New 19p13.13 microdeletion/microduplication syndrome

Michelle Dolan, MD¹, Nancy J. Mendelsohn, MD^2,3, Mary Ella Pierpont, MD, PhD^2,3,4, Lisa A. Schimmenti, MD⁴, Susan A. Berry, MD⁴, and Betsy Hirsch, PhD¹

Objective

Whole genome analysis by array-based comparative genomic hybridization has led to a rapid increase in the discovery of novel microdeletion and/or microduplication syndromes. Here we describe the clinical and cellular genomic correlations of novel microdeletions/microduplications of 19p13.13. METHODS: Among patients referred to the Cytogenetics Institute for array-based comparative genomic hybridization analysis, we identified four with deletions and one with a duplication within 19p13.13. Confirmatory fluorescent in situ hybridization and parental examination were performed. Detailed clinical findings and array profiles were reviewed and compared.

RESULTS: Patients with a deletion of 19p13.13 share a unique set of phenotypic abnormalities. In addition to developmental defects, the microdeletion was associated with overgrowth, macrocephaly, and ophthalmologic and gastrointestinal findings. In contrast, a single microduplication was associated with growth retardation and microcephaly. CONCLUSIONS: Consistent clinical findings associated with copy number variants in this region collectively justify the term 19p13.13 microdeletion/microduplication syndrome. A minimal region of approximately 311-340 Kb of overlap containing 16 genes was identified. Candidate genes include MAST1, NFIX, and CALR. The identification of this syndrome recommends that patients with this copy number variant be subjected to diagnostic close examination and follow-up. Integration of detailed clinical and array data is important to advance both patient care and human genome research.

Genet 2010:12(8):503-511.

Keywords:

Array CGH, chromosome 19p13, microdeletion, microduplication, syndrome

What is all autosomal whole region partial deletion/duplication syndrome?

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The incorporation of microarray technology into the routine evaluation of patients with unexplained developmental and/or phenotypic abnormalities has resulted in the rapid discovery of numerous repetitive microdeletions/microduplications. For example, in just two years, previously undetected losses and/or gains to the 1q21.11,2 and 16p11.23,4 genomic regions have become widely recognized as potential etiologic factors in autism and related disorders. Clinically significant copy number variants (CNVs) with chromosomal regions too small to be detected by conventional cytogenetic testing have been identified for all chromosome pairs of the human karyotype. For some copy number variants, variation in clinical manifestations and penetrance complicates the establishment of clinical significance. In others, specific phenotypic findings more consistent with copy number variants and association with novel inheritance facilitate demonstration of clinical significance. Here we describe a copy number variant of chromosome 19p13.13 that meets the latter criteria. Despite the fact that chromosome 19 is one of the most gene-rich chromosomes (~2000 genes, 59 Mb), for individuals with deletions involving 19p.5-10, to date, we have only been able to identify this microdeletion/microduplication syndrome with significant deletions by four clinical geneticists The clinical findings and characteristics of the individual reports were nearly identical and their microarray data were correlated.

Materials and Methods

Subject

Five patients were referred to the University of Minnesota Amplatz Children’s Hospital and the Genetics Clinic at Children’s Hospital of Minnesota for diagnosis. Array-CGH was ordered as a component of the standard thorough examination for patients with multiple malformations and/or developmental disorders of unknown cause. Patient ages ranged from 5 to 26 months at the time of initial testing and were evaluated by one of four clinical geneticists each. Participation in the study to allow for data sharing and publication of results was approved by the investigational review committees at both sites. Informed consent was obtained from the parents of these patients.

Array-based comparative genomic hybridization analysis

DNA from peripheral blood of patients was isolated, restriction enzyme digested, and labeled with the fluorescent dye cyanine 5 using random primers and exocrenow fragment DNA polymerase. DNA from pooled sex-matched controls was simultaneously labeled with the fluorescent dye cyanine 3. Patient and control DNA were combined and array-based comparative genomic hybridization (aCGH) was performed using customized 44K oligonucleotide arrays containing target regions of enriched coverage on the backbone with an average of 35 Kb overall median probe interval. To more accurately estimate the stop and start points for the patient with the smallest deletion (patient 3), a 180K array with an average tile spacing of 13 Kb was performed (Agilent Technologies, Santa Clara, CA). The ratio of patients to control DNA for each oligonucleotide was calculated using feature extraction software 9.1 or 10.5 (Agilent Technologies) and analyzed using DNA Analytics 4.0.85 (Agilent Technologies). Statistical algorithms used in the analysis included ADM1 and ADM2

(Agilent Technologies) The threshold is set to an absolute value of 0.3 on a logarithmic scale, with a requirement for three consecutive oligos that meet the threshold criteria.

