Duplication of 12q24.21q24.33 in a Girl with Epilepsy, Expanding the Phenotype

Abstract

Introduction

Duplication of 12q is characterized by craniofacial dysmorphia, growth failure, occasional brain malformations, abnormalities of the extremities, skeletal and thoracic malformations, cardiovascular defects, anogenital abnormalities like cryptorchidism, psychomotor delay, and intellectual disability.

Case presentation

We describe a female patient with typical manifestations of duplication 12q and epilepsy. She had a normal 46,XX karyotype. The microarray assay exhibited a 19.35-Mb gain at 12q24.21q24.33 due to ins(21;12)(p11.2;q24.21q24.33)mat.

Discussion and Conclusion

The duplicated region in the patient encompasses 219 genes, 24 considered as pathological. No relation between epilepsy and the genes reported as pathological has been reported.

Established Facts

• Duplication of 12q is well characterized.

• Features have been identified based on a small number of cases.

Novel Insights

• Few pure 12q duplication cases have been described to date.

• Epilepsy is a novel finding not previously reported.

• An association of the THRAP2 gene with congenital heart defects can be excluded in our patient.

Introduction

Several abnormalities in chromosome 12, especially in 12p, can occur commonly and result in well-known phenotypes, but trisomy 12q is rarely reported [Doco et al., 2006]. Most cases have duplications involving the region 12q24qter due to segregation of a maternal balanced translocation [Lagier et al., 2004]. Other rearrangements involve translocations with chromosomes 2, 4, 5, 9, 11, 17, 18, 21, mosaicism or pericentric inversions [Doco et al., 2006]. Trisomy 12q can be characterized by a clinically recognizable syndrome including craniofacial dysmorphias, growth failure, occasional brain malformations, abnormalities of the extremities, skeletal and thoracic malformations, cardiovascular defects, anogenital abnormalities, psychomotor delay, and intellectual disability [Vaglio et al., 2007; Paspaliaris et al., 2017].

In the present study, we report the case of a girl with partial trisomy 12q24.21q24.33 and epilepsy, not previously reported. We also present a review of cases reported with duplication 12q.

Case Report

The proband, a 5-year-old female, was referred for the presence of developmental delay, epilepsy, and patent ductus arteriosus with interventricular communication. She was the second child of young, healthy, and nonconsanguineous parents. No family history for congenital malformations or intellectual disability was registered. At birth, she had a weight of 2,700 g (15th percentile), a length of 51 cm (85th percentile), and an Apgar score of 8 at minute 1 and 9 at minute 5. She presented developmental delay and hypotonia. She was diagnosed with patent ductus arteriosus and interventricular communication. At the age of 5 years she presented focal seizures with epileptic aura-like nausea, gaze deviation to left, behavior arrest, duration of 1–5 min, monthly pattern. At physical examination, the proband had a weight of 14 kg (3rd percentile), a height of 97 cm (3rd percentile), an occipitofrontal head circumference of 49 cm (3rd percentile), downturned mouth, low-set ears, short neck, genital hypoplasia, sacral dimple, and single palmar creases (Fig. 1). The EEG showed spikes and spike-slow-wave complex in the right hemisphere, predominating over the frontotemporal area (Fig. 2). Initial management was with VPA, achieving control of epileptic seizures. As side effect of VPA she presented significant anemia, so treatment was discontinued. At that age abdominal ultrasound, brain MRI, as well as ophthalmic and auditory assessments were normal.

Fig. 1.

Phenotype of our patient showing facial dysmorphism like downturned mouth, low-set ears, and short neck.

Fig. 2.

EEG showing spikes and spike-slow-wave complex in the right hemisphere, predominating over the frontotemporal area.

About twice a year she had nonconvulsive status epilepticus (with behavior arrest), requiring management with intravenous infusion of benzodiazepines. She was treated with LEV 58 mg/kg/day, TPM 4 mg/kg/day, OXC 23 mg/kg/day, and PHT 6 mg/kg/day for 4 years. Actually, she has dual therapy with LEV and PB managing to control epileptic seizures.

