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These proteins are expressed throughout the body, but their physiological function is only beginning to be understood. It is known that ABCA transporters are important in the immune system, helping macrophages release lipid debris from bacteria and other particles that they engulf (phagocytose) as part of immune response. 1 Emerging evidence also suggests that ABCA transporters, including ABCA6, may play both positive and negative roles in cancer progression, by modulating the activity of lipid-responsive growth pathways. 2 3


rsID Number Major Allele Minor Allele Minor Allele Frequency (%) Major Amino Acid Minor Amino Acid
rs77542162 a g 2 Cys Arg

Risk Description

Increased total cholesterol and low-density lipoprotein (‘bad cholesterol’) levels in the carriers of the risk allele that may be counteracted by fish oil supplementation.

A rare SNP resulting in a modified ABCA6 protein sequence (Cys->Arg at position 1359) and potentially affecting the expression levels of ABCA5, ABCA6 and ABCA10 genes has been linked with total cholesterol and triglyceride levels. 4 5 What makes this unusual is that unlike many such variants, this SNP was specifically found to affect these traits in a manner that may be augmented by fish oil supplementation. 6

The Gene x Environment genome-wide association study (GxE GWAS) for lipid levels with and without fish oil supplementation that detected this variant 6 was high-powered and used a replication cohort, followed by a joint meta-analysis of both cohorts. Therefore, these results deserve our attention. However, it must be noted that interpreting GxE interaction effects such as this one can be tricky, and the true phenomena behind them may sometimes be counterintuitive. 7 Therefore, acting on their results should be done with some caution.

Indirect Nutrients:*

Ingredient Active Ingredient Effect
Fish Oil Omega-3

Fish oil may be particularly beneficial for the carriers of the AG and GG alleles of rs77542162, whose cholesterol levels tend to be higher, in particular given the detected interaction effect of fish oil supplementation on cholesterol levels for this SNP.

Discuss this information with your doctor before taking any course of action.

  1. Dean M, Moitra K, Allikmets R. The human ATP-binding cassette (ABC) transporter superfamily. Hum Mutat. 2022 Sep;43(9):1162-1182. doi: 10.1002/humu.24418.
  2. Pasello M, et al. ABCA6 affects the malignancy of Ewing sarcoma cells via cholesterol-guided inhibition of the IGF1R/AKT/MDM2 axis. Cell Oncol (Dordr). 2022 Dec;45(6):1237-1251. doi: 10.1007/s13402-022-00713-5
  3. Alketbi L, Al-Ali A, Talaat IM, Hamid Q, Bajbouj K. The Role of ATP-Binding Cassette Subfamily A in Colorectal Cancer Progression and Resistance. Int J Mol Sci. 2023 Jan 10;24(2):1344. doi: 10.3390/ijms24021344.
  4. Hoffmann TJ, et al. A large electronic-health-record-based genome-wide study of serum lipids. Nat Genet. 2018 Mar;50(3):401-413. doi: 10.1038/s41588-018-0064-5.
  5. Klarin D, et al. Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program. Nat Genet. 2018 Nov;50(11):1514-1523. doi: 10.1038/s41588-018-0222-9.
  6. Francis M, et al. Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci. PLoS Genet. 2021 Mar 24;17(3):e1009431. doi: 10.1371/journal.pgen.1009431.

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