Table 1 Clinical and cytogenetic characteristics of patients lost or gained within 19p13.12-p13.13

patient	1	2	3	Four	Five	Patient 8 of Lysy et al.	Patient 9 of Auvin et al.	Patient 10 of Jensen et al.	Patient 7 of Engels et al.	Patient 6 of Stratton et al.
cytogenetic imbalance	Deletion 19p13.13-p13.2	Deletion 19p13.13-p13.2	Deletion 19p13.13	Deletion 19p13.13-p13.2	Duplicate 19p13.12-p13.2	Deletion 19p13.13-p13.2	Deletion 19p13.13	Deletion 19p13.12	Deletion 19p13.12	Duplicate 19p13.13-p13.2
Breakpoint (min)	12,498,237–13,126,508	12,536,641–13,794,080	12,793,474–13,104,643	12,411,017–13,120,904	12,601,112–14,488,238	10,256,871–13,188,698	12,615,927–13,280,259	13,838,264–16,357,778	not listed	No rating
Size (min)	0.6 Mb	1.3 Mb	0.3 Mb (311 Kb)	0.7 Mb	1.9 Mb	2.9 Mb	0.6 Mb	2.5 Mb	2.1 Mb	not listed
Breakpoint (maximum)	12,476,664–13,178,511	12,521,732–13,854,243	12,779,366–13,120,858	12,335,402–13,126,464	12,582,355–14,503,887	10,246,651–13,280,203	not listed	not listed	not listed	No rating
Size(max)	0.7 Mb	1.3 Mb	0.3 Mb (341 Kb)	0.8 Mb	1.9 Mb	3.0 Mb	0.7 Mb	not listed	not listed	not listed
First-stage exam
age	2 years old	2 years old	0.75 years old	0.5 years old	3 years old	Birth	Normal growth parameters at birth	Birth	Birth	Birth
length(%ile)	50th	>95th	90th	90th	<5th	<-2	SD	not listed	<3rd	25–50th
Weight (%ile)	75th	>95th	50–75th	90th	25th	<-2	SD	<1st	not listed	20th
Circumference of preoccipital cortex (%ile)	>97th	>95th	>98th	>98th	<-2 SD	-2	SD	not listed	<<3rd	15th
craniofacial	Macrocephaly, frontal prominence	Macrocephaly, frontal prominence, and downward cleft palate	Macrocephaly, frontal prominence, and downward cleft palate	Macrocephaly, frontal prominence	Microcephaly, frontal protuberance, and downward cleft palate	Complex craniosynostosis, frontal bulge, small nose, low nasal bridge	Macroceph, high, large forehead, flat philtrum, small mouth	Flat occiput, high forehead, drooping PF, long tongue, short nose	micro/blackie, thin upper lip, long philtrum, small mouth	Microceph, bilateral ridges, upward PF
ophthalmology	Esotropia, nystagmus, poor fixation	Optic nerve hypoplasia, exotropia	Optic nerve hypoplasia, exotropia	Optic nerve atrophy, exotropia	Optic nerve hypoplasia, exotropia, nystagmus	Orbital hypoplasia, binophthalmia, proptosis, strabismus	no button	Strabismus, optic disc cupping, ptosis, redundant inner canthus skin	medial canthus redundant skin	Intermittent proptosis
G.I.	chronic diarrhea	Abdominal pain, vomiting, poor feeding	none	abdominal pain, vomiting, celiac disease	Abdominal pain, vomiting, FTT (G tube)	not listed	severe constipation	not listed	not listed	Colic after birth
brain	normal	Mild atrophy, frontal lobe	Cystic lesion with no rostral corpus callosum	Chiari I malformation with syrinx	normal magnetic resonance imaging	Moderate ventricular enlargement	Conventional magnetic resonance imaging	Mild hypoplasia of the corpus callosum and cerebellar parenchyma, early rupture of membranes 4th vent	usually	Normal head CT
seizure	–	–	+	+	+	not listed	+	not listed	not listed	not listed
hypotonia	+	–	+	+	torticollisShakei	+	+	not listed	+	not listed
developmental delay	Full scale IQ 49	18 months of skill in 3 years. significant speech delay	mostly nonverbal	Moderate speech delay, special education needs.	21-29 months of skill in 4.5 years. significant speech delay	It was 33 months. No language in 3.7 years	Saturday in 2 years “Psychomotor retardation”	Full scale IQ 63	Crawl at 16 months. no speech	Motor milestone not reached, 4 months
final exam
age	6 years old	3 years old	14.5 years old	9.5 years old	7 years old	3.7 years old	2 years old	not listed	1.5 years old	0.75 years old
Elongation (percentile)	86th	>95th	50th	75th	<3rd	-3 SD	>+3 SD	not listed	<3rd	50th
Weight (percentile)	55th	>95th	10–25th	50–75th	50th	-0.9 SD	+2 SD	not listed	<3rd	5th
Occipitofrontal circumference (percentile)	>97th	>95th	>98th	>98th	-2 SD	-0.7 SD	+2.5 SD	not listed	<<3rd	<5th