Materials and Methods

Chromosome analysis was performed by routine GTG-banding at a resolution of approximately 500 bands. Genomic DNA from the proband and her parents was isolated from peripheral blood samples using the Gentra PureGene Blood Kit and Qiagen extraction kits. The oligonucleotide-SNP array analysis with the GeneChip Human Cytoscan HD was carried out for the patient and her parents following the provided protocol (Affymetrix, Santa Clara, CA, USA) and using the Affymetrix GeneChip Scanner 3000 7G. The data were analyzed using GTYPE (GeneChip Genotyping Analysis Software, version 1.0.12) to detect copy number aberrations. The resolution of this procedure was estimated at 1.15 kb with 2.67 million probes. CNV breakpoints were determined by inspecting the log2 intensity ratios of SNPs within and flanking the detected regions of gain or loss. The interpretation of the clinical significance of all detected CNVs was analyzed with the Database of Genomic Variants (DGV; https://projects.tcag.ca/variation/), the UCSC genome browser (http://genome.ucsc.edu/), Ensembl Resources, OMIM, ClinGen, and ClinVar. The included genes in the CNVs of importance were determined with the UCSC browser (human genome NCBI build 37, hg37). The assessment of the regions that involved at least 1 gene included searches for similar cases in DECIPHER (https://decipher.sanger.ac.uk/) and a review in PubMed (http://www.ncbi.nlm.nih.gov/pubmed/).

Results

Conventional GTG-banding of the proband's metaphase chromosomes reported a normal karyotype 46,XX (Fig. 3). The microarray assay result was arr[GRCh37] 12q24.21q24.33(114,465,567_133,817,901)×3 exhibiting an approximately 19.35-Mb gain of the long arm of chromosome 12. FISH analysis in the mother showed ish ins(21;12)(p11.2;q24.21q24.33)(RP11-946G22+) (Fig. 4). These data show a chromosomal unbalance in the proband with a partial trisomic component 12q24.21q24.33 of maternal origin. The conventional karyotype of the father was normal (46,XY).

Fig. 3.

GTG-banded 46,XX karyotype of the patient with no visible numerical or structural aberrations.

Fig. 4.

a, b FISH with chromosome 12- and 21-specific probes in the patient's mother showing ish ins(21;12)(p11.2;q24.21q24.33)(RP11-946G22+).

Discussion and Conclusion

We describe a 19.35-Mb duplication of 12q24.21q24.3 (Fig. 5) in a patient with developmental delay, dysmorphisms, and epilepsy, the latter not previously reported in 12q duplication.

Fig. 5.

Region 12q24.21q24.3. The segments duplicated in patients with pure 12q duplications are shown.

Liveborn cases of partial trisomy 12q are rare; few fetuses carrying this translocation in the unbalanced form survive to term [Vaglio et al., 2007]. Only few cases with pure 12q duplication have been described, the majority are associated with other chromosomal abnormalities [Paspaliaris et al., 2017]. This condition is thought to result primarily from familial translocation. It has been proposed that a trisomy distal to 12q24 is associated with increased survivability [Roberts et al., 2016]. Duplications may arise during recombination events in meiosis, also creating a deletion in the chromosome [Ruiter et al., 2006].

Clinical features in 12q duplication have been identified based on a small number of case studies, and they include abnormally shaped cranium, hypertelorism, epicanthal folds, flat nasal bridge, micrognathia, down-turned mouth, low-set ears with prominent antihelix, widely spaced nipples, short neck with loose skin, clinodactyly, single palmar crease, genitourinary defects, skeletal and limb anomalies, intellectual disability, heart defects, cryptorchidism, and nervous system defects. Rare manifestations include pilonidal dimple, spina bifida occulta, planovalgus positioning of the feet, large mouth, down-turned tip of the nose, excess hair, and limited elbow movement [Ieshima et al., 1984; Roberts et al., 2016].

