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     Long Response


    USH2A Phenotype Audit (Graph-first): p.Glu767Serfs*21 vs p.Cys759Phe

    Goal: Create graphs + extract tables from the provided raw research excerpts.
    Critical limitation: In the provided data, p.Glu767Serfs*21 is explicitly present with cohort-level and clinical correlation information, but p.Cys759Phe is not present with phenotype/audiology outcomes. Therefore, any direct “variant-to-variant phenotype comparison” for p.Cys759Phe cannot be evidenced from the supplied sources.

    1) Where p.Glu767Serfs*21 appears in USH2A mutation spectra

    Evidence: p.Glu767SerfsX21 reported as the most common USH2A allele, accounting for 31% of all USH2 alleles in the UK National Collaborative Usher Study sequencing cohort.

    2) Truncating-mutation genotype patterns (proxy for p.Glu767Serfs*21 class)

    Important: p.Glu767Serfs*21 is a truncating frameshift; however, the provided Hearing Research excerpt quantifies phenotypic differences by mutation truncating-class combinations (2T vs 1T vs 2nT), not by individual named variants.
    Evidence for baseline HI ranges and truncating-mutation combination effects:

    3) Variant-level phenotype audit: what is known vs not evidenced from provided data

    Audit logic (skeptical):
    • If the provided research excerpts explicitly mention a named variant and any phenotype/audiology outcomes, we mark it as evidenced.
    • If p.Cys759Phe is not mentioned in the provided excerpts, we mark its phenotype as not available in supplied sources (no speculation).

    Table extraction (from supplied sources): named variant presence + phenotype linkage

    Variant Explicitly mentioned in provided excerpts? Phenotype/audiology outcomes in provided excerpts? What can be graphed/evidenced Evidence
    USH2A p.Glu767Serfs*21 Yes Partially: cohort-level mutation spectrum + truncating-class HI differences (proxy) (a) Allele-share bar; (b) truncating-combination HI effect-size bars (class-level)
    USH2A p.Cys759Phe Not in supplied excerpts Not evidenced in provided sources No direct p.Cys759Phe phenotype graphs can be generated from the supplied data
    No provided excerpt in the research data mentions p.Cys759Phe with phenotype/audiology outcomes; therefore no evidence-backed phenotype audit is possible here.

    4) What would change this conclusion (falsifiability / missing-information map)

    • If a provided (or newly supplied) USH2A-focused genotype–phenotype report contains p.Cys759Phe with segregation/clinical audiology endpoints, then direct variant-level comparison becomes evidence-complete.
    • If future datasets show that truncating-class effects (2T vs 1T/2nT) do not generalize to this specific frameshift allele (p.Glu767Serfs*21) at the same magnitude, then only the class-level association would remain robust, not allele-specific inference.
    • Potential bias sources in supplied evidence: the Hearing Research study is retrospective and uses last-available audiograms per patient, which can bias progression/trajectory inference; subgroup sizes vary; and center-specific testing methods may differ.
    Directly useful next step
    If you can provide (or ask BGPT to retrieve) a paper/database excerpt that includes USH2A p.Cys759Phe with phenotype endpoints, BGPT can regenerate the audit with true variant-level graphs.


    Feedback:    

    Updated: April 26, 2026

     Top Data Sources ExportMCP


     Analysis Wizard



    It extracts variant-level and genotype-class phenotype endpoints from supplied excerpts, aggregates allele-frequency and hearing-loss effect-size summaries, then generates audit tables and Plotly-ready series for visualization.



     Science Art


    Create Graphs: USH2A p.Glu767Serfs*21 vs p.Cys759Phe Phenotype Audit with Table Extraction Science Art

     Science Movie


    Make a narrated HD Science movie for this answer ($32 per minute)




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