Fluorescence in situ hybrid analysis

Fluorescence in situ hybridization (FISH) was performed to confirm the presence of deletions and/or duplications in the proband and to identify interchromosomal rearrangements in the parents that, if discovered, would have a significant impact on recurrence risk. was excluded. BACs selected for FISH probes were RP11-654K9 (contains MAST1), RP11-963I8 (contains NFIX), RP11-14L14 (contains CACNA1A), and for patient 5 RP11-56K21 (PKN1). (including). Stubs for RP11-654K9, RP11-14L14, and RP11-56K21 were obtained from CHORI BAC/PAC resources, grown on Luria broth plates using chloramphenicol, and nick-translated (Abbott Molecular, Abbott Park, IL). RP11-963I8 prelabeled with Enzo-Green was obtained from Empire Genomics (Empire Genomics, Buffalo, NY). A probe against the 19q subtelomeric region (D19S238E; Abbott Molecular) was also used as a control. Ten metaphase cells were scored to assess the presence or absence of deletions , and 75-100 interphase cells were scored to assess the presence or absence of duplications .

Result

Clinical findings

Detailed medical history and findings for each patient are shown below and summarized in Table 1.

Patient 1

This baby girl was born at term (birth weight 4026 g) (Figure 1). Her neonatal abnormalities included jaundice and an inability to breastfeed requiring amputation of the frenulum of the tongue. Her parents had concerns about her development at three months of age, but it became apparent as she got older, and over time her gross motor movements and her included a language delay. Ophthalmological and visual problems included esotropia, jerky eye movements, end-gaze nystagmus, and poor fixation. The patient had delayed visual acuity that improved over time and underwent two surgeries to correct strabismus. Gastrointestinal disorders characterized by chronic diarrhea of unknown etiology were present for the first 4 years. Physical examination after 22 months showed macrocephaly (>97th percentile), height at the 50th percentile, and weight at the 75th percentile. A prominent frontal protuberance with a supraorbital bulge and deeply set eyes was noted, along with a depressed nasal bridge, an upturned nasal tip, and a small mouth with a relatively high arched palate. Her fingers and toes were long, and there were deep wrinkles on the soles of her feet. The patient was hypotonic and had good deep tendon reflexes. At examination at 30 months, her height and weight were above the 80th percentile, and her occipitofrontal circumference was >97th percentile, but at 22 months she was only 0.3 cm larger. Follow-up at 6 years of age showed height in the 86th percentile, weight in the 55th percentile, and preoccipital circumference 1 SD above the 97th percentile. In Wechsler’s most recent evaluation, her preschool battery verbal IQ was 61, performance IQ was 47, and full scale IQ was 49. Her fine motor and visual motor skills have been repeatedly assessed and are relatively delayed. Radiological examination of her cranial and bone age was normal with X-ray and CT.   Magnetic resonance imaging (MRI) of the brain showed mild hypoplasia of the prechiasmatic optic nerve, but the brain was structurally normal

It was. Echocardiography and renal ultrasound were normal. Laboratory tests showed a normal 46,XX karyotype (550 band level resolution), normal urine metabolic screen, and normal serum amino acids, ammonia, lactate, and pyruvate.

