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Interesting case report

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies

Marjolein H. Willemsen, Nicole de Leeuw, Arjan P.M. de Brouwer, Rolph Pfundt, Jayne Y. Hehir-Kwa, Helger G. Yntema, Willy M. Nillesen, Bert B.A. de Vries, Hans van Bokhoven, Tjitske Kleefstra


Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients.We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (w1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic.  

History File

Previously published Interesting case reports

De novo microdeletions of chromosome 6q14.1-q14.3 and 6q12.1-q14.1 in two patients with intellectual disability - further delineation of the 6q14 microdeletion syndrome and review of the literature  
2p21 Deletions in hypotonia-cystinuria syndrome  
Duplication of 8q12 encompassing CHD7 is associated with a distinct phenotype but without duane anomaly  
A de novo 4.4-Mb microdeletion in 2p24.3/p24.2 in a girl with bilateral hearing impairment, microcephaly, digit abnormalities and Feingold syndrome  
A novel de novo 1.8 Mb microdeletion of 17q21.33 associated with intellectual disability and dysmorphic features  
An atypical 0.8 Mb inherited duplication of 22q11.2 associated with psychomotor impairment  
Molecular cytogenetic characterization of 2p23.2p23.3 deletion in a child with developmental delay, hypotonia and cryptorchism  
A newborn with a 790 kb chromosome 17p13.3 microduplication presenting with aortic stenosis, microcephaly and dysmorphic facial features - Is cardiac assessment necessary for all patients with 17p13.3 microduplication?  
Interstitial 16p13.3 microduplication: Case report and critical review of genotype-phenotype correlation  
Prenatal diagnosis of the duplication 17p11.2 associated with PotockieLupski syndrome in a foetus presenting with mildly dysmorphic features  
2q23.1 microdeletion of the MBD5 gene in a female with seizures, developmental delay and distinct dysmorphic features  
A de novo 163 kb interstitial 1q44 microdeletion in a boy with thin corpus callosum, psychomotor delay and seizures  
Delineating the 17q24.2eq24.3 microdeletion syndrome phenotype  
A 1 Mb de novo deletion within 11q13.1q13.2 in a boy with mild intellectual disability and minor dysmorphic features  
A de novo 3.57 Mb microdeletion in 8q12.3q13.2 in a patient with mild intellectual disability and epilepsy  
5p13 microduplication syndrome: A new case and better clinical definition of the syndrome  
Blepharophimosis, ptosis, epicanthus inversus syndrome with translocation and deletion at chromosome 3q23 in a black African female  
Sporadic male patients with intellectual disability: Contribution of X-chromosome copy number variants  
2007-2013 (1)
Partial trisomy 1q, region 1q31->qter  
2007-2013 (2)
Deletion 13q14.3 to q21.32  
2007-2013 (3)
Deletion 1p36.33-36.31::36.22-21  
2007-2013 (4)
Deletion of 3.2Mb on chromosomeband 4q24