The principal manifestations in our patient are developmental delay, downturned mouth, low-set ears, short neck, congenital heart disease, genital hypoplasia, sacral dimple, and single palmar creases, compatible with most of the common manifestations published before. Nevertheless, it is important to mention the epilepsy as a novel clinical feature which probably expands the phenotype of 12q duplication.

DECIPHER shows 17 patients with 12q24 duplications of different sizes. Of these 17 patients, 9 are males and 8 females; 12 have complex chromosomal imbalances, only 5 are reported as 12q duplication alone. Of those patients with duplication alone, all have a larger duplication (24.29 Mb), and those patients with similar duplication sizes have complex chromosomal imbalances. Our case is not in this database, but in Table 1 we compare patients published in PubMed, DECIPHER patients with pure duplication, and our case.

Table 1.

Physical and cytogenetic features reported in patients with pure 12q duplication

	Referenced	Sex	Duplicated segment	Parental origin	Skull/CNS	Facial appereance	Ears	Neck	Extremities/skeletal findings	Thorax/cardiac anomalies	GI/renal/ano-genital anomalies	Psychomotor delay	Growth retardation
Hobolth et al., 1974	M	12q24	Yes (mat)	Square-built	Broad-bridged and prominent nose with the tip turned downwards	Low-set and poorly lobulated	Redundant skin	Single palmar creases, big toes in a hammertoe position, prominent xiphoid process	No/NM	Cryptorchidism	Yes	Yes
Harrod et al., 1980	F	12q24.1q24.5, mosaic	No	Dolichocephaly, cerebral atrophy	Epicanthal folds, hypertelorism, flat nasal bridge, prominent nasal tip with slightly anteverted nares, downturned mouth, micrognathia	Abnormal shape/low-set	Short, redundant skin	Single palmar creases, hyperflexion at the wrists, ulnar deviation of both hands, clinodactyly of both 5th digits, sacral dimple, hypertonia	Wide-spaced nipples, pectus excavaturn	Hydronephrosis on the left with blunting of the calyces, ureterocele	Yes	Yes
	M	12q24.1q24.5, mosaic	No	Dolichocephaly, occipital prominence, cerebral atrophy	Prominent forehead, flat nasal bridge, prominent nasal tip, hypoplastic midface, small mandible, downturned mouth, deep horizontal crease below the lower lip	Low-set, posteriorly rotated ears with small lobules	No	Limitation of extension, pronation, and supination at both elbows/ulnar deviation, single palmar creases, index finger clinodactyly	Wide-spaced nipples, cardiomegaly, mild congestive heart failure, patent ductus arteriosus	No	Hypertonia	Yes
Ieshima et al., 1984	F	12q24.2qter	No	Brachycephaly, mild dilation of third and lateral ventricles, and cortical atrophy	Hypertelorism, flat nasal bridge, downturned mouth, micrognathia	Abnormal shape	Short	Mild brachydactyly and hypoplastic nails, sacral dimple	Wide-spaced nipples/ventricular septal defect	NM	Yes	Yes
MacDonald and Holden, 1985	M	12q24.1qter	Yes (pat)	Frontal bossing, Dandy-Walker cyst, agenesis of the corpus callosum	Mild right facial hypoplasia, strabismus	NM	Left torticollis	Hip dysplasia, spastic quadriplegia	Marked thoracic kyphosis	Small, nonfunctioning left kidney with hydronephrosis and bladder neck obstruction	Yes	Yes
Ireland et al., 2004	M	12q24.31qter	No	Yes	Hypertelorism, epicanthal folds, broad nasal bridge, anteverted nares, micrognathia	NM	NM	Sacral dimple, scoliosis, mildly altered distal flexion creases of the fingers	NM	NM	Yes	NM
Ruiter et al., 2006	F	12q24.21q24.23	No	Hypertonia and ataxia	Epicanthal folds, hypertelorism, arched eyebrows, short	Low-set	NM	Clinodactyly of the fifth fingers, distal brachydactyly and	NM	NM	Yes	Yes
