Allele expression at CPN2 p.304 remains undetermined

Determine whether the reference or alternative allele is expressed at residue p.304 (A>T) of the human CPN2 protein in the analyzed samples from the PRIDE PXD010154 healthy human tissues dataset processed with the ProHap workflow, given that no peptides covering this site were identified in the mass spectrometry data.

Background

In the CPN2 case study, ProHap Explorer revealed three amino acid substitutions (p.304:A>T, p.508:Q>R, p.535:V>M) observed across haplotypes. Peptide evidence indicated expression of the alternative allele at p.508 and the reference allele at p.535 in specific tissues.

However, the protein region containing residue p.304 lacked peptide coverage in the analyzed dataset, preventing determination of whether the reference or the alternative allele is expressed at this site. This leaves a concrete unresolved question about allele-specific expression at p.304 in the processed samples.

References

We could not determine whether the reference or the alternative allele is expressed for the substitution at position 304, as this part of the protein was not covered by peptides at all.

— ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets  (2504.06282 - Vašíček et al., 25 Mar 2025) in Section 6.1, Case Studies: Common Haplotypes of CPN2