Background and aims Last five years more than 50 novel microdeletion and microduplication syndromes were described. Sometimes we find rare chromosome anomalies, which clinical significance is not always known.

Our aim was to describe the new phenotype of rare chromosome disorders in patient with mental retardation caused by genotype combined with different microdeletion

Methods Boy, 5 years old, was observed with developmental delay with the first year of life. Clinical features: upslanting palpebral fissures, epicanthal folds, short philtrum, synophrys, microstomia, low set ears, prominent forehead, high borderline of hair growth, sensorineural and conductive deafness. We used the CytoScan HD Array solution (Affymetrix) for detecting of chromosomal pathological variants lager than 50 kb.

Results We detected a 7,4 Mb pathogenic deletion in chromosome region 7 p21.1–7 p15.2 and a smaller one 494 kb deletion in the chromosome region 22q12.1 spanning the genes TTC28 and CHEK2. This deletion has not been described previously. According to the literature, deletions in this chromosomal region larger than 300 kb was described in patients with mental retardation and multiple malformations including conductive deafness.

Conclusions It is known that the patients with deletions in 7 p21–p14.3 chromosome region have mental retardation and facial features similar to Greig syndrome and patients with 22q12 deletions have mental retardation, hearing loss and heart disease. All of these clinical features were present in phenotype of our patient. The results of our molecular cytogenetic research allow to reveal the combination of two microdeletions which fully explain the existing phenotype of patient. The Affymetrix microarray solutions is a powerful flexible method for detection of rare chromosomal aberrations which can help to paediatricians and clinical geneticists explain and describe new phenotype in patients with rare chromosome disorders.