Cohen syndrome in family members: a case report

Levchenko O. A.; Zinchenko R. A.; Lavrov A. V.

COHEN SYNDROME IN FAMILY MEMBERS: A CASE REPORT

Levchenko OA1, Zinchenko RA1>2, Lavrov AV1>2E3

1 Laboratory of Mutagenesis,

Research Centre for Medical Genetics, Moscow, Russia

2 Department of Molecular and Cellular Genetics, Biomedical Faculty, Pirogov Russian National Research Medical University, Moscow, Russia

Cohen syndrome is a rare autosomal-recessive disorder characterized by intellectual disability, myopia, hypotonia, and skeletal malformations. Its clinical diagnosis is impeded by marked inter- and intrafamilial phenotypic variability. Gene VPS13B that carries disease-associated mutations has 62 exons, making Sanger sequencing of the entire gene unsuitable for routine clinical use due to high costs. In this work we report a case of Cohen syndrome in a brother and sister born to a mixed Abazin-Circassian marriage and diagnosed with moderate mental retardation. Both patients had psychomotor retardation, were unable to study at school, and never learned to read, write and count. Although the patients shared a few nonspecific phenotypic characteristics, phenotypic differences made it impossible to arrive at a clear diagnosis. Therefore, whole exome sequencing was performed revealing the single nucleotide variant a7603C>T that results in the premature stop codon R2535* in VPS13B. This mutation was found in the mother, the affected sibs and one of the two other healthy sibs. The second mutation remained undetected. Considering the identified mutation and the analyzed phenotypic traits, we concluded Cohen syndrome in both patients.

Keywords: intellectual disability, familial nonspecific intellectual disability, whole exome sequencing, Cohen syndrome, nonsyndromic intellectual disability

Correspondence should be addressed: Alexander Lavrov

ul. Moskvorechie, d. 1, Moscow, Russia, 115478; [email protected]

Received: 02.08.2017 Accepted: 15.08.2017

СЕМЕЙНЫЙ СЛУЧАЙ СИНДРОМА КОЭНА: КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ

О. А. Левченко1, Р. А. Зинченко1'2, А. В. Лавров1,2 и

1 Лаборатория мутагенеза, Медико-генетический научный центр, Москва

2 Кафедра молекулярной и клеточной генетики, медико-биологический факультет,

Российский национальный исследовательский медицинский университет имени Н. И. Пирогова, Москва

Синдром Коэна — редкое аутосомно-рецессивное заболевание, характеризующееся умственной отсталостью, миопией, гипотонией, ожирением и деформацией костей. Заболевание имеет выраженный меж- и внутрисемейный клинический полиморфизм, что затрудняет его клиническую диагностику. Ген УРБ13Б, мутации в котором приводят к развитию синдрома, имеет 62 экзона, и полный его анализ в практике не применяется. Нами описан семейный случай синдрома Коэна. Брат и сестра из метисированного абазино-черкесского брака имеют диагноз «умственная отсталость в стадии имбецильности». У обоих пробандов с рождения отмечена задержка психомоторного развития. В школе учиться не смогли, писать, читать, считать не научились. Несмотря на некоторые общие неспецифические признаки, различия в фенотипе не позволили установить диагноз, и был назначен полноэкзомный анализ. Найдена однонуклеотидная замена с.7603С>Т, приводящая к образованию преждевременного стоп-кодона Я2535* в гене УРБ13Б. Носителями мутации оказались мать, больные сибсы и один из двух здоровых сибсов. Вторую мутацию найти не удалось. По итогам детального анализа фенотипа и с учетом выявленной мутации установлен синдрома Коэна у обоих пациентов.

Ключевые слова: умственная отсталость, семейная неспецифическая умственная отсталость, полноэкзомный анализ, синдром Коэна, несиндромальная умственная отсталость

Е><] Для корреспонденции: Лавров Александр Вячеславович

ул. Москворечье, д. 1, г Москва, 115478; [email protected]

