Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report

BMC Neurol. 2021 Apr 28;21(1):180. doi: 10.1186/s12883-021-02204-w.


Background: The present study aimed to determine the underlying genetic factors causing the possible Warburg micro syndrome (WARBM) phenotype in two Iranian patients.

Case presentation: A 5-year-old female and a 4.5-year-old male were referred due to microcephaly, global developmental delay, and dysmorphic features. After doing neuroimaging and clinical examinations, due to the heterogeneity of neurodevelopmental disorders, we subjected 7 family members to whole-exome sequencing. Three candidate variants were confirmed by Sanger sequencing and allele frequency of each variant was also determined in 300 healthy ethnically matched people using the tetra-primer amplification refractory mutation system-PCR and PCR-restriction fragment length polymorphism. To show the splicing effects, reverse transcription-PCR (RT-PCR) and RT-qPCR were performed, followed by Sanger sequencing. A novel homozygous variant-NM_012233.2: c.151-5 T > G; p.(Gly51IlefsTer15)-in the RAB3GAP1 gene was identified as the most likely disease-causing variant. RT-PCR/RT-qPCR showed that this variant can activate a cryptic site of splicing in intron 3, changing the splicing and gene expression processes. We also identified some novel manifestations in association with WARBM type 1 to touch upon abnormal philtrum, prominent antitragus, downturned corners of the mouth, malaligned teeth, scrotal hypoplasia, low anterior hairline, hypertrichosis of upper back, spastic diplegia to quadriplegia, and cerebral white matter signal changes.

Conclusions: Due to the common phenotypes between WARBMs and Martsolf syndrome (MIM: 212720), we suggest using the "RABopathies" term that can in turn cover a broad range of manifestations. This study can per se increase the genotype-phenotype spectrum of WARBM type 1.

Keywords: PCR-RFLP; RAB3GAP1; Tetra-primer ARMS-PCR; WARBM type 1; Whole-exome sequencing.

Publication types

  • Case Reports

MeSH terms

  • Abnormalities, Multiple / genetics*
  • Cataract / congenital*
  • Cataract / genetics
  • Child, Preschool
  • Cornea / abnormalities*
  • Exome Sequencing
  • Female
  • Humans
  • Hypogonadism / genetics*
  • Intellectual Disability / genetics*
  • Iran
  • Male
  • Microcephaly / genetics*
  • Mutation
  • Optic Atrophy / genetics*
  • Pedigree
  • RNA Splicing
  • rab3 GTP-Binding Proteins / genetics*


  • RAB3GAP1 protein, human
  • rab3 GTP-Binding Proteins

Supplementary concepts

  • Warburg Sjo Fledelius syndrome