Table 2 Filtering of SNPs and indels

Called in entire larger sample (n =669)

817,028

75,781

  → Found in all 10 TMAU subjects, with at least one subject homozygous for the minor allele

94,535

5,251

   → Pathogenic by SIFT or PolyPhen-2

1,867

163

    → Pathogenic in oxidoreductase pathways

57

4

     → Pathogenic in oxidoreductase pathways and with MAF < 0.05

4

1

    → Pathogenic in genes with no known choline metabolism function and shared by 2 subjects

762

63

     → Pathogenic rare variant homozygous in two subjects within genes with no known choline metabolism function

9

1