A 2018 study measured 139 serum metabolites and their ratios in over 1,000 people with chronic kidney disease, finding genetic loci that illuminate how the kidney handles specific molecules.
The kidneys generate, transport, and excrete metabolites as a core part of their function, and chronic kidney disease (CKD) changes how well those functions work. Measuring the concentrations of specific small molecules — serum metabolites — in people who already have CKD offers a way to study kidney biology directly in the population it affects, rather than inferring it from healthy people.
Li et al. 2018, the GCKD study, measured 139 serum metabolites and 41 urine metabolites, along with their pairwise ratios, in up to 1,168 people who already had chronic kidney disease. After correcting for multiple testing, the study found genome-wide significant associations for 25 serum metabolites, 2 urine metabolites, and 259 serum plus 14 urinary metabolite ratios.
Several findings stood out. A variant near AOC1 was tied to the uremic toxin putrescine, a compound that builds up as kidney function declines. Rare missense variants in ACADM, carried by about 2% of the cohort, were collectively associated with ratios of medium-chain acylcarnitines. And a common variant in SLC7A9 showed a much stronger association with ratios between lysine and other amino acids in urine than with lysine concentration alone — a pattern consistent with SLC7A9 acting as an exchanger of amino acids at the kidney's proximal tubule, the segment responsible for reabsorbing most of what the kidney filters.
This page's own variants include rs12134854 in ACADM, directly one of the paper's own highlighted genes, alongside FADS1, FADS2, ACADS, and NAT8 — genes this site's separate, general-population Blood Metabolite Levels page also covers, now confirmed specifically in a cohort of people who have kidney disease.
Serum metabolite levels are measured directly with laboratory testing, not estimated from genotype, and none of the variants here is used to diagnose or stage chronic kidney disease. Standard CKD diagnosis and monitoring rely on measures like estimated glomerular filtration rate and albuminuria — not on the variants listed here.
This page's variants describe genetic influences on metabolite levels specifically within a population that already has chronic kidney disease. They are a research tool for understanding kidney physiology and tubular transport mechanisms, not a genetic test for CKD itself.
What a 23andMe/AncestryDNA export or raw VCF can and can't tell you about Serum Metabolites in Chronic Kidney Disease comes down to these specific, well-studied positions — not a diagnosis. 31 positions are linked to this page; the ones this page's own text discusses are shown first.
TMEM229B · rs1077989
See detailed info →PRODH · rs117935223
See detailed info →FADS1 · rs174560
See detailed info →ASPG · rs2282377
See detailed info →DNAH17 · rs55888180
See detailed info →MAGEL2 · rs850799
See detailed info →PYDC2 · rs1066621
See detailed info →ACADM · rs12134854
See detailed info →CDH18 · rs17253658
See detailed info →NAT8 · rs375811360
See detailed info →SLIT2 · rs57802047
See detailed info →PTPRN2 · rs1242780
See detailed info →ZNF618 · rs814698
See detailed info →TMEM229B · rs1885041
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 29 of 31 linked studies with a resolved discovery ancestry.
Databases, guidelines and references
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Serum Metabolites in Chronic Kidney Disease. MyGeneLog™. https://www.mygenelog.com/conditions/serum-metabolites-ckd
Serum metabolites are small molecules circulating in blood, many of them generated, transported, or excreted by the kidneys. Measuring them in people who already have chronic kidney disease offers a direct way to study how kidney disease affects these processes.
In up to 1,168 people with CKD, it found genome-wide significant associations for 25 serum metabolites, 2 urine metabolites, and hundreds of metabolite ratios, including notable findings in AOC1, ACADM, and SLC7A9.
No. CKD is diagnosed and monitored using measures like estimated glomerular filtration rate and albuminuria, not the variants on this page. These variants describe genetic influences on metabolite levels within a population that already has the condition.
Several are. FADS1, FADS2, ACADS, ACADM, and NAT8 all also appear on this site's separate Blood Metabolite Levels page, which covers a general, non-CKD population — this page confirms similar genetic influences specifically in people who have kidney disease.
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.