Objective To improve the understanding of the genotype of 3 - methylcrotonyl-CoA carboxylase deficiency (MCCD) caused by uniparental disomy. Methods Clinical data of a patient diagnosed with MCCD was retrospectively analyzed and relevant literature was reviewed. Results A 9 -month-old boy presented with external rotation of his right leg for one week. Physical examination showed dysplasia, right lower extremity external rotation and slightly low muscle strength of lower extremity. His score after psychological and behavioral development assessment of children aged 0 - 6 was 66 points. Blood tandem mass spectrometry and urine gas chromatography-mass spectrometry indicated MCCD. Whole genome sequencing found a c. 1853 _ 1856 delTTTA homozygous variation of MCCC1 gene not reported in the literture, inherited from his mother. Chromosomal microarray confirmed that the proband was maternal uniparental disomy on chromosome 3p24- 3 q 29 , which contained MCCC 1 gene. Conclusion It is firstly found that MCCD was of caused by uniparental disomy. and a novel homozygous variation c. 1853 _ 1856 delTTTA in MCCC 1 gene was found.