Case of interstitial 12q deletion in association with Wilms tumor

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.

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.

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.

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.

Characterization of a Wilms tumor in a 9-year-old girl with trisomy 18

This is a report of a trisomy 18 patient who developed Wilms tumor in conjunction with perilobar nephroblastomatosis (NB) at 9 years and 5 months of age. Review of the literature revealed that most patients with trisomy 18 who develop Wilms tumor, do so at a later than expected age for a tumor related to NB, and are females. In this case, no chromosome 11 WT1 mutation was detected by PCR/SSCP analysis, but the tumor had in addition to the trisomy, an isochromosome 7q and loss of heterozygosity at 16q, two mutations that have been linked independently to Wilms tumorigenesis.

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.