Notable findings included p.Val617Phe in JAK2 (predicted GOF, rs77375493), which was associated with myeloproliferative disease (phecode = 200, OR = 40.6, P = 1.29 × 10–29), p.Trp620Arg in PTPN22 (predicted GOF, rs2476601), displaying an association with type 1 diabetes (phecode = 250.1, OR = 1.78, P = 4.08 × 10–6), as well as a predicted GOF variant in LRRK2, p.Asn2081Asp (rs33995883), which demonstrated an association with regional enteritis (phecode = 555.1, OR = 2.33, P = 4.28 × 10–7). This evidence concerns the gene PTPN22 and type 1 diabetes mellitus.