Expanding the phenotype of reciprocal 1q21.1 deletions and duplications: a case series

In recent years, the introduction of new technologies such as comparative genomic hybridization (CGH) allows for the routine detection of submicroscopic deletions and duplications. Several studies of patients with global developmental delay, intellectual disability and/or congenital malformation of unknow cause have led to the identification of new genomic disorders [1‐4].

Recurrent reciprocal 1q21.1 deletions and duplications have been associated with variable phenotypes. Phenotypic features described in association with 1q21.1 microdeletions include developmental delay, craniofacial dysmorphism and congenital anomalies. Developmental delay is usually mild and may involve global or specific areas. Psychiatric and behavioral abnormalities, such as autism spectrum disorders (ASD), schizophrenia and attention deficit hyperactivity disorder (ADHD), are also described in a minority of patients. Dysmorphic features are a common finding; they may include microcephaly (almost 50% of patients), frontal bossing, deep-set eyes, epicanthal folds, large nasal bridge, long philtrum and highly arched palate. Several congenital anomalies may be associated with the deletion: congenital heart disease (CHD), eye abnormalities (microphthalmia, chorioretinal and iris colobomas, strabism, various type of cataracts), skeletal and genitourinary malformations. In some cases, seizures are also described (15%) [5‐9]. As it is clear, the phenotype of 1q21.1 microdeletion has a high variability, so it is not possible to define a clinically recognizable syndrome.

Few individuals with 1q21.1 reciprocal duplication have been reported in literature. Most recognizable features are macrocephaly or relative macrocephaly, frontal bossing, hypertelorism, developmental delay, intellectual disability and autism spectrum disorder [6, 7]. Individuals with 1q21.1 copy number variations (CNVs) may also have a normal phenotype.

The 1q21.1 critical region spans approximately 1.35 Mb (from 145 to 146.35 Mb) [6] and includes at least 12 genes, among which PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B. Deletions and duplications can be inherited from a parent in an autosomal dominant manner or occur de novo.

Our study describes seven patients, who were referred to us for developmental delay/intellectual disability, dysmorphic features and, in some cases, congenital anomalies, in whom we identified 1q21.1 CNVs by array-CGH. The aim of this study is to contribute to the definition of the phenotype associated with reciprocal 1q21.1 deletions and duplications.

Among our seven patients we detected, using array-CGH, four 1q21.1 deletions, two 1q21.1 duplications and a double rearrangement on the long arm of a chromosome 1, with a 1q21.1 duplication and a 1q21.1-q21.2 deletion.

Before undergoing to array-CGH analysis, a karyotype study was performed in patient 2, 4 and 7: all patients have a normal male karyotype (46,XY).

We detected a 1q21.1 deletion in patient 2, 4, 5 and 7. Patient 2 and 4 have a 1q21.1 deletion that spans approximately 1,2 Mb (146.564.743–147.786.706). Array-CGH analysis in both parents of patient 2 shows that the rearrangement has a paternal origin, while these data are not available for the parents of patient 4. Patient 5 and 7 have a 1q21.1 deletion, of approximately 1,1 Mb (146.641.601–147.786.706)(Fig. 1). The rearrangement is inherited from his mother in patient 7, while it is de novo for what concerns patient 5. This deleted region includes numerous genes: PRKAB2, PDIA3P, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, PDZK1P1, NBPF11, NBPF24. Patients with a microduplication are patient 1 and 6. Patient 1 has a 1q21.1 duplication of approximately 932 kb (145.632.334–146.564.802), involving the genes: GPR89A, PDZK1, CD160, RNF115, POLR3C, NUDT17, PIAS3, ANKRD35, PEX11B, ITGA10, RBM8A, LIX1L, POLR3GL, HFE2, NBPF10, NOTCH2NL. The origin of this rearrangement is unknown, because array-CGH analysis data concerning parents are not available. Patient 6 has a 1q21.1 duplication that spans approximately 456 kb (145.291.711–145.747.269)(Fig. 2). Array-CGH analysis in both parents shows that the rearrangement has a maternal origin. The duplicated region involves genes such as NBPF20, GPR89A, PDZK1, CD160 and RNF115.

Finally, patient 3 is the only one with a prenatal diagnosis. Fetal karyotype on amniotic cells revealed a chromosomal insertion involving the short arm of a chromosome 3 and the short arm of a chromosome 1: 46, XY, ins(1;3)(p22;p13p23). This rearrangement was confirmed by Fluorescent in-situ Hybridization (FISH): ish ins(1;3)(p22;p13p23)(pVYS218C+;wpc3+). The karyotype study in both parents was normal, this showing that the rearrangement was de novo. In order to better define this chromosomal abnormality, array-CGH analysis was performed. We detected a double rearrangement on the long arm of a chromosome 1: a 1q21.1 duplication extended for 1.2 Mb (from 144.612.681 to 145.799.573) and a 1q21.1-q21.2 deletion extended for 1,7 Mb (from 146.155.983 to 147.824.178). These complex rearrangements were confirmed by Dye-swap. Both rearrangements are de novo. The duplicated region includes many genes: NBPF9, PDE4DIP, NBPF10, HFE2A, TXNIP, RBM8A, PEX11B, ITGA10, PIAS3, CD160, PDZK1, GPR89A. The 1q21.1-q21.2 deletion comprises the 1q21.1 microdeletion syndrome critical region. This region includes genes such as PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8 and GPR89B. Though karyotype and FISH analysis performed prenatally revealed a chromosomal insertion involving the short arm of a chromosome 3 and the short arm of a chromosome 1, array-CGH analysis did not show gain or loss of genetic material of these regions. So we can affirm that it is a balanced rearrangement. At the same time, array-CGH allowed us to highlight a double rearrangement involving the long arm of chromosome 1.

