Coding variants in four genes prioritized from our gene-mapping strategy associated with reduced risk of hypothyroidism—ZAP70 (PAVs, MAF < 0.001%—OR = 0.33, 95% CI = 0.19–0.57, P = 6.4 × 10−5), ARHGAP9 (PAVs, MAF < 1%—OR = 0.76, 95% CI = 0.66–0.87, P = 1.3 × 10−4), TYK2 (PAVs, MAF < 1%—OR = 0.78, 95% CI = 0.69–0.88, P = 6.9 × 10−5) and IFIH1 (pLoF, MAF < 1%—OR = 0.81, 95% CI = 0.75–0.86, P = 2.2 × 10−6). Here, IFIH1 is linked to hypothyroidism.