Introduction

Reports of isolated subtelomeric deletions of the long arm of chromosome 20 are rare, but a few cases have been reported in the literature over the past 30 years.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 Traylor et al.12 provided an overview of these cases alongside six others with clinical similarities including skeletal and growth abnormalities, developmental delay and seizures.12 Butler et al.13 suggested that common abnormalities seen in 20q13 deletion patients were intellectual disability, speech problems, pre- and postnatal growth retardation, microcephaly, hypotonia, a high forehead and broad nasal bridge, a thin upper lip and a small chin, malformed ears, hypertelorism, a bulbous nasal tip and malformed hands and feet.13 Solomon et al.14 described a patient with a 0.7 Mb deletion at 20q13.33, and proposed that the deletion of GTPB5 makes it a candidate gene for tracheoesophageal fistula/esophageal atresia.

We present a patient with a 2.6 Mb interstitial deletion of chromosome 20q, spanning a region more centromeric than the majority of cases previously published and within the region of deletion reported by Butler et al.,13 and just proximal to the deletion reported by Solomon et al.14 We describe the clinical phenotype of this child in the context of his microarray-based comparative genomic hybridization (arrayCGH) deletion at 20q13.32–q13.33, and define a possible minimal region of overlap for a common phenotype.

Materials and methods

This patient is a 2-year-old boy, first child of healthy, non-consanguineous, White North European parents. Pregnancy was complicated by concerns regarding oligohydramnios and poor growth. The 20-week anomaly scan showed a single umbilical artery and he was delivered by emergency cesarean section at 36+2 weeks gestation, owing to fetal distress. He did not require any resuscitation immediately after birth and Apgar scores were 9 and 9 at 1 and 10 min, respectively, of age. Birth parameters were: weight ~1.56 kg (0.4th–2nd centile), length ~40 cm (<0.4th centile) and head circumference ~28.2 cm (<0.4th centile). He spent the first 6 weeks of his life in the Special Care Baby Unit because of poor feeding and was diagnosed to have bilateral positional talipes, which resolved with physiotherapy. Cranial ultrasound at the time of birth showed a grade 1 subependymal hemorrhage. He was subsequently discharged home and continued to have significant problems with feeding and gastroesophageal reflux needing antireflux medications. His growth continued to remain well below the 0.4th centile, with some preservation of head circumference.

In terms of his development, he smiled at 2 months of age, sat at 7 months, walked at 13 months and there were no concerns with his vision, hearing and speech. On examination at 2 years of age, he was facially dysmorphic, with bilateral low-set ears, thin skin, reduced subcutaneous fat, grayish sclerae and a spooned-out appearance of his nails (Figures 1a and b). He had a mild degree of developmental delay, but there were no concerns with his vision, hearing or speech. Measurements included: weight ~6 kg (2 cm below 0.4th centile), height ~69.5 cm (1 cm below 0.4th centile) and head circumference ~42 cms (1.5 cm below 0.4th centile), with no evidence of asymmetry.

Figure 1
figure 1

Patient as an infant (a) and at 18 months of age (b), demonstrating grayish sclerae, thin skin and facial dysmorphism. A full color version of this figure is available at Journal of Human Genetics online.

Investigations before arrayCGH included metabolic tests including urine organic and amino acids, plasma lactate, plasma acylcarnitine profile, serum amino acids, lipid profile, VLCFA (very long chain fatty acids), serum calcium and parathormone levels, which were all reported as normal. Echocardiogram and an abdominal ultrasound were also reported as normal. Cytogenetics showed a normal male karyotype (46,XY) and 11p15 methylation analysis and UPD7 (uniparental disomy on chromosome 7) to exclude Russell–Silver Syndrome (due to his small stature), methylation testing for Prader–Willi syndrome (in view of his feeding difficulties), all of which were negative. Skeletal survey demonstrated slender ribs and the long bones appeared osteopenic with normal bone age.

