases, plus one with a deletion with an overlap of the chromosomal region and phenotypic similarities. As far as we know our patient is the fourth reported with this cytogenetic abnormality. This additional report allows us to support a genotype-phenotype correlation for this chromosomal abnormality.

Noonan syndrome: clinical features, diagnosis, and management guidelines

Noonan syndrome (NS) is a common, clinically and genetically heterogeneous condition characterized by distinctive facial features, short stature, chest deformity, congenital heart disease, and other comorbidities. Gene mutations identified in individuals with the NS phenotype are involved in the Ras/MAPK (mitogen-activated protein kinase) signal transduction pathway and currently explain ∼61% of NS cases. Thus, NS frequently remains a clinical diagnosis. Because of the variability in presentation and the need for multidisciplinary care, it is essential that the condition be identified and managed comprehensively. The Noonan Syndrome Support Group (NSSG) is a nonprofit organization committed to providing support, current information, and understanding to those affected by NS. The NSSG convened a conference of health care providers, all involved in various aspects of NS, to develop these guidelines for use by pediatricians in the diagnosis and management of individuals with NS and to provide updated genetic findings.

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

We demonstrate the successful application of exome sequencing1–3 to discover a gene for an autosomal dominant disorder, Kabuki syndrome (OMIM %147920). The exomes of ten unrelated probands were subjected to massively parallel sequencing. After filtering against SNP databases, there was no compelling candidate gene containing novel variants in all affected individuals. Less stringent filtering criteria permitted modest genetic heterogeneity or missing data, but identified multiple candidate genes. However, genotypic and phenotypic stratification highlighted MLL2, a Trithorax-group histone methyltransferase4, in which seven probands had novel nonsense or frameshift mutations. Follow-up Sanger sequencing detected MLL2 mutations in two of the three remaining cases, and in 26 of 43 additional cases. In families where parental DNA was available, the mutation was confirmed to be de novo (n = 12) or transmitted (n = 2) in concordance with phenotype. Our results strongly suggest that mutations in MLL2 are a major cause of Kabuki syndrome.

12q interstitial deletion with bilateral cleft lip and palate: case report and literature review

The authors report the case of a Japanese girl with interstitial deletion of chromosome 12q15-q21.2 who had multiple congenital anomalies including bilateral cleft lip and palate (BCLP) with intrauterine onset of growth retardation and severe psychomotor developmental delay. Only two other patients with a similar deletion have been reported previously. However, these two patients showed such different clinical features that defining the karyotype-phenotype correlation has remained unfeasible. The additional case presented here reveals that two of the three cases with an overlapping deletion in 12q show the phenotype of BCLP, suggesting the correlation between this area of gene deletion and cleft lip and palate.

New case of interstitial deletion 12(q15-q21.2) in a girl with facial dysmorphism and mental retardation

Interstitial deletions of the long arm of chromosome 12 are rare rearrangements with only 15 cases reported in the literature. The phenotype may include facial dysmorphism, developmental delay, ectodermal abnormalities, cardiac and renal malformations depending on breakpoints' position. Here, we describe a third case of 12(q15-q21.2) deletion ascertained through CGH-array analyses and provide a 5-year follow-up. The patient presented with pre- and postnatal growth retardation, congenital heart defect, developmental delay, and facial dysmorphism changing with age, underlining the importance of long-term follow-up. We compared this new case with previous observations of 12q deletions in order to propose phenotype-karyotype correlations.

Prenatal diagnosis of an interstitial 12q chromosome deletion

Rearrangements involving long arm of chromosome 12 are rare events. To our knowledge, we present the first case of an interstitial deletion of the long arm of chromosome 12 in a prenatal diagnosis. A review of the literature is included in our report.

Interstitial deletion of chromosome 12q: Genotype-phenotype correlation of two patients utilizing array comparative genomic hybridization

Interstitial deletions of chromosome 12q are rare, with only 11 reported cases in the literature. We recently described two cases with cytogenetically identical interstitial deletions of the long arm of chromosome 12. Here, we report on a third patient, a 26-month-old male with a cytogenetically-identical interstitial deletion: 46,XY,del(12)(q21.2q22). Phenotypic features of this male proband included craniofacial and ectodermal anomalies, genitourinary anomalies, minor cardiac abnormalities, mild ventriculomegaly on brain MRI, hyperopia, and developmental delay. To further define the extent of the chromosomal aberration, microarray-based comparative genomic hybridization (array CGH) analysis was performed and the array data was compared to one of our previously reported cases. Although cytogenetic analysis of the two patients was concordant, molecular analysis by array CGH revealed that the patients had discordant distal breakpoints. The determination of molecular breakpoints and phenotypic analyses in these two patients, in conjunction with previously reported cases, leads us to propose a 12q deletion phenotype and a possible genetic locus for hyperkeratosis pilaris/ulerythema ophryogenes.

