De Novo Subtelomeric 6p25.3 Deletion with Duplication of 6q23.3-q27: Genotype–Phenotype Correlation

Abstract

Duplications of 6q and deletions of 6p have been reported in more than 30 cases of live born infants and given rise to widespread abnormalities recognizable as a specific clinical syndrome. Different phenotypes have been described with variable clinical signs. Most cases involve the coexistence of unbalanced translocations affecting one or the other of the chromosomes. However, duplication of both chromosome 6q and deletion of 6p regions have been reported in only a few cases. Here, we report the first duplication of chromosome band 6q23.3–q27 with deletion of 6p25.3. This is the first case in the literature involving changes to these specific chromosomal regions; a medium size duplication of the distal long arm and smaller deletion of the terminal short arm of chromosome 6. In the literature, there are no other cases where these two specific chromosomal aberrations are observed together. Conventional chromosome analysis was performed to investigate the patient. Chromosome structure was identified using fluorescence in situ hybridization for subtelomeric regions of chromosome 6 and array comparative genomic hybridization analysis (array-CGH).

Introduction

Duplication (partial trisomy) of the distal long arm of chromosome 6 has several clinical characteristics. Similarly, deletion of the 6pter results in many clinical abnormalities. These two aberrations have been reported to occur in more than 30 cases of live born infants. ¹

A variety of different phenotypes have been described with varying clinical signs for each of these chromosomal aberrations. In the case of duplication of 6q21–27, intellectual disability, pre- and postnatal growth restriction, microcephaly, prominent forehead, downward slanting palpebral fissures, clinodactyly, syndactyly, talipes equinovarus, cardiac anomalies, hypertelorism, flat/broad nasal bridge, “carp” mouth, small mandible, low set/posteriorly rotated ears, short/webbed neck, joint contractures, cerebral anomalies, abnormal palmar creases, cleft palate, eye abnormalities, and genital abnormalities have been observed. ² Terminal deletions of 6p are rarer but also present a variety of clinical features. ³

Partial duplication has been described for all chromosomes and many cases show maternal inheritance. ⁴ Most cases represent the coexistence of unbalanced translocations. However, duplication of chromosome band 6q23.3–q27 is reported only in a few cases and they have well-defined phenotypes. Partial duplication of 6q is also reported only in a few cases ^{5 6} and these reports generally have duplication of 6q accompanied by other chromosomal abnormalities, e.g., chr16p and others, with duplications found more often than deletions. The size of duplication is directly related to the severity of the clinical phenotypes.

Sheth et al reported a medium size duplication of the distal long arm of chromosome 6 and small size deletion of terminal short arm. ⁷

The case reported here is the first in the literature involving the duplication of 6q23.3–q27 and deletion of the 6p25.3 chromosomal region.

Case Presentation

Our case is of an 8-month-old girl, the third child of a nonconsanguineous Turkish couple. Her mother and father are 28 and 31 years old, respectively. The proposita was delivered by Cesarean section at 38 ^5/7 weeks of gestation because of polyhydramnios. The pregnancy was uncomplicated. Birth weight was 2,670 g (10th centile) with a length of 48 cm (25th centile) and a head circumference of 33 cm (≥3rd and <97th). At the age of 2 months, the infant was noted to have bilateral exophthalmos, large fontanelle, bilateral overlapping toes ( Fig. 1 ), nail clubbing of the hand, retroperitoneal anus, and dysplastic ears.

Fig. 1.

Case image after physical examination.

At the age of 5 months, the main physical findings were head circumference 37.0 cm (<3rd centile), could not sit unsupported, cleft soft palate, blue sclerae, large prefrontal cortex (8 cm × 6 cm), and was fed with baby food. Stenosis of the patent foramen ovale and peripheral pulmonary artery was demonstrated by echocardiographic examination.

At age of 8 months, the infant had a head circumference of 39 cm with anterior fontanelles and open sutures. She was able to make good eye contact, was unable to sit unaided but could hold up her head. Abdominal ultrasonographic imaging was performed and a full abdominal examination was noted as normal (spleen, kidneys, liver, gall bladder, urinary bladder, pancreas, and bilateral adrenal gland). Right and left kidney sizes were 35 and 40 mm, respectively. The sizes of the liver and spleen were 41 and 39 mm. Society for Fetal Urology grade I dilation was detected in the bilateral pelvicalyceal system. The now 9-month-old patient underwent the Denver II Developmental Screening Test and was evaluated as abnormal.