					philtrum, open mouth appearance, full lips, irregular position of the lower teeth, broad gums and a flat palate with a normal uvula			short toenails
Cappellacci et al., 2006	M	12q22q24.33	de novo	Macrocephaly, flat occiput, Dandy-Walker malformation	Hypertelorism, long palpebral fissures, long eyelashes, protruding nasal root, anteverted nostrils, thin lips, high-arched palate, mild prognathism, malar hypoplasia	Abnormal shape/low-set	NM	Femoral fibrous chondrodysplasia, short stubby hands	NM	NM	Yes	NM
Doco et al., 2006	F	12q24.1q24.2	de novo	Microcephaly, hypoplasia of corpus callosum	Upslanting palpebral fissures, hypertelorism, epicanthal folds, large downturned mouth, micrognathia, flat nasal bridge, nose prominent tip, anteverted nares	Low-set	Short, redundant skin, congenital right torticollis	Single palmar creases, hip dislocation	Wide-spaced nipples, pectus excavatum/pseudo-coarctation of aorta	Severe constipation	Yes	Yes
Shchelochkov et al., 2008	F	12q24.11q24.23	No	Microcephaly with mild occipital flattening	Ptosis, hypertelorism, epicanthal folds, anteverted nares, velopalatal incompetence, downturned mouth, retrognathia	Cupped, simple ears	NM	Levoconvex thoracic scoliosis, hip dysplasia	Pectus excavatum in the lower half of the sternum, hypoplastic aortic arch with coarctation, atrial septal defect, and ventricular septal defect	NM	Yes	Yes
Present case	F	12q24.21q24.33	Yes (mat)	Epilepsy	Downturned mouth	Low-set	Short	Sacral dimple, single palmar creases	Intraventricular communication, patent ductus arteriosus	Hypoplasia	Yes	No
DECIPHER 397223	M	12q (24.29 Mb)	Yes	Microcephaly, EEG abnormality	Downslanted palpebral fissures, ptosis, strabismus, prominent nose, thick upper lip vermilion, tooth malposition	NM	Webbed and short neck	Ulnar deviation of the hand, abnormal thumb, flexion contractures, sacral dimple	Wide-spaced nipples	Cryptorchidism, micropenis	Yes	NM
DECIPHER 394813	M	12q (24.29 Mb)	Yes	Trigonocephaly	Hypertelorism, epicanthus, short and upslanted palpebral fissure, anteverted nares, depressed nasal bridge, long philtrum, narrow mouth, micrognathia	Low-set, attached earlobe, hearing impairment	Webbed and short neck	Postaxial polydactyly, scoliosis	Wide-spaced nipples	Hypospadias	Yes	NM
DECIPHER 402696	F	12q (24.29 Mb)	Unknown	Microcephaly, hypoplasia of the corpus callosum	Epicanthus, upslanted palpebral fissure, downturned mouth, thin lip vermilion, prominent glabella, prominent and wide nasal bridge	Low-set, microtia, prominent ear helix	Short	Single palmar creases, 2-3 toe syndactyly, clinodactyly, sacral dimple	Wide-spaced, hypoplastic nipples	Gastroesophageal reflux	NM	Yes
DECIPHER 392773	M	12q (24.29 Mb)	de novo	Dolichocephaly, frontal bossing, macrocephaly, cerebral atrophy	Bulbous nose, depressed nasal bridge, downturned mouth, midface retrusion, micrognathia	Hypoplasia of the earlobes, low-set and posteriorly rotated ears	NM	Single palmar creases, skin dimple, ulnar deviation of the hand, clinodactyly, radioulnar synostosis, sacral dimple	Wide-spaced nipples, patent ductus arteriosus	NM	Yes	NM
DECIPHER 392795	F	12q (24.29 Mb)	de novo	Dolichocephaly, macrocephaly	Hypertelorism, epicanthus, anteverted nares, bulbous nose, depressed nasal bridge, downturned mouth, micrognathia	Low-set	Webbed and short neck	Single palmar creases, talipes equinovalgus, ulnar deviation of the hand, clinodactyly, coxa valga	Pectus excavatum	Hydronephrosis, uretral atresia	Yes	Yes

GI, gastrointestinal tract; NM, not mentioned.