Patient 2

This baby girl was born at term (birth weight 2835 g). After 6 months, she was noted to have delayed gross and fine motor development, and she was unable to visually focus and track. Her patient was macrocephalic with a preoccipital circumference of 46.5 cm (95th percentile) and had a downward-pointing palpebral fissure. The Bayley Infant Development Test for infant development at 7 months of age was 3 months, gross motor level was 2 to 5 months, and fine motor level was 1 month. After 15 months, her brain waves were normal and her hearing was normal. At 17 months, the patient presented with chronic and transient abdominal pain associated with vomiting. Magnetic resonance imaging of the brain showed mild atrophy, particularly in the frontal lobes. Exotropia persisted, and ophthalmological examination showed bilateral optic nerve hypoplasia. Heart and renal sounds were normal. Cytogenetic analysis showed a normal 46,XX karyotype. The clinical findings suggested Sotos syndrome, so NSD1 was sequenced and the results were negative. there were. At follow-up evaluation, language and developmental delays persisted, with a proficiency level of approximately 18 months at age 3 years, significant language delay (apraxia of language), and preoccipital circumference persisted above the 95th percentile. He was shown to have sexual macrocephaly.

Patient 3

This boy was born with a birth weight of 3884 g and presented with large macrocephaly in infancy, a wide forehead, a frontal prominence, an inferior oblique palpebral fissure, hypotonia, and marked developmental delay. (Figure 1). The patient developed epilepsy at the age of 4 years and has been medically controlled. He underwent two surgeries to correct strabismus and upper eyelid retraction (sunken eye sockets and decreased blinking). From infancy to age 14, his macrocephaly persisted (preoccipital circumference >98th percentile), but height gradually increased from the 90th to the 50th percentile and weight from the 50th to 75th percentile to the 10th to 25th percentile. It declined to . Ophthalmological follow-up revealed optic atrophy with onset between the ages of 8 years (normal optic nerve by magnetic resonance imaging) and 11 years (retrobulbar, prechiasmatic, and chiasmatic optic nerve hypoplasia). At the most recent examination (age 14.5 years), he was in the 25th to 50th percentile for height, 10th to 25th percentile for weight, and 98th percentile for head circumference. Characteristics of transformation

They had low facial tone, large ears, a high palate, crowded teeth, large hands, and flat feet. He had severe speech delay and was nonverbal except for a few selected words. Magnetic resonance imaging of his brain showed a chronic occipital cystic lesion of unknown origin and a rostral absence of the corpus callosum. Serial renal ultrasound revealed left renal pelvis dilatation or bulge, interpreted as extrapelvic, which remained stable. Cytogenetic testing showed a normal 46 XY karyotype (550 band level resolution), and molecular testing showed deletions or mutations were negative.

Patient 4

This baby girl was born at term (birth weight 4097 g) and exhibited hypotonia, macrocephaly, prominent eyes with large blue irises, and exotropia during infancy, and optic nerve pallor was noted within 1 year ( Figure 1). Other clinical findings include an upturned nose, low facial tone, six crescent-shaped cafe-au-lait spots, and myoclonic jerks, once at age 9 years. The patient developed a prolonged seizure. EEG did not detect epilepsy. She had motor and speech delays including gait at 2-3 years and nonverbal dysarthria 2 years ago. In her fourth year she underwent strabismus surgery, but her early visual inattention improved over time. She developed symptoms of celiac disease between 7 and 9 years and was on a gluten-free diet. At her most recent visit at age 9.5, she requires special education services, but her vocabulary has expanded significantly. Magnetic resonance imaging of her brain after 5 months was normal, but repeat examination 4 years later showed Chiari type I malformation (syringomyelia, surgically decompressed at age 5 years) and chiasm and intracranial lesions. Optic nerve hypoplasia was demonstrated. Laboratory tests include metabolic testing (serum amino acids, blood long chain fatty acids, urine organic acids, muscle biopsy, and mitochondrial DNA testing), cytogenetic testing (750 band level resolution), and NF1 mutation analysis. The results were normal.

