Novel heterozygous pathogenic variants in CHUK in a patient with AEC-like phenotype, immune deficiencies and 1q21.1 microdeletion syndrome: a case report

Ectodermal dysplasias (ED, OMIM:604292) are a group of diseases affecting the teeth, hair, nails and exocrine and sebaceous glands. In some cases, part of the skin, eyes, inner ears, fingers, toes and central nervous system can also be affected. There are approximately 150 different types of ED, the most commonly recognized syndromes being the ectrodactyly-ectodermal dysplasia-clefting syndrome (EEC, OMIM: 129900), Rapp-Hodgkin syndrome (OMIM: 129400) and ankyloblepharon-ectodermal defects-cleft lip/palate syndrome (AEC, OMIM:106260) [1]. AEC syndrome, also known as Hay-Wells syndrome, is caused by heterozygous pathogenic variants in TP63 [2, 3]. A classical feature of AEC syndrome is the presence of skin erosions affecting the palms, soles and scalp. Other clinical manifestations include ankyloblepharon filiforme adnatum, cleft lip, cleft palate, craniofacial abnormalities, and ectodermal defects such as sparse wiry hair, nail changes, dental changes, and subjective hypohydrosis [4‐6].

IRF6-related disorders are a group of inherited disorders associated with heterozygous pathogenic variants in IRF6, including Van der Woude syndrome (VWS, OMIM:119300) and popliteal pterygium syndrome (PPS, OMIM:119500). VWS is characterized by orofacial clefting and lip pits whereas PPS is characterized by similar lip/palate abnormalities in combination with ankyloblepharon in some cases, as well as digital and genital abnormalities [7, 8]. Bartsocas-Papas syndrome (BPS, OMIM: 263650), a severe form of PPS, is associated with homozygous pathogenic variants in RIPK4 and CHUK [9‐11]. Recently, a de novo missense variant in CHUK was reported in one patient with ectodermal dysplasia, orofacial clefting, limb anomalies and hypogammaglobulinemia [12].

Copy number variants affecting the 1q21.1 region have been associated with genomic disorders. Phenotypic features of 1q21.1 deletion syndrome include microcephaly (50%), mild intellectual disability (30%), mildly dysmorphic facial features, and eye abnormalities (26%). Other findings can include cardiac defects, genitourinary anomalies, skeletal malformations, and seizures (~ 15%). Psychiatric and behavioral abnormalities can include autism spectrum disorders, attention deficit hyperactivity disorder, and sleep disturbances (OMIM: 612474). The majority of microdeletions are inherited, and incomplete penetrance and variable expressivity have been noted [13‐15]. In this report, we describe, for the first time, a patient with compound heterozygous variants in CHUK. Interestingly, one variant arose de novo. To our knowledge, this is the second patient with CHUK-deficiency and immune abnormalities associated with de novo variant in CHUK. However, based on our data, it is unclear if, in some cases, de novo heterozygous CHUK variants are sufficient to cause disease. Clinical features of the patient are consistent, although less severe, with previously reported cases. This patient is also carrier of a 2 MB deletion on chromosome 1 which might contribute to some of his features.

Our patient is a male born to healthy non consanguineous parents weighing 2.375 kg, measuring 48 inches at birth. Maternal and paternal age were 27 and 25 years old, respectively. During the pregnancy there were no exposures to drugs, alcohol, tobacco or medications. The fetal movements were described as normal up until approximately 32 weeks gestation, when they were noted to be decreased. He was delivered by induced vaginal delivery at 37 + 4 weeks gestation due to intrauterine growth retardation and reduced fetal movements. He was transferred to the Children’s Mercy Hospital Neonatal Intensive Care Unit (NICU) on day 1 of life due to cleft lip and palate and ankyloblepharon filiforme adnatum. Physical examination revealed sparse eyelashes and eyebrows, hypoplasia of the teeth, abnormal palmar creases, 5^th finger clinodactyly, mild 2^nd, 3^rd toe syndactyly and hypohidrosis (Fig. 1). The patient had recurrent bacterial and viral infections. His infections included recurrent otitis media despite bilateral myringotomy and tube placement, Staphylococcus aureus impetigo, coxsackie hand foot mouth disease, recurrent upper and lower respiratory infections including respiratory syncytial virus (RSV) bronchiolitis and multiple episodes of non-RSV viral bronchiolitis. His immune work up showed mild abnormalities including low immunoglobulin (Ig) M (31 mg/dL) and low normal IgG levels (355 mg/dL). His IgA was normal (17 mg/dL). His lymphocyte subsets showed normal T cells (CD3; 1860 mm³) but mildly low CD4 (1333 mm³) and CD8 (372 mm³) subsets. The patient’s developmental history was appropriate. He had a head ultrasound, abdominal ultrasound, echocardiogram and bone survey which were unremarkable. This clinical presentation led to the suspicion of an ectodermal dysplasia syndrome such as AEC syndrome, Bartsocas-Papas syndrome or Van der Woude syndrome. Gene testing for TP63, RIPK4 and IRF6 was negative. Microarray analysis revealed a 2 MB deletion on chromosome 1 encompassing 18 genes (arr [hg19] 1q21.1q21.2 (145,885,645–147,929,115)). Parental studies were requested but not performed.

