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From Next Generation Sequence to the Phenotype: Exploring the Bainbridge-Ropers Syndrome with Loss of Function Variants in ASXL3

Silvina Noemí Contreras-Capetillo1*, Melania Abreu-González2

1Laboratorio de Genética, Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Mérida, Yucatán, México

2Laboratorio de Biología Molecular y Secuenciación Masiva. Genos Médica, Centro Especializado en Genética, Ciudad de México, México

In 2013, Bainbridge-Ropers syndrome (MIM #615485) was described in patients with severe global developmental delay, postnatal microcephaly and feeding problems due to heterozygous loss of function variants in the ASXL3 gene. The ASXL3 is part of the ASXL gene family involved in gene expression during embryogenesis and they participate as epigenetic scaffolds capable of interacting with complex modifiers of chromatin and diverse transcription factors. Germline variants in ASXL1, ASXL2 and ASXL3 have been associated with neurodevelopmental disorders which clinical phenotypic presentation resembles to Bainbridge-Ropers syndrome thus elucidating these types of overlapping genetic disorders is challenging. Up to now, approximately forty patients have been confirmed with this syndrome by next generation sequencing. The implementation of whole exome sequencing allows early identification and definitive diagnosis of patients with clinically unestablished phenotypes, as seen in AXL3 gene. This review discusses clinical and molecular features of variants in AXL3 gene associated with Bainbridge-Ropers syndrome.

Neurodevelopmental disorders without specific phenotype are highly undiagnosed, fortunately, next-generating sequencing (NGS) platforms are now able to confirm clinical phenotypes that in the past remained unknown1. These types of technologies have allowed for the discovery of new genes and new associations with diseases. In 2011, Mathew Bainbridge, a computational biologist, identified an abnormal copy of the ASXL3 gene in a patient who, after multiple genetic tests remained without diagnosis. After collaboration between Bainbridge and other experts in NGS, three additional individuals with variants in ASXL3 gene associated with neurodevelopment disease were found. Finally, in 2013 Bainbridge and colleagues reported ASXL3 variants in four patients with similar clinical features to Bohring-Opitz syndrome (MIM *612990, BOS) without the classic posture. Global development delay, postnatal microcephaly and feeding difficulties with heterozygous loss of function mutations in ASXL3 gene (MIM *615115) were detected by whole-exome sequencing (WES) and whole genome sequencing (WGS)2. These findings have led to the identification of nearly forty patients in large scale NGS project (Deciphering Developmental Disorders Study,, cohorts of clinical exome (CES)4,5 or isolated cases of nonspecific developmental delay6,7 which required WES or CES as molecular approaches.

The ASXL3 gene is part of the ASXL (Additional Sex Combs-Like) family in vertebrates (ASXL1, ASXL2 and ASXL3 genes) that encodes regulatory proteins of the trithorax and polycomb enhancers. The ASXL modulates the expression of homeotic genes during embryogenesis and functions as epigenetic scaffolds capable of interacting with complex modifiers of chromatin and diverse transcription factors8. ASXL1, ASXL2 and ASXL3 genes present common domains (ASXN, ASXH, ASXM1, ASXM2 and one PHD-finger) with thirteen exons and twelve introns9. The ASXL1, ASXL2 and ASXL3 genes express ubiquitously but, ASXL3 is predominantly expressed in the brain. These genes are involved in hereditary neurological disorders and the somatic presentation is associated with different types of cancers8. As more patients are described, it will be possible to determine if there is an increased risk of developing cancer in constitutional carriers.

Previously, studies have shown that ASXL1 gene is primarily involved in transcriptional activation and repression. In addition, somatic nonsense and frameshift variants have been frequently described in myelodysplastic syndrome and other hematological malignancies since, ASXL1 is essential for erythroid development and differentiation10. Germline de novo ASXL1 variants in PHD and ASXM2 domains have shown to cause BOS9,11.

Dominant-negative effect variants in ASXL2 gene have recently been linked to neurodevelopmental disorder (Shashi-Pena syndrome; MIM #617190, SHAPNS), as presented in six unrelated probands with de novo truncating variants. Reported patients demonstrated common clinical characteristics including delayed psychomotor development, variable intellectual disability, macrocephaly, prominent eyes, arched eyebrows, hypertelorism, glabellar nevus flammeus and hypotonia12.