Materials and Methods

Conventional chromosome analysis was performed on 72 h lymphocyte cultures according to standard techniques. ⁸ Preparations were performed using Leishmann-pancreatin banding. At a 400- to 500-band level of resolution, the extra chromosomal material was seen clearly a direct duplication. Subtelomeric 6p/6q probe (Chromoprobe Multiprobe-T device Panel, Aquarius Subtelomere Specific Probes Cat. No. PMP 803) was applied by for confirmation of the karyotype result. Genomic DNA was isolated from patient lymphocytes using the Qiagen DNA extraction kit (Santa Clara, CA). The investigation of copy number changes was performed by array comparative genomic hybridization (aCGH) using the Whole Human Genome Comparative Genomic Hybridization Microarray 60K (Agilent Technologies, Santa Clara, CA, United States) as recommended by the manufacturer. Scanned images of the arrays were processed by the Feature Extraction software (Agilent Technologies).

Written informed consent form was signed by the legal guardian of the baby. The research was reviewed and approved by an institutional review board.

Results

The patient was found to have a chromosomal aberration on chromosome 6 that contained a medium size duplication of the long arm. Her karyotype was 46,XX,der(6)(qter- > q23::p25.3- > qter; Fig. 2 ). Her parents have normal karyotypes. Subtelomeric fluorescence in situ hybridization showed three red signals for 6qter (indicating three copies of 6q) and a green signal for 6pter on normal chromosome 6 ( Fig. 3 ). Array comparative genomic hybridization analysis showed that the extra material on the patient's abnormal chromosome 6 was derived from chromosome 6. A deletion was observed on the 6p25.3-pter, approximately 329 kb in size that contained 20 probes. The deletion region was located between 206.749 bp and 588.213 bp. This region contains three genes (arr[GRCh37] 6p25.3[206749–588213]x1).

Fig. 2.

Case karyotype.

Fig. 3.

Case FISH (fluorescence in situ hybridization) image.

Array comparative genomic hybridization results generated expansion test/reference ratios for the 6q23.3q–27 region, supporting duplication (arr [GRCh37] 6q23.3-q27[138,180,512–170,906,796]x3). The gain in size was 32,726 kb and was detected by 525 probes/174 genes ( Fig. 4 , Table 1 ). The duplication region was located between 138.180.512 bp and 170.906.796 bp. Her array result is 46,XX,[GRCh38]6p25.3(206749–588213)x1 dn, 6q23.3-q27(138,180,512–170,906,796)x3 dn.

Fig. 4.

Array-CGH (comparative genomic hybridization) results.

Table 1. Gene list in duplication region 6q23.3q27.

TNFAIP3	PERP	KIAA1244	PBOV1	HEBP2	NHSL1	MIR3145
FLJ46906	CCDC28A	ECT2L	REPS1	C6orf115	HECA	TXLNB
CITED2	LOC645434	MIR3668	NMBR	VTA1	GPR126	LOC153910
HIVEP2	AIG1	ADAT2	PEX3	FUCA2	LOC285740	PHACTR2
LTV1	C6orf94	PLAGL1	HYMA	SF3B5	STX11	UTRN
EPM2A	FBXO30	SHPRH	GRM1	RAB32	C6orf103	LOC729176
LOC729178	STXBP5	SAMD5	SASH1	UST	TAB2	SUMO4
ZC3H12D	PPIL4	C6orf72	KATNA1	LATS1	NUP43	PCMT1
LRP11	RAET1E	RAET1G	ULBP2	ULBP1	RAET1K	RAET1L
ULBP3	PPP1R14C	IYD	PLEKHG1	MTHFD1L	AKAP12	ZBTB2
RMND1	C6orf211	C6orf97	ESR1	SYNE1	MYCT1	VIP
FBXO5	MTRF1L	RGS17	OPRM1	IPCEF1	CNKSR3	SCAF8
TIAM2	TFB1M	CLDN20	NOX3	ARID1B	C6orf35	ZDHHC14
MIR3692	SNX9	SYNJ2	SERAC1	GTF2H5	TULP4	TMEM181
DYNLT1	SYTL3	MIR3918	EZR	OSTCL	C6orf99	RSPH3
TAGAP	FNDC1	SOD2	WTAP	LOC100129518		ACAT2
TCP1	SNORA20	SNORA29	MRPL18	PNLDC1	MAS1	IGF2R
LOC729603	SLC22A1	SLC22A2	SLC22A3	LPAL2	LPA	PLG
MAP3K4	AGPAT4	NCRNA00241		PARK2	PACRG	LOC285796
DKFZp451B082		LOC100526820		QKI	C6orf118	PDE10A
C6orf176	LOC441177	PRR18		SFT2D1	BRP44L	RPS6KA2
MIR1913	RNASET2	MIR3939		FGFR1OP	CCR6	GPR31
TCP10L2	UNC93A	TTLL2		TCP10	C6orf123	C6orf124
MLLT4	HGC6.3	KIF25		FRMD1	DACT2	SMOC2
THBS2	WDR27	C6orf120		PHF10	TCTE3	C6orf70
NCRNA00242	C6orf208			DLL1	PDCD2	LOC154449
FAM120B	PSMB1	TBP