Статья получена: 02.08.2017 Статья принята к печати: 15.08.2017

Cohen syndrome is an inherited autosomal recessive disorder (OMIM# 216550). It was first reported in 1973 by Cohen et al. who noticed a shared pattern of anomalies in a few patients, including hypotonia, obesity, intellectual disability, limb and facial dysmorphisms, and ocular anomalies [1]. As early as 1994 a group of Finnish researchers mapped the VPS13B (COH1) gene to chromosome 8 [2], but it was not until 2003 that it became clear that the syndrome is caused by mutations in this

particular gene [3]. An extensive search for COH1 mutations was carried out in 76 patients from 59 families preliminarily diagnosed with Cohen syndrome [4]. In the course of their study, the researchers described a total of 22 mutations, 19 of which were reported for the first time. A number of studies were dedicated to the study of Cohen syndrome in Finnish and British patients [4, 5]; but altogether the literature reports only a few hundreds of verified cases in different countries and across

different populations, including Germany and Poland [6], Italy [7], Greece [8], Belgium [9], Middle East and Africa [6, 10, 11], Japan [10, 12] and the US [6, 11, 13]. Therefore, the assumed rarity of the disease makes it difficult to accurately access its prevalence. The variability of clinical manifestations both within and between families impedes accurate diagnosis, resulting in the underestimation of real prevalence of the syndrome. For example, Rauch et al. [14] diagnosed Cohen syndrome in 0.7 % of patients with undifferentiated intellectual disability, while clinical exome sequencing verified Cohen syndrome only in 0.1% of patients showing signs of genetic disorder [15].

Cohen syndrome is an inherited disorder affecting many parts of the body and characterized by mild microcephaly, high degree myopia, progressive retinal dystrophy, joint hyperextensibility and specific facial features. Patients tend to have thick hair and eyebrows, long lashes, a peculiar eye shape (down slanting palpebral fissures and almond-shaped eyesantimongoloid slant or arched eyelids), a rounded nasal tip, a short philtrum, maxillary hypoplasia, and prominent upper incisors. A combination of the three latter signs often causes open mouth appearance [16]. Other signs and symptoms may include narrow hands and feet and long fingers. Lab tests reveal low levels of leukocytes (neutropenia) leading to recurrent infections [17]. Patients can show various combinations of the aforementioned symptoms which do not have to co-occur in Cohen syndrome.

Differential diagnosis is often hindered by the variability of clinical manifestations, including those accompanying age-related changes. Cohen syndrome should be differentiated from such syndromes as Prader-Willi, Bardet-Biedl, Alstrom, Angelman, Marfan, and Sotos. A rare Mirhosseini-Holmes-Walton syndrome (OMIM# 268050) is considered to be allelic to Cohen syndrome, and their clinical manifestations overlap to a great extent [18, 19].

Genetically, the syndrome is caused by mutations in the gene VPS13B (COH1) [3]. Mutations in this gene can also lead to non-syndromic intellectual disability [20] and autism [21]. The gene VPS13B encodes for a transmembrane protein constituting the Golgi apparatus. Its major role is to regulate vesicular transport and sort proteins inside the cell. Besides, VPS13B is involved in glycosylation. The expression analysis has demonstrated the highest levels of VPS13B production in the cortical neurons of the brain [22].

Most often, patients with Cohen syndrome have mutations that cause protein shortening and therefore loss of protein function. It has been shown that reduced protein synthesis leads to a drop in the amount of neurons in hypoccampal cultures, which may explain microcephaly and intellectual disability. The abnormal distribution of body fat in such patients may be caused by disrupted glycosylation [23].

Targeted sequencing can be very instrumental in the verification of Cohen syndrome in populations where mutations are frequent. For example, in Finnish patients with Cohen syndrome 75 % of mutant alleles are represented by the deletion c.3348_3349delCT [3], and in the isolates obtained from the American Amish suffering from this disorder the founder pathogenic variants c.8459T>C and 9258_9259insT account for 99 % of all alleles. Other diagnostic options include multiplex ligation-dependent probe amplification (MLPA) and chromosomal microarray analysis, considering that up to 30 % of cases are caused by deletions/duplications [24]. Sanger sequencing of the entire gene is not recommended because the gene in question has 62 exons rendering the whole procedure too costly. NGS-panels and exome sequencing may also be good alternatives; the latter is increasingly used to as part of

the diagnostic routine in patients with intellectual disability [25]. Exome sequencing can confirm Cohen syndrome in 70 % of patients [5].

