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Background  Ataxia with oculomotor apraxia type 1 is an autosomal-recessive neurodegenerative disorder characterized by a childhood onset of slowly progressive cerebellar ataxia, followed by oculomotor apraxia and a severe primary motor peripheral axonal motor neuropathy. Ataxia with oculomotor apraxia type 1 is caused by bi-allelic mutations in  APTX  (chromosome 9p21.1).    Case presentation  Our patient has a clinical presentation that is typical for ataxia with oculomotor apraxia type 1 with no particularly severe phenotype. Multiplex Ligation-dependent Probe Amplification analysis resulted in the identification of a homozygous deletion of all coding  APTX  exons (3 to 9). SNP array analysis using the Illumina Infinium CytoSNP-850 K microarray indicated that the deletion was about 62 kb. Based on the SNP array results, the breakpoints were found using direct sequence analysis: c.-5 + 1225_*44991del67512, p.0?. Both parents were heterozygous for the deletion. Homozygous complete  APTX  deletions have been described in literature for two other patients. We obtained a sample from one of these two patients and characterized the deletion (156 kb) as c.-23729_*115366del155489, p.0?, including the non-coding exons 1A and 2 of  APTX . The more severe phenotype reported for this patient is not observed in our patient. It remains unclear whether the larger size of the deletion (156 kb vs 62 kb) plays a role in the phenotype (no extra genes are deleted).    Conclusion  Here we described an ataxia with oculomotor apraxia type 1 patient who has a homozygous deletion of the complete coding region of  APTX . In contrast to the patient with the large deletion, our patient does not have a severe phenotype. More patients with deletions of  APTX  are required to investigate a genotype-phenotype effect.    Electronic supplementary material  The online version of this article (doi:10.1186/s12881-015-0213-y) contains supplementary material, which is available to authorized users.

Complete APTX deletion in a patient with ataxia with oculomotor apraxia type 1