Furthermore, pathogenic truncating de novo loss of- function4 variants in ASXL3 gene are associated with Bainbridge-Ropers syndrome (BRS). Frameshifts included 62% of the variants described, nonsense were reported in 34% and one report a splicing variant was identified (0.03%)6 (Table 1). These types of changes are consistent with the haploinsufficiency mechanism as proposed previously4. Missense variants were also reported in ASXL3 associated within the autistic spectrum13,14. Three variants presented recurrence in BRS. The c.3106C>T(p.Arg1036*)4,14,15, present in both BRS and in an individual with autism spectrum disorder16. The c.4330C>T(p.Arg1444*)3,5 and the c.3039+1G>A6,15 which were described in unrelated patients (Table 1). In 2013, Bainbridge and colleagues generated the polarity hypothesis in relation to the location of the mutations associated with BRS. This suggested that truncated variants, which occur at end 5´of the gene, are associated with a more severe phenotype. Nonetheless, this hypothesis was eliminated5,6,7 after accumulated evidence was examined. Despite the fact that the majority of the mutations are located on the largest exon, as in ASXL117, to date, two clusters of variants have been proposed both equally affected (~43%) (Table 1). One in the N-terminal region located between the codons 404 to 659 and another in the C-terminal (functional domain of chromatin-DNA recognition) between the codons 1045 to 14446,17. Additionally, transcriptomes of fibroblasts from patients with BRS demonstrated >500 genes involved in transcriptional regulation, development and proliferation of the differentially expressed genes, establishing that BRS is associated with defects in transcriptional regulation3,5.

Table 1. Loss of function variants associated with BRS phenotype
NM_030632.2 NP_085135.1 Cluster BRS Phenotype Reference
Nonsense Variants n=11/32 (34%)
c.1074T>A p.Tyr358* N + 3
c.1210C>T p.Gln404* N + 2
c.1369G>T p.Glu457* N + 4
c.1396C>T p.Gln466* N + 2
c.1783C>T p.Gln595* N + 3
c.3106C>T p.Arg1036*   + 4,14,15
c.3364C>T p.Gln1122* C + 5
c. 3613G>T p.Glu1205* C + 4
c.3635T>G p.Leu1212* C + 3
c.4144C>T p.Gln1382* C + 3
c.4330C>T p.Arg1444* C + 3,5
Indels (Frameshift Variants) n=20/32 (62%)
c.1082dup p.Leu362Alafs*23   + 3
c.1201del p.Ala401Glnfs*8   + 3
c.1219delA p.Ser407Alafs*2 N + 4
c.1314_1316delinsA p. Ser439Argfs*7 N + and hyperventilation induced athetosis 8
c.1318dup p.Glu440Glyfs*7 N + and pontocerebelar hypoplasia 18
c.1422dup p.Pro475* N + 2
c.1448dupT p.Thr484Asnfs*5 N + 5
c.1484insTGAA p.Asp497* N + 3
c.1491dup p.Asn498* N + 3
c.1897_1898delCA p.Gln633Valfs*13 N + and trigonocephaly 19
c.1978_1981delGACA p.Asp660Asnfs*1   + 2
c.2992_2995del p.Glu998Lysfs*26   + 7
c.3028delC p.Pro1010Leufs*14 C + and prominence of the Sylvian Fissure 13
c.3127_3128dup p.Gly1045Valfs*99 C + 3
c.3178dup p.Arg1060Profs*50 C + 3
c.3313_3316delCAGA p.Thr1106Argfs*36 C + 15
c.3355dup p.His1119Profs*7 C + 3
c.3494_3495delGT p.Cys1165* C + 4
c.4072_4073delGT p.Val1358Leufs*8 C + 4
c.6697_6710dup p.Ser2238Thrfs*3   + 20
Splicing 1/32 (0.03%)
c.3039+1G>A ? C + 6,15

Of the 32 variants described in Table 1, ∼90% were detected by WES. This was likely due to a higher diagnostic yield compared to CES or other NGS gene panels for neurodevelopmental disorders21. Based on these findings, it is necessary to include the ASXL gene family in NGS analysis in patients with subtle dysmorphism and psychomotor delay.

Recently, a compound heterozygous patient with BRS like features and primary IGF1 deficiency which presented the genotype c.(2965C> G);(3078G> C) was reported. It was proposed that the additively effect of both changes impacted in ASXL3 gene function. Although, in silico analysis suggests that the variant c.2965C>G was responsible for the loss of function. Functional studies will be necessary to confirm the real pathogenicity of the c.2965C>G rare variant22.