Results

ArrayCGH and fluorescence in situ hybridization

ArrayCGH was performed on genomic DNA extracted from peripheral lymphocytes. This was applied to a BlueGnome oligonucleotide array, 8 × 60 K, International Standard Cytogenomic Array Consortium v2 configuration, according to the manufacturer’s instructions, using Promega pooled control DNA as a reference. Slides were scanned using a Genepix Personal 4100A scanner (Axon Instruments) and analyzed using BlueGnome BlueFuse-Multi (version 3.2) analysis software. Confirmatory fluorescence in situ hybridization was performed using the BlueGnome RP3-492J12 BAC probe. The arrayCGH results showed a 2.6 Mb heterozygous interstitial deletion of chromosome 20q13.32–q13.33 (chr20: 56 571 799–59 230 205 Build GRCh37) (Figure 2a) including 21 HGNC genes (Table 1). Fluorescence in situ hybridization confirmed the deletion showing an absence of the RP3-492J12 probe on one chromosome 20 homolog (Figure 2b). Examination of the parents revealed that this was a de novo finding and the most likely cause of this patient’s phenotype.

Figure 2
figure 2

Array CGH profile showing deletion on chromosome 20q13.32–q13.33 (a), which was confirmed by metaphase fluorescence in situ hybridization (FISH) using BAC probe RP3-492J12 (b), and representation of the de novo 2.6 Mb deletion of 20q13.32–q13.33 (chr20: 56 571 799–59 230 205 Build hg19), showing the array profile of our patient. Shown here is a schematic of the genes in the region, blue bars represent HGNC genes, green bars represent OMIM genes. The OMIM gene names are given in order in the track below. Also shown, represented by the gray bars, are the deletions reported by Butler et al.13 (chr20: 53 512 484–60 850 110 hg19), Genevieve et al.5 (delineated by FISH) and Solomon et al., 2011 (chr20: 59 671 821–60 329 092 hg18) (c). A full color version of this figure is available at Journal of Human Genetics online.

Table 1 Genes deleted from 20q13.32 to q13.33 Includes HGNC gene name, OMIM number, function according to uniprot and %HI.16

Discussion

We report a 2-year-old boy with poor growth, feeding difficulties, lack of adipose tissue with poor weight gain, facial dysmorphism and radiological evidence of low bone mass without a history of fractures, with a 2.6 Mb interstitial deletion on chromosome 20q13.32–q13.33. This region contains 21 HGNC genes and 12 OMIM genes, one of which, GNAS is a DD2GP (associated with a developmental disorder) gene (https://decipher.sanger.ac.uk).15 Interstitial deletions of the long arm of chromosome 20 are rare, but this has been reported with a proposed common phenotype comprising intellectual disability, speech problems, pre- and postnatal growth retardation, microcephaly, hypotonia, a high forehead and broad nasal bridge, a thin upper lip, small chin, malformed ears and hypertelorism.5, 13, 15

The patient reported here is perhaps more similar to the patients reported by Butler et al.,13 and Geneviève et al.5, 13 and Butler et al.13 described a 32-month-old girl of Peruvian origin with a 20q13.2–q13.33 deletion presenting with intellectual disability, low tone, absent speech, poor growth and a cleft lip.13 Geneviève et al.5 described two unrelated patients with a 6 Mb deletion of 20q13.2–q13.3 who presented with severe pre- and postnatal growth retardation, significant feeding difficulties, developmental delay, abnormal distribution of subcutaneous adipose tissue and facial dysmorphism with a non-Albright’s hereditary osteodystrophy (non-AHO) phenotype. In fact, our patient described here has a very similar phenotype and looks facially very similar to patient 2.5 Evidence from these manuscripts and our paper adds to the conclusion that interstitial deletion of 20q13.3 does not always result in an AHO phenotype, which is an important fact in the genetic counseling process, especially when the molecular karyotyping is carried out when young. Also, given the evidence that our patient did not have the AHO phenotype as with the patients described by Geneviève et al.,5 we would hypothesize that the deletion was likely to be of paternal origin. Table 2 provides a comprehensive comparison of the patients reported with similar deletions in the literature with the patient described here and it is clear that interstitial deletions of 20q13.3 have a similar clinical presentation and a non-AHO phenotype. The deletion described by Solomon et al.14 is a 0.7 Mb de novo deletion of 20q13.33, which is just distal to the patient reported here, and hence we would not expect a phenotypic overlap with this patient14 (Figure 2c).