Another case of interstitial del(12) involving the proposed cardio-facio-cutaneous candidate region

Recent reports of patients with interstitial deletions involving the long arm of chromosome 12 have led to the proposal of a candidate region for the cardio-facio-cutaneous syndrome (CFCS) at (12)(q21.2q22). We now report a patient with an interstitial deletion, del(12)(q21.1q21.3) that overlaps the proposed critical region. The patient is an 11-year-old female with developmental delay. Her growth was normal but she is microcephalic with low set ears. In common with other patients with deletions in this region, she had fine, sparse head and eyebrow hair and a hyperkeratotic follicular rash, which involved her face and limbs. She does not have the diagnostic features of the CFC syndrome.

Phenotype-genotype correlation in two patients with 12q proximal deletion

Proximal 12q deletion is a very rare chromosomal abnormality. Only five cases have been reported. Among the five, an Argentinian patient (Case 1) with del(12)(q11q13) and a Japanese patient (Case 2) with del(12)(q12q13.12) were analyzed because they shared several clinical features: growth and psychomotor developmental delay; strabismus; broad and short nose with anteverted nostrils; high, arched palate; large, lowset ears; widely set nipples; short fingers and clinodactyly of fifth fingers; and abnormality of the second and third toes. To clarify the correlation between the deleted genes and their phenotypes, we delimited their deleted regions by fluorescence in situ hybridization (FISH). The overlapped region in the deletions spanned 6.2 Mb where at least 15 genes were predicted to localize on the current human genome database. Among them, YAF2 and AMIGO2 were the most plausible candidates to affect growth and psychomotor retardation, respectively, in both cases. Regarding unique symptoms in each case, congenital fibrosis of the extraocular muscles found only in Case 1 may be caused by KIF21A deletion and hearing loss and cleft palate in Case 2 by COL2A1 defect.

Transient abnormal myelopoiesis in Noonan syndrome

An infant affected by Noonan syndrome and presenting with abnormal hemopoiesis is described. Cytogenetic analysis, molecular studies, and in vitro culture assays ruled out myelodysplasia or other hematologic malignancies but were consistent with transient abnormal myelopoiesis. At present, 3 years and 10 months after diagnosis, the patient shows a normal hematologic picture. Supportive treatment in such patients, unless refractory cytopenias or overt leukemia develops, is emphasized.

Additional patient with del(12)(q21.2q22): further evidence for a candidate region for cardio-facio-cutaneous syndrome?

Cardio-facio-cutaneous (CFC) syndrome is characterized by a distinct facial appearance, cardiac defects, ectodermal anomalies and developmental delay. Recently, we reported a 19-month-old girl with phenotypic manifestations consistent with the CFC syndrome who had an interstitial deletion of the long arm of chromosome 12, del(12)(q21.2q22), implicating a possible locus for CFC syndrome. Here, we report an additional patient with a cytogenetically identical interstitial deletion: 47,XYY,del(12)(q21.2q22). To further characterize this deletion we used microarray-based comparative genomic hybridization (array CGH). Array CGH confirmed both the deletion and the second Y chromosome. The deletion on chromosome 12q spanned at least 14 Mb as indicated by the positions on the genome sequence of the 4 BAC clones included in the deletion. While the proband did not have the classic features of CFC, he had some dysmorphic craniofacial characteristics, ectodermal anomalies and moderate developmental delay which were suggestive of CFC syndrome; however, this patient did not have classical CFC. The phenotypic differences between the two del(12)(q21.2q22) patients may be due to variability in the expression of the syndrome, or this deletion may present as a syndrome with overlapping features. Alternatively, the phenotypic differences may result from discordance at the molecular level, which may yield a critical minimal region of deletion for CFC. The region 12q21.2 --> q22 remains a possible candidate region for CFC syndrome. Additional characterization of these and other CFC patients may confirm and further refine this candidate region.

Temporal bone histopathological study of Noonan syndrome

Four temporal bone specimens, obtained from three individuals 1--6 years of age with Noonan syndrome (NS), were studied histopathologically. All four specimens were accompanied by similar inner ear abnormalities including the reduced number of spiral ganglion cells, enlarged lateral semicircular canal, and dislocated endolymphatic sac and vestibular aqueduct. The mean population of spiral ganglion cells (15,699 cells) was approximately half of those (32,978 cells) in four age-matched control cases. In addition, they had several middle ear abnormalities including the remaining mesenchyme and dehiscence of the facial canal. To our knowledge, this is the first report to describe the histopathological temporal bone findings in patients with NS. We discuss the implications of the observed abnormalities with regard to clinical issues.

Cardio-facio-cutaneous syndrome phenotype in an individual with an interstitial deletion of 12q: identification of a candidate region for CFC syndrome

We report on a 19-month-old girl who presented with the phenotype of cardio-faciocutaneous (CFC) syndrome including characteristic minor facial anomalies, cardiac defect, ectodermal anomalies, and developmental delay. Cytogenetic analysis showed the presence of an interstitial deletion of one chromosome 12, del(12)(q21.2q22), confirmed by fluorescence in situ hybridization with chromosome band specific probes. Controversy exists as to whether CFC and Noonan syndrome (NS) are distinct disorders, a contiguous gene syndrome, or allelic variants. The identification of the del(12) in this patient, in a region distinct from the putative NS locus, supports the view that CFC is a genetically distinct condition from NS. In addition, this implicates the region 12q21.2-->4q22 as a candidate region for the gene(s) causing CFC syndrome.