(The main characteristics of the patients are shown in Table 1).

Recurrent reciprocal 1q21.1 deletions and duplications have been associated with variable phenotypes. The 1q21.1 microdeletion syndrome is characterized by a high variable clinical phenotype. The most common features, even if not constant, are microcephaly, dysmorphism, developmental delay and mild intellectual disability. Several congenital anomalies may be associated with 1q21.1 deletion: CHD, eye abnormalities, skeletal and genitourinary malformations. Psychiatric and behavioral abnormalities, such as ASD, schizophrenia and ADHD, are also described in a minority of patients.

The 1q21.1 reciprocal duplication have been associated with macrocephaly or relative macrocephaly, dysmorphic features, developmental delay, intellectual disability and autism spectrum disorder. Individuals with 1q21.1 CNVs may also have a normal phenotype.

We describe seven patients, who were referred to us for developmental delay/intellectual disability, dysmorphic features and, in some cases, congenital anomalies, in whom we identified by array-CGH analysis: four 1q21.1 deletions, two 1q21.1 duplications and a double rearrangement on the long arm of a chromosome 1, with a 1q21.1 duplication and a 1q21.1-q21.2 deletion. Duplications detected in patient 3 and 6 involve also the proximal part of 1q21.1 region. 1q21.1 proximal microduplications are associated with variable and not defined phenotypes, including intellectual disabiliy, dysmorphic features and behavior problems.

Our data confirm the extreme phenotypic variability associated with 1q21.1 microdeletion and microduplication. We observed common phenotypic features, described in previous studies, such as microcephaly, mild dysmorphic features, developmental delay and intellectual disability. Three patients also have skeletal anomalies (clinodactyly of fingers and toes, broad thumbs and hallux), while two patients have genitourinary malformation (VUR, ectopic urethral meatus). Furthermore, in our cohort of patients we described, for the first time, congenital hypothyroidism in association with 1q21.1 deletion and trigonocephaly associated with 1q21.1 duplication. None of the patients in our study have CHD.

Disagreeing with the literature, one patient harbouring a duplication (patient 1) has microcephaly instead of relative/absolute macrocephaly.

Only one patient (patient 3), the one with a double rearrangement on the long arm of a chromosome 1 prenatally diagnosed, has no phenotypic manifestations: we suggest a careful follow-up in order to evaluate his psychomotor development and the possible occurence of psychiatric and behavioral abnormalities.

Array-CGH analysis in the parents show a parental origin in three patients: two patients inherited the rearrangement from their mother, while one has a paternal inheritance. Among these, only in one case (patient 7) the mother was affected, having intellectual disability, thyroid hypoplasia and hypothyroidism, while the father of patient 2 and the mother of patient 6 have a normal phenotype. In two of our patients the rearrangement occurs de novo; lastly, in two cases data about parents are not available, so the inheritance remains unknown.

CNVs detected in our patients have different size, ranging from 456 kb to 1,2 Mb (Fig. 3a and b). Many genes are included in the deleted region, but no single gene mutations or haploinsufficiency are known to cause the 1q21.1 microdeletion phenotype. The most studied genes are CHD1L, PRKAB2, GJA5, GJA8 and NBPF genes.

CHD1L has been implicated in chromatin remodelling, relaxation and decatenation. Haploinsufficiency or over-expression of CHD1L have been implicated in impaired chromatin remodeling during DNA single strand break repair, suggesting that it has a role in DNA Damage Response [10]. Despite that, the phenotypic consequences of alterations in DNA Damage Response in patients with 1q21.1 CNVs are not clear [11].

PRKAB2 encodes the β2-subunit of AMPK (AMP-activated protein kinase), a regulator of cellular response to a large number of external stimuli, which seems to have an important role in brain function [11].

GJA5 and GJA8 have been identified in subjects with cardiac defect and eye abnormalities, respectively [5, 12, 13].

The NBPF (neuroblastoma breakpoint family) gene family consists of 24 members. Deleted or duplicated regions involved in our patients include: NBPF9, NBPF10, NBPF11, NBPF20 and NBPF24.

This gene family encodes for the DUF1220 protein domains, that seem to be associated with pathological variations in brain-size and neocortex volume. In particular, the loss of DUF1220 copy number has been associated with microcephaly, while the increases in DUF1220 copy number underlie 1q21-associated macrocephaly [14].

In the duplicated region, the most studied gene is PDZK1. Over-expression of this gene has been described in association with an increased risk of ASD and psychiatric diseases [15, 16].

The duplicated region in patient 1 encompasses also the PEX11B (peroxisomal membrane protein 11B) gene. It seems to be involved in the regulation of neuronal differentiation and migration, so it could be responsible for pathological variations in brain-size [17].

Among the genes involved in patient 7 (PRKAB2, PDIA3P, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, PDZK1P1, NBPF11, NBPF24), with current knowledge, none seems to be related with congenital hypothyroidism. We believe it is important to report this finding in order to better define this complex phenotype, although we are aware that more studies are needed to explain the relationship between 1q21.1 deletion and hypothyroidism. Likewise, none of the genes duplicated in patient 6 (NBPF20, GPR89A, PDZK1, CD160, RNF115) are known to cause trigonocephaly.

In conclusion, our results confirm the high phenotypic variability of 1q21.1 deletions and duplications, extending the phenotype with the finding of congenital hypothyroidism and trigonocephaly in association with 1q21.1 deletion and duplication, respectively.

Further studies are needed to better define the 1q21.1 microdeletion/microduplication syndrome and to understand how haploinsufficiency or over-expression of genes included in this region can cause this complex phenotype.