Ruiter et al. [2006] reported another patient with a 12q24.21q24.23 duplication and severe mental retardation, epicanthal folds, hypertelorism, arched eyebrows, low-set ears, short philtrum, open mouth appearance, full lips, irregular position of the lower teeth, broad gums and a flat palate with a normal uvula, clinodactyly of the fifth fingers, distal brachydactyly and short toenails, 2 cafe-au-lait spots and hypertonia mainly in the legs. The duplicated region encompassed 16 genes expressed in the brain or during embryogenesis (like NOS1, RFC5, and THRAP2) supporting a pathogenic effect of the microduplication. Although clinical features in relation to THRAP2, RFC2, and NOS1 seem to be caused by a loss of function, it is known that genes involved in early development might cause similar clinical effects when they are overexpressed. Besides, our patient has a larger duplication excluding an association of the THRAP2 gene with congenital heart defects, at least in our patient.

MacDonald and Holden [1985] published a boy with Dandy-Walker syndrome and multiple congenital abnormalities. The chromosomal analyses revealed an abnormal chromosome 21, inherited from his father who had a balanced translocation involving chromosomes 12 and 21, similar to our case with the difference that our proband has no partial or complete loss of chromosome 21. Dysmorphic features included frontal bossing, mild right facial hypoplasia, inguinal hernia and a two-vessel umbilical cord, small, non-functioning left kidney with hydronephrosis, and bladder neck obstruction. They performed a computerized tomography of the head revealing a posterior fossa cyst communicating with the fourth ventricle, indicative of a Dandy-Walker cyst, left cerebellar hemisphere was absent and the right was malformed. The ventricles and subarachnoid space appeared large and corpus callosum was absent. In the analyses, they compared previous cases and found that abnormal skull shape, psychomotor retardation, downturned corners of mouth, hypertelorism, single palmar crease and undescended testes were the most common features. They did not argue if the manifestations could be attributed to 12q(dup) or 21(del).

The duplicated region in our patient, encompasses 219 genes, 27 considered as pathological (Fig. 5; Table 2). Some of them seem to be important for the clinical features of our patient. SETD1B is a component of a histone methyltransferase complex that produces trimethylated histone H3 at Lys4, which is enriched in gene promoters and is seen to be highly correlated with gene expression [Krzyzewska et al., 2019]. Diseases associated with SETD1B include syndromic intellectual disability and Kabuki syndrome 1 (https://www.genecards.org/cgi-bin/carddisp.pl?gene=SETD1B). MED13L causes the developmental delay-facial dysmorphism syndrome. MED13L (MED13L; MIM # 608771) is one of the subunits in the CDK8 module of the Mediator complex, a dissociable component of the Mediator complex that has been described to have an activating or repressing function in regulating transcriptions. The Mediator complex regulates gene expression by physically linking transcription factors to RNA polymerase II. There are studies that have identified structural variants and mutations affecting MED13L in some patients with heart defects, craniofacial anomalies, and intellectual disability [Utami et al., 2014]. Asadollahi et al. [2013] reported copy number variants encompassing MED13L in 3 patients, 2 had out-of-frame deletions, with conotruncal heart defect, moderate intellectual disability, hypotonia, and facial anomalies, and one had a triplication involving full-length MED13L and a neighboring gene MAP1LC3B2. The patient with the triplication had a milder phenotype with mild hypotonia, a clinically insignificant cardiac defect and mild developmental delay only. Comparing with our patient, both had cardiac defect, hypotonia, and developmental delay; as for the facial dysmorphism, they only reported broad nasal bridge.

Table 2.