Discussion

Partial trisomy of chromosome 6q causes a wide range of effects in patients. Most fetuses with these anomalies abort during pregnancy. The condition of live born infants is dependent on the severity of clinical manifestations and generally these children need special care and specific therapies. Partial trisomy of 6q is a variable syndrome, which needs further evaluation. An increased number of studies can help to identify chromosomal aberration cause and clinical effect more clearly. Duplicated regions of the long arm of chromosome 6 display many widespread anomalies but define a clinically specific syndrome ( Fig. 5 ; Table 2 ). ^{2 9 10 11 12 13 14 15 16} Hence, the observed variations in the syndrome characteristics between proximal ⁹ and distal duplication of chromosome 6q ¹⁰ might be because of the infrequent, potentially destructive genes mapped in the euchromatic band q21 and, in contrast, the clustering of genes related to brain differentiation, neuromuscular synapses, acetylcholine receptor expression, actin, and trace amine-associated receptor 4 in the telomeric region of the 6q23-qter. ¹¹ Five papers have been published, related to 6q23q26 duplication and our case showed the same breakpoints. ^{2 9 12 13 14} Some people are mildly affected by a duplication of 6q but others show more marked effects. Children with terminal duplications of the long arm of chromosome 6 (between band 6q23 and the end) need a moderate amount of support with their learning, but some will need more, especially when they have a particularly large duplication. Some part of the duplication that we detected in our patient corresponds to this range. Therefore, the patient may be expected to have the same clinical findings at later ages. Children/adults with a duplication of 6q have small hands and short fingers but different features can be seen, which include an extra finger and toe; and hands that are twisted outwards and toward the little finger. ^{15 16} Our patient had similar clinical signs of the toes except for the hand fingers. She has bilateral overlapping toes ( Fig. 1 ), nail clubbing of the hand. Children and adults with 6q duplication have a very small head (microcephaly) and cryptorchidism, hypospadias, and shawl scrotum have also been reported in the literature. In our case, microcephaly is similar to these findings. At age 8 months, the infant had a head circumference of 39 cm with anterior fontanelles and open sutures. Patients with 6q duplication were generally born with normal kidneys and well-functioning urine collection systems; however, slow growth (in some cases starting in the womb) has been observed. Feeding and eating problems occur in some but certainly not all babies and children. Abdominal ultrasonographic imaging was performed and a full abdominal examination was noted as normal (spleen, kidneys, liver, gall bladder, urinary bladder, pancreas, and bilateral adrenal gland). Right and left kidney sizes were 35 and 40 mm, respectively. The sizes of the liver and spleen were 41 and 39 mm. Society for Fetal Urology grade I dilation was detected in the bilateral pelvicalyceal system in our patient's findings.

Fig. 5.

Diagram of normal and abnormal chromosome 6 of patient. Most likely features in literature.

Table 2. Comparison of physical findings of a duplication of chromosome 6q, deletion 6p, and the findings in our patient ^{2 9 22 23 24 25} .