Patient 5

This boy was born at 36 weeks gestation (birth weight 2835 g). Two months later, he developed anorexia, constipation, frequent vomiting, marked irritability, multiple infections, and a paler complexion than his siblings. After 14 months, his weight, height, and preoccipital circumference were all below the 5th percentile. Other clinical findings included a tilted forehead, narrow nasal wings, inverted nipples, and abnormal fat distribution in the buttocks. The patient had epilepsy, with approximately 4 to 5 seizures occurring daily from a focus in the left frontotemporal lobe. Because of continued difficulty in feeding and aversion to oral intake, Nissen fundoplication with G-tube placement was performed. Ophthalmological examination revealed horizontal nystagmus. By 3 years, his head circumference remained significantly below the 5th percentile, with persistent growth failure and developmental delay (only a few words, walking at 2 years). Neuropsychological testing at age 4.5 years showed development comparable to ages 21 to 29 months, with hyperactivity, sleep disturbances (delayed sleep onset with approximately 3 hours of sleep per night), tantrums, obsessive-compulsive behaviors, and Self-injurious behavior was observed. His receptive language was mildly impaired and expressive communication significantly impaired, and he first spoke in sentences at age 6. There has been some improvement over the past 2-3 years. The patient’s growth rate is slow (3.2 cm/year, < 1st percentile) and his height at age 7 years is currently below the 3rd percentile, but his weight has increased to the 50th percentile as his oral feeding aversion improves. did. His family history was significant in that the patient’s father had nystagmus and reported learning difficulties. Radiological examinations included chest X-ray, abdominal ultrasound, upper gastrointestinal tract, flexible sigmoidoscopy, and brain magnetic resonance imaging, all of which were normal. Laboratory tests including electrolytes, complete blood count with differential, liver and thyroid function tests, immunoglobulins, sweat chloride, serum amino acids, and urinary organic acids were all reported as normal. Cytogenetic analysis showed a normal 46,XY karyotype with 850 band level resolution. FISH testing (fluorescence in situ hybridization) is used to detect Williams syndrome, telomere FISH, and external BAC aCGH performed at the reference laboratory was normal.

Array-CGH analysis

Array-CGH showed ratio profiles matching the loss areas of patients 1 to 4, and the gain area of patient 5. As shown in Figure 2, the area of loss ranged from approximately 0.31 Mb (patient 3) to 1.3 Mb (patient 2). Patient 5’s gain area was ~1.9 Mb. The minimal region of overlap (SRO) separated by the deletions seen in patient 3 is ~ It spans 311 Kb and is localized to band 19p13.13. Based on Human Genome Build 18, the start and stop points of this SRO were 12793474 and 13104643 (minimum breakpoint) and 1279366 and 13120858 (maximum breakpoint). Parents of all patients were followed up with aCGH (Figure 3). The ratio profile of the 19p13 region was within normal range for each of the parental specimens.

Inspection

aCGH identified 4 patients with microdeletions and microduplications involving 19p13.12-19p13.2 . SRO was delimited by patient 3 with a minimal deletion of approximately 311 Kb (maximum 340 Kb) within 19p13.13 . The smallest SRO ranges from approximately 12793474bp to 13104643bp (Build 18). To date, there are only two published case reports of patients with deletions encompassing this SRO (the patient reported by Auvin et al. ⁹ ). One case was reported by Lysy et al ^{. 8 with} a deletion of approximately 740 Kb . with a larger 3 Mb deletion . Patients in this study and in the study of Auvin et al . show consistent phenotypic correlations supporting the designation of this 19p13.13 clinical-cytogenomic entity as a microdeletion/microduplication syndrome . Lysy et al.’s patient ⁸ , however, the phenotype was significant, as this deletion affected the telomeres in the present report by nearly 3 Mb, nearly three times the size of the largest deletion and nearly 10 times the size of the critical region. 

19p13.13deletionsThe clinical findings in patients are a cluster of three recurrent abnormalities. It’s worth noting. First, there is overgrowth. Patients 1-4 and Auvin et al.’s patient ⁹ Both of these patients were macrocephalic for their age, and their height and weight were consistent with their craniofacial dimensions. Of particular interest are patients 2 and 3 and patient 9 of Auvin et al. To exclude Sotos syndrome, NSD1 testing was performed. Therefore, this region of 19p13.13 has a differential diagnosis of Sotos syndrome, but NSD1 It may be related to other patients with negative test results. The second most common clinical manifestations are ophthalmological abnormalities (particularly strabismus) and optic nerve atrophy or hypoplasia, the latter detected by formal ophthalmological examination and/or magnetic resonance imaging. A third finding is gastrointestinal symptoms, particularly abdominal pain and vomiting. Although the only finding in this triad is not specific to 19p13.13 abnormalities, this set of findings is similar to other Microdeletion/Microduplication This is not one of the many reports currently reported. However, these 19p13.13 patients also showed some nonspecific findings. Neurological abnormalities (eg, seizures, myoclonic spasms, hypotonia) were present in some, and developmental and/or mental retardation was present in all. For comparison, within 19p13.12-19p13.2 microdeletions or A few other published patients with microduplication are included in Table 1 (Reference (See also literature). 6, 7, 10. None of these overlap with the critical region delimited by patient 3, and their phenotype There are some notable differences. Our deletion patient and Auvin et al.’s deletion In contrast to patient ⁹ theseduplicationNodeletionPatient^7,10 are small with age, supporting the conclusion that genes within the 310 Kb SRO that we defined are responsible for the large body size. Our deletion patients do not have hearing loss, but these Do not duplicate19pMissed There is significant hearing loss for aphrodisiacs, suggesting that genes within these proximal and distal regions explain this aspect of their phenotype. However, some similarities exist (e.g. strabismus and optic disc cupping).

