Splice effect of a synonymous variant in AP4B1: multiomics approach establishes the diagnosis in two sisters with spastic paraplegia.

Synonymous AP4B1 variant driving aberrant splicing, in trans with a nonsense variant: biallelic loss of function of the AP-4 adaptor complex.

Two sisters with complex spastic paraplegia remained undiagnosed after exome sequencing, which had identified only monoallelic nonsense variants in AP4S1 and AP4B1, suggesting a digenic inheritance never established for AP-4-associated disorders. A multiomics approach combining genome sequencing, RNA sequencing and proteomics re-prioritised a predicted synonymous variant, NM_006594.5:c.969G>A, compound heterozygous with the AP4B1 nonsense variant and previously called benign, by demonstrating aberrant splicing. Proteomics showed reduced abundance of the AP-4 components AP4B1 and AP4M1 together with upregulation of the cargo protein ATG9A, confirming AP-4 deficiency. The AP4S1 variant underwent nonsense-mediated decay, and identification of biallelic causative AP4B1 variants established autosomal recessive spastic paraplegia 47, refuting the initial digenic hypothesis.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

The value here is not a new gene but a reasoning discipline: two monoallelic variants in two subunits of the same complex should raise suspicion of a missed second hit on one allele before invoking digenic inheritance, which must remain a last-resort hypothesis. The causal variant was already in the exome data and had been filtered out as synonymous, confirming that splicing annotation, not coverage, is the bottleneck, and that RNA sequencing earns its place whenever segregation does not add up. Caveat: a single family, and targeted proteomics remains out of reach for most diagnostic laboratories.

Analysis by Dr Thibaut Benquey