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Background:

Common genetic variation in the arsenic methyltransferase (AS3MT) gene region is known to be associated with arsenic metabolism efficiency (AME), measured as the percentage of dimethylarsinic acid (DMA%) in the urine. Rare, protein-altering variants in AS3MT could have even larger effects on AME, but their contribution to AME has not been investigated.

Objectives:

We estimated the impact of rare, protein-coding variation in AS3MT on AME using a multi-population approach to facilitate the discovery of population-specific and shared causal rare variants.

Methods:

We generated targeted DNA sequencing data for the coding regions of AS3MT for three arsenic-exposed cohorts with existing data on arsenic species measured in urine: Health Effects of Arsenic Longitudinal Study (HEALS, $n=\mathrm{2,434}$), Strong Heart Study (SHS, $n=868$), and New Hampshire Skin Cancer Study (NHSCS, $n=666$). We assessed the collective effects of rare (allele frequency $<1\%$), protein-altering AS3MT variants on DMA%, using multiple approaches, including a test of the association between rare allele carrier status (yes/no) and DMA% using linear regression (adjusted for common variants in 10q24.32 region, age, sex, and population structure).

Results:

We identified 23 carriers of rare-protein-altering AS3MT variant across all cohorts (13 in HEALS and 5 in both SHS and NHSCS), including 6 carriers of predicted loss-of-function variants. DMA% was 6–10% lower in carriers compared with noncarriers in HEALS [$\mathrm{\beta }=-9.4$ (95% CI: $-13.9$, $-4.8$)], SHS [$\mathrm{\beta }=-6.9$ (95% CI: $-13.6$, $-0.2$)], and NHSCS [$\mathrm{\beta }=-8.7$ (95% CI: $-15.6$, $-2.2$)]. In meta-analyses across cohorts, DMA% was 8.7% lower in carriers [$\mathrm{\beta }=-8.7$ (95% CI: $-11.9$, $-5.4$)].

Discussion:

Rare, protein-altering variants in AS3MT were associated with lower mean DMA%, an indicator of reduced AME. Although a small percentage of the population (0.5–0.7%) carry these variants, they are associated with a 6–10% decrease in DMA% that is consistent across multiple ancestral and environmental backgrounds. https://doi.org/10.1289/EHP8152