Table 2 Comparison of published cases with current patient

Table 1 provides a list of the HGNC genes involved with their corresponding OMIM number and gene function in 20q.16, 17 As is evident from the table apart from GNAS complex, the other genes are less commonly implicated in human disease and most of them are not associated with a phenotype in the heterozygous state. The genes with the lowest haploinsufficiency scores are: STX16, VAPB, GNAS and SLMO2, which have been discussed further. Of significance, the deleted region contains GNAS and STX16, part of the GNAS complex that is a complex imprinted locus that produces multiple transcripts through the use of alternative promoters and alternative splicing. We know that genomic imprinting, by which maternal and paternal alleles of some genes have differing levels of activity depending on parent of origin, have profound effects on growth and development in humans. Inactivating loss-of-function mutations in GNAS are known to cause pseudohypoparathyroidism (PHP type 1a), also known more commonly as AHO, whereas activating mutations in this gene are associated with the McCune–Albright syndrome and polyostotic fibrous dysplasia.18 AHO is an autosomal-dominant condition characterized by obesity, short stature, round face, short bones in the fingers, especially the 4th and 5th metacarpals, and subcutaneous calcification. Intellectual disability is reported in about 70% of these patients.19 In contrast, PHP type 1b is characterized by isolated renal parathyroid hormone resistance without any of the physical characteristics seen in AHO. PHP type 1b is caused because of methylation and imprinting defects of the GNAS complex from the maternal allele with subsequent loss of expression of Gs-α protein in proximal renal tubules (as only the maternal allele is expressed in the proximal renal tubules).20 Another cause of PHP type 1b is because of microdeletions of STX16, a long-range control element of methylation at the GNAS locus.21 Our patient did not have the AHO or PHP type 1b phenotype (in terms of the physical characteristics and the bone biochemistry) and hence is perhaps phenotypically more similar to the Peruvian patient reported Butler et al.,13 with a non-AHO phenotype.

Of the other potential genes of interest, VAPB (vesicle-associated membrane protein-associated protein B) has a role in unfolded protein response, which is a process that suppresses the accumulation of unfolded proteins within the endoplasmic reticulum.22 Heterozygous mutations in VAPB have been implicated in amyotrophic lateral sclerosis and late-onset, Finkel-type spinal muscular atrophy.23 SLMO2 is not a protein-coding gene and its function is not yet known. Of the other genes implicated in human disease within this deletion are, EDN3 (Endothelin-3), mutations in which have been identified in Waardenburg type 4b (Shah-Waardenburg syndrome), congenital central hypoventilation syndrome (CCHS) and also, in some cases, of isolated Hirschsprung disease.24, 25 TUBB1 codes for a major β-tubulin expressed in platelets and megakaryocytes and mutations in this gene are known to cause macrothrombocytopenia.26 Therefore, although, the patient reported here does not have an AHO phenotype, and GNAS is the most likely candidate gene contributing to this phenotype in the deleted region.

In conclusion, this patient has clinical features that overlap those previously reported in association with 20q13 deletions. The 2.6 Mb interstitial deletion of chromosome 20q13.32–q13.33 is smaller than that previously reported by Butler et al.,13 and therefore helps to narrow the minimum deleted region that may be responsible for the ‘common’ features of a 20q13.3 deletion syndrome. Further case reports of a similar nature are required to try and delineate the exact phenotypic variations in interstitial deletions within the long arm of chromosome 20.