Duplicationwas observed in only one case, and caution should be taken in generalizing the clinical symptoms. Currently well-established reciprocals, including 17p11.2 and 22q11.2Microdeletion/microduplication syndromeNow, eachdeletionA set of phenotypic findings associated with Duplicationare sufficiently different from those associated with 17p11.2 deletionaboutSmith-Magenis syndrome、Duplicate of 17p11.2aboutPotocki-Lupski syndrome is clearly justified.

Additionally, patients with duplications may have findings opposite to those seen in patients with deletions, as seen with disequilibrium involving the Williams-Beuren locus . 13,14 In this series, this is similarly demonstrated by the striking difference in head circumference between macrocephalic 19p13.13 deletion patients and microcephalic duplication patients. This was also true for the duplicate patients reported by Stratton et al . However, deletions and duplications in the same region may also share some common features, as demonstrated by the finding of velopharyngeal dysfunction in both 22q11.2 deletions and duplications . Similarly, several clinical findings (e.g., ocular findings, gastrointestinal symptoms, and seizures) were observed in 19p cases, regardless of the presence or absence of deletions or duplications .^15-17

The 16 genes mapped to SRO are involved in diverse processes such as transcription, DNA repair, and hematopoiesis. DNASE2 ¹⁸ and KLF1 ^{19, 20} are involved in fetal hematopoiesis. The absence of overt hematological abnormalities in these five patients is not unexpected, as the presence of one functional KLF1 allele is sufficient for human erythropoiesis. Other genes within this region are involved in autosomal recessive diseases : GCDH and glutaric acidemia/aciduria (GA-1) ^21-24 and RNASEH2A and Aicardi-Goutieres syndrome. Deletion of these genes is not expected to be associated with clinical symptoms unless accompanied by mutations in the non-deletion homologues . Some of the SRO genes are expressed in the brain and nervous tissue and are candidate genes for clinical manifestations. MAST1, microtubule-associated serine/threonine kinase 1, is such a candidate. It is a member of the microtubule-associated serine/threonine kinase family that is highly expressed in the brain. Of particular interest is the fact that MAST1 interacts with and helps stabilize PTEN. Mutations in PTEN are associated with both macrocephaly and autism. NFIX, a member of the NF1 transcription factor family, is another candidate gene. ^26-28 Mouse models have shown that Nfix is ​​essential for normal brain development, and one experiment showed that hemizygosity resulted in agenesis of the corpus callosum, 30 which supports this ^finding . The findings are similar to those seen in patient 3. As mentioned above, gastrointestinal problems were prominent in our patient. The gene of interest for these findings is CALR. CALR encodes calreticulin, a protein that binds and stores calcium in the endoplasmic reticulum, acts in the nucleus, and regulates gene transcription by nuclear hormone receptors. Interestingly, it is also localized to neurons in the human small intestine and may therefore be involved in the gastrointestinal symptoms seen in four out of our five patients. In previously published reports of deletions of 19p13, including Auvin et ^{al. , CACNA1A and CC2D1A have been hypothesized to play important roles in the resulting phenotype. 9, 31} Since neither CACNA1A nor CC2D1A are included in our critical 310-340 Kb region, they are candidates for a specific phenotypic constellation associated with this 19p13.13 deletion/duplication in our patient. I can’t think of that.

