Rare, protein-altering variants in as3mt and arsenic metabolism efficiency: A multi-population association study

Dayana A. Delgado, Meytal Chernoff, Lei Huang, Lin Tong, Lin Chen, Farzana Jasmine, Justin Shinkle, Shelley A. Cole, Karin Haack, Jack Kent, Jason Umans, Lyle G. Best, Heather Nelson, Donald Vander Griend, Joseph Graziano, Muhammad G. Kibriya, Ana Navas-Acien, Margaret R. Karagas, Habibul Ahsan, Brandon L. Pierce

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


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 = 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 [ β = - 9.4 (95% CI: - 13.9 , - 4.8 )], SHS [ β = - 6.9 (95% CI: - 13.6 , - 0.2 )], and NHSCS [ β = - 8.7 (95% CI: - 15.6 , - 2.2 )]. In meta-analyses across cohorts, DMA% was 8.7% lower in carriers [ β = - 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.

Original languageEnglish (US)
Article number047007
JournalEnvironmental health perspectives
Issue number4
StatePublished - 2021

Bibliographical note

Funding Information:
The authors thank all the men and women who participated in the Health Effects of Arsenic Longitudinal Study, the New Hampshire Skin Cancer Study, and the Strong Heart Study and all the research staff who contributed to data collection. This work was supported by National Institutes of Health grants R01 ES023834 (to B.L.P.), R35 ES028379 (to B.L.P.), R21 ES024834 (to B.L.P. and M. Argos), P42ES010349 (to J.H.G.), R01 CA107431 (to H.A.), P30 ES027792 (to H.A. and G. Prins), R24 ES028532 (to H.A.) and R24 TW009555 (to H.A.).

Publisher Copyright:
© 2021, Public Health Services, US Dept of Health and Human Services. All rights reserved.


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