Create a predicate to test if variant affects a codon that encodes an aminoacid of interest

[ielis]

Create a predicate to test if variant affects a codon that encodes an aminoacid of interest.

[pnrobinson]

ZMYM3, amino acid 441 might be a good test, although the cohort size is small

[pnrobinson]

There is a significant result here:

r441w = VariantPredicates.variant_key("X_71249610_71249610_G_A") #c.1321C>T	p.Arg441Trp
r441q = VariantPredicates.variant_key("X_71249609_71249609_C_T") #c.1322G>A	p.Arg441Gln	
r441 = r441w | r441q

is_r441 = monoallelic_predicate(
    a_predicate=r441,
    b_predicate=~r441,
    a_label="R441",
    b_label="other"
)
r441_result = analysis.compare_genotype_vs_phenotypes(
    cohort=cohort,
    gt_predicate=is_r441,
    pheno_predicates=pheno_predicates,
)
summarize_hpo_analysis(hpo=hpo, result=r441_result)

yields a corrected p value of 0.003839 for Cupped ear [HP:0000378].

Note that I added a lot of curation for this cohort, which previously was one of the early efforts and did not include all of the HPOs. The data is not yet in an official phenopacket-store release.