Case description

A mixed Abazin-Circassian family sought advice of a medical geneticist. Both parents were healthy; of their 4 children two were also healthy, while the other (a son of 36 and a daughter of 23 years of age) were disabled and diagnosed with moderate mental retardation back in childhood. Both probands had suffered psychomotor retardation since birth and had been unable to study at school failing to learn to read, write and do simple sums. Their speech was impoverished, with a tendency to primitive grammatical structures. Mental development matched that of a 3 to 5-year old child. Physical examination showed intellectual disability, microcephaly (52.5 cm in the man and 53 cm in the woman). The patients had thick bushy hair and eyebrows, low hairlines, high degree myopia, short philtra, thin upper lips, hypoplasia of the maxilla (more prominent in the man), and beak-shaped noses with rounded tips. Both had pronounced limbar scoliosis, planovalgus feet, and long fingers. The male patient had a long proximal phalanx of the little finger, low-set protruding ears, and synophrys. The woman was 158-160 cm tall and obese (first to second degree), had a more severe intellectual disability, attached earlobes, a widow's peak, an open mouth with prominent front incisors, dental caries, hypotonia, striae all over the body, lack of menarche (see the Figure).

Due to the differences in the clinical manifestation, the diagnosis had not been arrived at by the time of the consultation, therefore we suggested that the male patient should undergo massively parallel whole-exome sequencing, which revealed a previously described mutation, namely rs386834107 [6, 26]. It is a single nucleotide variant (c.7603C>T) which results in a premature stop-codon R2535* in exon 42 of VPS13B. Since VPS13B has 62 exons, the encoded protein is only two-thirds of its natural length. We also conducted Sanger sequencing to test all family members for this particular mutation. The mother, the diseased sibs and one of the two other healthy sibs turned out to be carriers, which does not contradict the autosomal recessive manner of inheritance.

In an effort to detect the second mutation, all single nucleotide variants identified in the sequenced gene were analyzed, and a manual search for possibly undetected mutations was performed. The following variants were found: M3265*, G3432R, and D903N. They are not pathogenic, nor were they confirmed by Sanger sequencing in our study. The analysis of evenness of coverage and the presence of heterozygous variants did not allow us to conclude an allelic deletion.

Sibs with Cohen syndrome: the sister, 23 years of age (on the left), and the brother, 32 years of age (on the right)

Phenotypes of both patients were additionally analyzed using the Face2Gene app (FDNA, Israel). The clinical signs (intellectual disability, microcephaly, myopia, thick hair, a low hairline, a rounded nasal tip, prominent front incisors) were also suggestive of Cohen syndrome.

Based on the complex clinical examination, we assume that Cohen syndrome has been verified in our patients.

Case discussion

The considerable variability of clinical manifestations in patients with Cohen syndrome hinders its accurate diagnosis, especially when verification lab tests cannot be run straightaway (e. g., in expeditionary research and genetic counselling). In these cases, high-throughput methods of molecular genetic testing are the only diagnostic solution. Molecular genetic testing demonstrated considerable allelic heterogeneity of the syndrome which was thought to be the reason of clinical variability [6, 16]. However, intrafamilial variability was almost ignored (OMIM# 216550) and published photos of the affected sibs were conclusive of mainly similar phenotypes [6, 16].

The studied family demonstrated a marked variability of clinical manifestations against the background of many shared features. The second mutation could have provided a possible explanation for clinical heterogeneity, had it been detected.

Further diagnostic tests might include a search for deletions or duplications in the gene. However, given the gene length and the absence of robust methods for its analysis, this would be very difficult. Deletions and duplications of one or two exons, as well as inversions, have been described in many patients with Cohen syndrome: 9 (53 %) out of 17 cases [27]. However, there have been a few cases in which only one of two heterozygous mutations was detected (including the one that we identified in our patients) [6]. Therefore, molecular genetic testing for Cohen syndrome requires the use of various methods in order to accurately detect and identify point and lengthy mutations or inversions. Previously we proposed an algorithm for diagnosing intellectual disability, which includes the use of whole-exome sequencing or chromosomal microarray analysis [25]. Still, in some cases both of these methods fail to detect the second mutation.

CONCLUSIONS

Cohen syndrome is characterized by a considerable variability of the phenotypes within a family, which may present a problem for clinical diagnosis. Massively parallel sequencing is very instrumental in arriving at an accurate diagnosis, as it helps to differentiate this disease from other syndromes involving intellectual disability.

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