MISSED BY OTHERS, DETECTED BY US
Genomic Unity® Case Study

Compound heterozygous partial exon deletion provides a complete molecular diagnosis

Clinical presentation

A 6-year-old male presented with poor growth, developmental delays and the following additional symptoms:

  • Microcephaly, cleft lip & palate
  • Chronic respiratory disease, hydronephrosis
  • Bilateral hearing loss

Previous genetic testing

Testing was performed with negative results. Including exome testing that identified a pathogenic indel in the recessive UBE3B gene, but no second variant:

  • Chromosomal microarray
  • Whole exome sequencing

Genomic Unity® Testing

was ordered because of its ability to identify all major variant types in a single test.

Results and interpretation

Variantyx Genomic Unity® testing identified a maternally inherited, pathogenic, 219 bp partial exon deletion in the UBE3B gene together with the previously identified, paternally inherited UBE3B indel – finally providing a complete molecular diagnosis.

Diagnosis: Kaufman oculocerebrofacial syndrome

IGV view of UBE3B variants

Uniform data from WGS clearly shows both the indel (left) and 219 bp deletion (right) variants.

The Variantyx Difference

Why was this partial exon deletion detected by Genomic Unity® testing, and not detected by other tests?

  • CMA tests are unable to detect deletions smaller than 25 kb.

  • Exomes are typically unable to detect deletions smaller than 3 exons in size.
    Variantyx genome analysis has a detection range from 1 bp to whole chromosomal events, easily detecting this 219 bp deletion.

  • One of the deletion breakpoints is intronic, adding to the complexity of detection.
    Variantyx genome analysis includes intronic regions, enabling breakpoint detection regardless of location.

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