Sixteen genes mapped to the SRO are involved in diverse processes including transcription, DNA repair, and hematopoiesis. DNASE2¹⁸ and KLF1^{19, 20} are involved in fetal hematopoiesis. Since the presence of one functional KLF1 allele is sufficient for human erythropoiesis, the absence of overt hematological abnormalities in these five patients is not unexpected. Other genes within this region are implicated in autosomal recessive disorders: GCDH and glutaric acidemia/aciduria (GA-1)^21-24 and RNASEH2A and Aicardi-Goutieres syndrome. Deletions of these genes are not expected to be associated with clinical symptoms unless accompanied by non-deletion homolog mutations. Several of the SRO genes are expressed in brain and nervous tissue and are candidate genes for clinical manifestations. MAST1, a microtubule-bound serine/threonine kinase 1, is such a candidate. It is a member of the microtubule-associated serine/threonine kinase family that is highly expressed in the brain. Of particular interest is the fact that MAST1 interacts with PTEN and helps stabilize it; PTEN mutations are associated with both macrocephaly and autism. NFIX, a member of the NF1 transcription factor family, is another candidate gene.^26-28 Mouse models have shown that Nfix is essential for normal brain development, with one experiment showing that unilateral zygosity leads to aplasia of the corpus callosum,³⁰ a finding that is This finding is similar to that seen in patient 3. As noted above, gastrointestinal problems were prominent in our patient. A gene of interest in these findings is CALR, which encodes calreticulin, a protein that binds and stores calcium in the endoplasmic reticulum and acts in the nucleus to regulate gene transcription by nuclear hormone receptors. Interestingly, it is also localized to neurons in the human small intestine and may therefore be involved in the gastrointestinal symptoms seen in four of our five patients. In previously published reports on deletions of 19p13, including Auvin et al.⁹, CACNA1A and CC2D1A have been postulated to play an important role in the resulting phenotype.^{9, 31} Since neither CACNA1A nor CC2D1A are included in our critical 310-340 Kb region Since neither CACNA1A nor CC2D1A is included in our critical 310-340 Kb region, they are not considered candidates for the specific phenotypic constellation associated with this 19p13.13 deletion/reduplication in our patient.

Mouse models and mutation screens are proposed to further investigate potential candidate genes MAST1 and CALR. As previously mentioned, the start and stop points involved in deletions and duplications were unique to each patient. This fact, coupled with the absence of low-copy repeats or segmental duplications within or adjacent to the deletion/duplication region, makes them unlikely mechanisms for generating 19p13 copy number variants . Opposes allelic homologous recombination. Recently, it has been suggested that microhomology at breakpoint junctions involved in strand break repair is involved in the formation of copy number variants with non-repetitive breakpoints. ^32,33 However, detailed sequencing of the breakpoint will be required to further explore this possibility and further characterize the underlying molecular mechanism. The Center for Applied Genomics Research (TCAG) (http://projects.tcag.ca/variation/) has a database of ³⁴ genomic variants (DGV) that are well-documented in cytogeneticists and control populations to identify benign variants. will be invaluable to other researchers working with arrays to help identify copy number variants that may be Note that in DGV, part of this region (from the starting point to 12919491) was identified by Wong ^{et al} . Based on the BAC array, it was removed in 3 out of 95 patients. Notably, among the large control cohorts published in the literature and cited in the DGV (representing over 4000 control individuals) ^, only one identified deletions or duplications of a large proportion of this region. No way. Furthermore, as the deletion and duplication in our case were proven to be de novo, the single 2007 accession in DGV outweighs the data supporting the clinical importance of this copy number variant. isn’t it. Validating the copy number variant breakpoints reported in the 2007 BAC array may also provide further insight.

In summary, close collaboration between clinical geneticists and cytogeneticists, and correlation of genotype and phenotypic data, led to the identification of microdeletion/microduplication syndrome in 19p13.13. made it easier. This leads to a diagnostic workup on identified patients (e.g., a complete ophthalmological examination to detect strabismus and a thorough evaluation including magnetic resonance imaging of the optic nerve, magnetic resonance imaging to detect structural brain abnormalities). Resonance imaging, continuous monitoring of the occipitofrontal area, elucidation of the history of gastrointestinal symptoms including poor feeding, abdominal pain, and vomiting), as well as research to elucidate the relationship with further functions and clinical features of this syndrome. This led to the identification of the gene.

Acknowledgments

The authors would like to thank the patients and their families who actively participated in this study. We also thank Heather Zierhut, MS, Genetic Counselor, for her support of this project, and the technicians at the Cytogenetics Laboratory at Fairview, University of Minnesota Medical Center, for their assistance in performing the array-CGH assay.

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