To date, fewer than 40 patients with variants in ASXL3 with the BRS phenotype have been reported3,4,5, 6,7,12, 13, 14, 15, 19. Usually, BRS presents as de novo truncating mutations in all patients with the exception of two siblings with the same mutation, which was not present in their parents. Germline mosaicism was not ruled out in this case. BRS patients are described from the prenatal stage18 to the age of 4720 with consistent phenotype features such as facial dysmorphisms with a broad and prominent forehead, arched eyebrows, downslanting palpebral fissures and anteverted or hypoplastic nares. These characteristics are shown to be present in less than 50% of the patients described. The principal manifestations are those related with neurological development. Global development delay, intellectual disability, from moderate to severe, late or absent language skills and hypotonia are present in more than 80% of the affected individuals. Feeding difficulties are also prevalent among these patients and more frequent during the neonatal period. 2,3,5, (Table 2).

Table 2. Clinical characteristic of 36 patients with variants in ASXL3 compared with phenotype reported in pathological variants in ASXL2 and ASXL1 in the literature.
Phenotype ASXL3 (n=36) ASXL2 (n=6)12 ASXL1 (n=7)17
Age Prenatal-47 years 11 months – 31 years Neonatal-14 years
Global developmental delay/Intellectual disability 100% 100% 100%
Late/absent language skill 92% 33% NR
Hypotonia 83% 100%* 21%
Feeding difficulties 75% 100% 100%
Autism spectrum disorder/Autism 47% NR NR
Seizures 39% 83% 50%
Brain abnormalities   83% 71%
Craneofacial features.
Microcephaly 36% 0 100%
Macrocephaly 0 100% 0
Downslanting palpebral fissures 50% 0 0
Broad/prominent forehead 42% 16% (1 ) 0
Glabellar nevus flammeus 0 100% 86%
Arched eyebrows 31% 100% 0
Low-set/ posteriorly rotated ears 22% 100% 43%
Anteverted nares/hypoplastic nares 22% 16% (1) 29%
Ocular hypertelorism 19% 100% 57%
Upslanting palpebral fissures 8% 0 57%
Systemic features
Ulnar deviation 17% 0 0
Hypertrichosis 16% 16% (1) 86%
BOS posture 0 0 100%
  Neonatal macrosomy in one patient Structural cardiopathy, hypoglicemia Atresia choanal, atrial septal defect, hepatomegaly, thoracolumbar scoliosis, ocular abnormalities

*In one case limb hypertonia was described. NR: Not reported

Both BOS and SHAPNS show intellectual disability and neurodevelopmental delay as a main characteristic. However, development delay is mild in SHAPNS compared to the others2,4,13. BOS was first described in patients with feeding problems with primary or secondary microcephaly and severe neurodevelopmental delay. “BOS posture” consistent to exrotation and/or adduction of the shoulders, flexion at the elbows, flexion at the wrists, and ulnar deviation of the wrists and/or fingers at the metacarpophalangeal joints, was described in those patients. This phenotype was associated to ASXL1 gene variants and was classified as a distinct condition from BRS, based on the absence of BOS posture in patients with ASXL3 gene variants23,24. SHAPNS is described as a neurological disease caused by ASXL2 gene variants. The overlapping features are identified by global developmental delay and feeding problems. But, macrocephaly instead of microcephaly seems to be SHAPNS most distinctive clinical sign12.

The relevance of the discovery of BRS and the diagnostic route lies in the reversibility of the daily routine of the patient with genetic conditions2, given that the majority of these patients have been diagnosed through molecular findings, which subsequently allowed them to be grouped in a similar phenotype. Clinical differences within the ASXL were identified between the ASXL1, ASXL2 and AXL3 genes phenotype. Differences in epigenetic regulating function factors that contribute to phenotype and temporality of the presentation of gene variants (germinal or somatic) could play an important role14. Primarily, described ASXL3 gene phenotypic variants have been classified as de novo. However, findings support a <1% possibility of recurrency in germline mosaicism respectively.

Five years after the initial BRS description, it has been possible to provide answers to an ever-increasing number of families thanks to the significant achievement of obtaining a definite genetic diagnosis. The phenotypic definition associated with the ASXL gene family presents the challenge of the importance to use massive sequencing analysis in order to obtain more timely diagnosis associated with neurodevelopmental disorders.

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Article Notes

  • Published on: January 12, 2019


  • Postnatal microcephaly
  • Trithorax


Dr. Silvina Noemí Contreras-Capetillo
Centro Regional de Investigaciones “Dr. Hideyo Noguchi”, Universidad Autónoma de Yucatán. Calle 96 s/n x Av. Jacinto Canek y calle 47 Paseo de Las Fuentes. C.P. 97225. Mérida, Yucatán, México; Telephone No: +52 (999) 9245809; Fax No: +52 (999) 923612

©2019 Contreras-Capetillo SN. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.