Key findings	Duplication 6q (the findings reported in the literature)	Subtelomeric deletion 6p (the findings reported in the literature)	Patient
Short webbed neck	+
Microcephaly	+	+	+
Prominent forehead	+	+	+
Down-slanting palpebral fissures	+	+
Acrocephaly	+		+
Abnormal palmar creases	+		±
Transient neonatal diabetes mellitus	+
Joint contractures	+
Foot anomaly	+	+	+
Growth retardation	+	+	+
High/cleft palate	+	+	+
Low birth weight	+		+
Flat facies	+	+	+
Hypertelorism	+	+	+
Carp shaped mouth	+		+
Micrognathia	+		+
Hand/finger anomaly	+	+	+
Kyphoscoliosis(kyphosis)	+
Severe psychomotor retardation	+		+
Low set ears	+	+
Cardiac: murmur/anomaly	+		+
Genitourinary anomaly	+		+
Cerebral anomaly	+
Flat/broad nose	+		+
Nail clubbing in hand			+
Bilateral overlapping toes			+
Bilateral exophthalmos			+
Large fontanelle			+
Retroperitoneal anus			+
Patent foramen ovale			+
Peripheral pulmonary artery stenosis			+
Short/smooth/flat philtrum		+
Long philtrum			+
Blue sclerae	+		+
Intellectual disability		+
Language impairment		+
Hypotonia		+
Hearing loss		+
Heart defect		+
Structural eye abnormality		+
Dandy–Walker		+
Hydrocephalus/abnormal skull shape		+
White matter abnormalities		+
Slender long bones and tall foreshortened vertebral bodies		+
Epiphyseal dysplasia		+
Hip dysplasia		+
Hernia (umbilical or inguinal)		+
Dental abnormalities		+

Babies with duplications of other bands of 6q have been born with clubfoot or fixed contractures of the ankles. ¹⁷ The 6q duplication interval contains at least ten OMIM listed genes, of which four have OMIM morbid entries ( SMOC2, THBS2, ERMARD , and TBP ). Burnside et al report extensive CNS developmental abnormalities in a 2-month-old infant with duplication of THBS2 . This gene encodes thrombospondin 2, an astrocyte-secreted protein essential for synaptogenesis and neurite growth. The clinical features described in our proband are largely common to other case reports of duplication of 6q. ^{2 13 14 15 16 17} No such findings were observed in our patient at the time of admission to the clinic. However, she will be followed for further developmental periods.

Over 25 cases with variable deletions of 6p25-pter have been reported. Submicroscopic deletions of 6p, especially at 6p25 to 6pter, lead to develop hearing impairment, ocular dysgenesis, brain abnormalities, and dysmorphic features including hypertelorism, downslanting palpebral fissures, small nose, low nasal bridge, tented mouth, and a short neck. Other features include skeletal, renal, and cardiac malformations. ¹⁸ All previous reports of 6p25 cytogenetic abnormalities are consistent with the concept that altered doses of a gene or genes in the duplicated ( Table 1 ) or deleted regions give rise to the clinical symptoms ( Table 2 ). She has main physical findings: head circumference, 37.0 cm (less than third centile); could not sit unsupported; cleft soft palate; blue sclerae; large prefrontal cortex (8 cm × 6 cm); and was fed with baby food. Stenosis of the patent foramen ovale and peripheral pulmonary artery was demonstrated by echocardiographic examination. The clinical findings in our patient were more similar to the 6p deletion findings than the effects of the duplication of the sixth chromosome. As already known in classical knowledge, the phenotypic effects of chromosomal deletions compared with duplications produce more severe and more serious clinical effects. ¹⁹ Interferon regulatory factor-4(IRF4), dual specificity phosphatase 22 (DUSP22) , exocyst complex component 2(EXOC2) coding genes are normally present in the deleted region found in our patient at 6p25.3; however, such deletions in the literature usually also include the FOXC1 gene and because of this the clinical prognoses of patients are poor. ^{18 20 21 22} The deletion region in our patient did not include this gene.

IRF4 is located on chromosome 6 at the telomeric extremity of the short arm and occurs in the region between the DUSP22 and EXOC2 genes. ^{20 21 22} The loss of these genes ( IRF4, DUSP22 , and EXOC2 ) in the 6p25.3 region is reported as benign at ISCA. ^{23 24} The number of genes in the duplicated region is larger than the deleted region.

Conclusion

Here we report the first recognized case of duplication of chromosome 6q23.3-q27, a medium size duplication of the distal long arm, with deletion of 6p25.3, a small size deletion of the terminal short arm of chromosome 6. The patient described will be followed up clinically and correlation of developmental parameters with the cytogenetic findings will be performed. We hope to be a guide in the clinical evaluation of prospective patients and phenotypic and chromosomal findings will add to the exiting literature.

Funding Statement

Funding None.