Clinical exome sequencing was performed on the affected individual with methods as previously published [16‐18]. Variants were filtered to 1% minor allele frequency, then prioritized by the American College of Medical Genetics (ACMG) categorization [19], OMIM identity and phenotypic assessment. This individual was found to be compound heterozygous for a frameshift variant c.1365del (p.Arg457Aspfs*6) and a missense variant c.1388C > A (p.Thr463Lys) in CHUK (NM_001278.3) (Fig. 2a). Both variants are located in exon 13 and occurred in trans, as visualized by the Integrative Genomics Viewer (IGV) tool (Additional file 1: Figure S1) [20, 21]. Sanger sequencing confirmed that the p.Arg457Aspfs*6 variant was maternally-inherited and the p.Thr463Lys was not detected in either parental sample (Fig. 2b). Paternity was confirmed using short-tandem repeat analysis. This indicates that the p.Thr463Lys variant arose de novo, but germline mosaicism in the father can’t be excluded. These variants were absent from population databases.

Pathogenic variants in CHUK have been reported in 3 families to date (Table 1; Additional file 2: Figure S2): In 2010, Lahtela et al., described a Finnish family in which a homozygous loss of function variant in CHUK (c.1264C > T; p.Gln422*) was associated with Cocoon syndrome, an autosomal recessive lethal condition characterized by severe fetal malformations. Prenatal ultrasound of 2 fetuses revealed an abnormal cyst in the cranial region, a large defect in the craniofacial area, an omphalocele and immotile and hypoplastic limbs. Abnormalities of the heart, lungs, skin, bones and skeletal muscles were also observed. Both parents were heterozygous for this variant and genealogical analysis revealed a common ancestor [22]. In 2015, Leslie et al., reported a homozygous variant in the splice acceptor site of exon 10 (c.934-2A > G) in a female patient with Bartsocas-Papas syndrome born to healthy first degree cousins. Clinical manifestations included alopecia totalis (with absent eyebrows and eyelashes), wide cranial suture and fontanelle, nose and ear dysmorphisms, bilateral microophthalmia, ankyloblepharon, bilateral cleft lip and palate, genital hypoplasia, popliteal webs and skeletal abnormalities [11]. In 2017, Khandelwal et al., reported a 10-year-old female born to non-consanguineous Caucasian parents with a de novo missense variant in CHUK (c.425A > G, p.His142Arg). Clinical features of the patient included sparse hair, absent eyebrows and eyelashes, ankyloblepharon and dysplastic nails. X-rays of the hands and feet showed complex anomalies consisting of, among others, hypoplastic thumbs and 3^rd–5^th toe syndactyly. Other features included posterior cleft palate, retrognathia, buccal synechia, hypoplastic external genitalia, conical and fragile primary teeth and short stature (height -3.5SD and weight -3SD). Her development was marked by growth retardation, gastrointestinal reflux with swallowing problems and lower respiratory tract infections. She also had hypogammaglobulinemia. To our knowledge, a second pathogenic variant was not detected in this patient, but additional screening methods such as deletion/duplication analysis were not performed [12].

The CHUK gene encodes for Ikka (Inhibitor of nuclear factor kappa-B kinase subunit alpha), a catalytic subunit of the multiprotein complex IbK kinase. Studies in mice show that the Ikka protein is ubiquitously expressed with the highest levels in the developing spine, limb buds and head. It plays an important role in limb development, apoptosis of interdigital tissue and proliferation and differentiation of epidermal keratinocytes. Embryos from the Ikka-deficient mice developed to term, but died shortly after birth. The fetuses displayed several skeletal abnormalities affecting the size and the morphology of the spine, skull, forepaws and the hindpaws. Limb bones were relatively smaller and of normal shape. Microscopic evaluation of the skin revealed hyperplasia of the suprabasal layer (stratum spinosum) and absent stratum granulosum and stratum corneum. Mice heterozygous for the CHUK gene deletion are normal, viable and fertile [23].

In this report, we describe a male patient presenting with an AEC syndrome-like phenotype and recurrent infections suggestive of immune deficiency. Targeted sequencing of TP63, RIPK4 and IRF6 was negative. Microarray analysis identified a 2 MB deletion on chromosome 1 covering the distal part of the 1q21.1 region deletion. Although this pathogenic deletion is unlikely to account for all the clinical features of the patient, it could contribute to his dysmorphic facial features, small size and failure to thrive (Fig. 1, Additional file 3: Figure S3). Additionally, exome sequencing revealed that he was compound heterozygous for two novel variants in CHUK. The c.1365del (p.Arg457Aspfs*6) frameshift variant, was inherited from his unaffected mother and the c.1388C > A (p.Thr463Lys) missense variant arose de novo. This genotype is compatible with autosomal recessive inheritance and consistent with previously reported families [11, 22]. To our knowledge, only one patient has been reported so far with a de novo missense variant in CHUK [12]. Since deletion/duplication testing was not performed, the presence of a second undetected variant cannot be ruled out. Interestingly, our patient shares several clinical features with this individual. However, skeletal defects appeared less severe in our patient and we cannot rule out progressive hypogammaglobulinemia needing Ig replacement at follow up. Therefore, based on our findings, it is unclear if, in some cases, the inheritance pattern could be dominant and that de novo heterozygous CHUK variants are sufficient to cause the disease. Even if the majority of pathogenic de novo variants are involved in dominant genetic disorders, there are growing examples of recessive disorders that can be caused by the combination of an inherited variant on one allele and a de novo variant on the other.