A 2010 study of Filipino women found a variant in CPS1 that raises homocysteine only in females, plus a much stronger MTHFR effect in young adults than in their mothers.
Homocysteine is an amino acid produced as a byproduct of processing another amino acid, methionine, obtained from protein in the diet. Elevated plasma homocysteine has long been linked to cardiovascular disease risk and is thought to contribute to vascular damage, a precursor to atherosclerosis. Levels are shaped by both diet — particularly folate and B-vitamin intake, which the body uses to clear homocysteine — and genetics.
Lange et al. 2010 ran a genome-wide association study of homocysteine in 1,786 unrelated Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The single most strongly associated variant, rs7422339 in CPS1, encodes an amino-acid change in the CPS1 protein and explained 3.0% of the variation in homocysteine level — but was significant only in females, not when men were included in the analysis.
The widely studied MTHFR C677T variant, rs1801133, was also highly significant and explained 1.6% of the trait variation in the mothers. When the researchers genotyped the same MTHFR variant separately in 1,679 CLHNS young-adult offspring, its effect was markedly stronger — explaining about 5.1% of variation in that younger generation, a difference the authors suggest reflects how genetic effects on homocysteine can shift across developmental stages, possibly tied to differences in diet or folate status between generations.
This page's own variants include the paper's exact headline SNP, rs7422339 in CPS1, alongside two variants in CBS — a gene central to the same homocysteine-clearing pathway — and MTR, DPEP1, NOX4 (twice), SLC17A3, and CUBN, all part of the broader folate and homocysteine metabolic network this study examined. (rs1801133 itself is catalogued separately on this site under its own folate-metabolism trait, rather than as one of this page's variants.)
Homocysteine is measured directly with a blood test, not estimated from genotype. The variants here describe genetic contributions to homocysteine level found in a specific study population — they are not used clinically to diagnose or predict cardiovascular risk on their own.
Elevated homocysteine (hyperhomocysteinemia) can arise from genetic, nutritional (particularly B12 or folate deficiency), or other medical causes, and clinical evaluation relies on measured levels and the broader clinical picture rather than genotype. The sex-specific CPS1 effect and the age-related MTHFR effect described here are findings from one cohort study, not established clinical rules.
What a 23andMe/AncestryDNA export or raw VCF can and can't tell you about Homocysteine Levels comes down to these specific, well-studied positions — not a diagnosis.
CPS1 · rs1047891
See detailed info →GNMT · rs9296404
See detailed info →The studies behind these variants recruited participants from different ancestries — a result found in one population doesn't always transfer to another. Based on 11 of 11 linked studies with a resolved discovery ancestry.
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Homocysteine Levels. MyGeneLog™. https://www.mygenelog.com/conditions/homocysteine-levels
Homocysteine is an amino acid produced when the body processes methionine from dietary protein. Elevated plasma homocysteine has long been linked to cardiovascular disease risk and vascular damage.
In 1,786 Filipino women, a variant in CPS1 (rs7422339) explained 3.0% of homocysteine variation but only in females. The well-known MTHFR variant (rs1801133) explained 1.6% of variation in the mothers and about 5.1% in their young-adult offspring — a notably stronger effect in the younger generation.
The study found this sex-specific pattern but did not establish the underlying biological reason for it.
No individual variant does. These are population-level statistical associations from one cohort study, and homocysteine is measured directly with a blood test, not estimated from genotype.
Free to reuse. This page's text is original writing from freely-available research, licensed CC BY 4.0 — reuse it, including commercially, with attribution to MyGeneLog™. It's general research-derived information, not medical advice or a diagnosis — see Terms of Use.