Pathological genes located in the duplicated region of our patient

Gene	Disease	Inheritance
TBX5	Holt-Oram syndrome	AD, haploinsufficiency
TBX3	Ulnar-mammary syndrome	AD, LOF
MED13L	Transposition of the great arteries, dextro-looped 1	AD, deletion, duplication
	Mental retardation and distinctive facial features with or without cardiac defects	AD
HSPB8	Neuronopathy, distal hereditary motor, type IIA	AD
	Charcot-Marie-Tooth disease, axonal, type 2L	AD, GOF
CIT	Microcephaly 17	AR, LOF
COX6A1	Charcot-Marie-Tooth disease, recessive intermediate D	AR, haploinsufficiency
COQ5	Coenzyme Q10 deficiency, primary, 9	AR, GOF
ACADS	Deficiency of Acyl-CoA dehydrogenase, short-chain	AR, LOF
ORAI1	Immunodeficiency 9	AD, LOF
	Myopathy, tubular aggregate, 2	AD, GOF
SETD1B	Intellectual developmental disorder with seizures and language delay	AD, GOF
GATC	Combined oxidative phosphorylation deficiency 42	AR, LOF
HPD	Hawkinsinuria, tyrosinemia, type III	AR, LOF
CFAP251	Spermatogenic failure 33	AR, deletion
ZCCHC8	Pulmonary fibrosis and/or bone marrow failure, telomere-related, 5	AD, LOF
EIF2B1	Leukoencephalopathy with vanishing white matter; VWM	AR
SCARB1	High density lipoprotein cholesterol level QTL6	Variable
DHX37	Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies	AR, missense
C12orf65	Combined oxidative phosphorylation deficiency 7	AR, LOF
	Spastic paraplegia 55	AR
TCTN2	Meckel syndrome 8	AR
	Joubert syndrome 24	AR, LOF
ATP6V0A2	Cutis laxa, autosomal recessive, type IIA	AR, LOF
	Wrinkly skin syndrome	AR, LOF
PUS1	Myopathy, lactic acidosis, and sideroblastic anemia 1	AR, LOF
ANKLE2	Microcephaly 16, primary	AR, not known
POLE	Susceptibility to colorectal cancer 12	AD
FILS syndrome
	IMAGE-I syndrome	LOF
HNF1A	Type 2 diabetes mellitus; T2D	AD
Hepatic adenoma, somatic Renal cell carcinoma, nonpapillary; RCC
Type 1 diabetes mellitus; T1D	AR
	MODY, type III Diabetes mellitus, insulin-dependent, 20
BCL7A	B-cell non-Hodgkin lymphoma, high-grade	Not known
DIABLO	Deafness, autosomal dominant 64	AD
VPS33A	Mucopolysaccharidosis-plus syndrome	AR

AD, autosomal dominant; AR, autosomal recessive; LOF, loss of function; GOF, gain of function.

In conclusion, we describe a patient with duplication of the 12q24.21q24.3 region and epilepsy, which has not been previously reported and seems to represent a novel clinical feature expanding the phenotype. In addition, also interesting, our patient had congenital heart defects with no duplication of the THRAP2 gene which seems to indicate that this gene is not strictly associated with this type of defect.

Statement of Ethics

Written informed consent was obtained from the patient's parents for publication of the details of their medical case and any accompanying images. This study protocol was reviewed and approved by Comite de Etica en Investigacion and Comite de Investigacion of Hospital General de Mexico, approval number DI/17/310A/04/083.

Conflict of Interest Statement

The authors have no conflicts of interest to declare.

Funding Sources

The study was funded by Programa de Posgrado en Ciencias Médicas, Odontológicas y de la Salud, Facultad de Medicina, UNAM. PAPIIT IN219419, DGAPA, Universidad Nacional Autonoma de México.

Author Contributions

Writing and original draft preparation: M.D.M.-S., S.A.C.-C., L.P.-B., C.G.S.-A., and O.M.-B. Critical review: M.D.M., S.A.C.-C. All authors analyzed and interpreted the data and approved the manuscript in its final form.

Data Availability Statement

All data generated or analyzed during this study are included in this article. Further inquires can be directed to the corresponding author.

Funding Statement

The study was funded by Programa de Posgrado en Ciencias Médicas, Odontológicas y de la Salud, Facultad de Medicina, UNAM. PAPIIT IN219419, DGAPA, Universidad Nacional Autonoma de México.