Small molecules the kidneys filter, reabsorb, or excrete into urine — three studies found 12 genetic contributors, on this page, most of them in the transporter proteins that move those molecules across kidney cells.
Blood carries thousands of small molecules — amino acids, sugars, vitamins, waste products — and the kidney decides, molecule by molecule, what to keep and what to let go into urine. Urinary metabolite levels are the measured output of that filtering and reabsorption process, captured by NMR spectroscopy of urine samples. Most of the genes behind them are transporter proteins that physically move specific molecules across the cells lining the kidney's filtering tubules.
A 2011 study of 862 men, replicated in 1,039 more (five years later) and 992 independent participants, found 5 genome-wide-significant urinary metabolite loci. Three had known clinical links: SLC7A9 — this page's rs8101881 — is a chronic kidney disease risk gene; SLC6A20 — this page's rs17279437 — causes iminoglycinuria, a benign amino-acid-transport variant, when disrupted more severely. At the time, blood metabolite GWAS had already found over 150 loci; urine had found only 11 in total across all prior small studies, reflecting how much harder urine is to study at scale.
A larger 2015 study of 3,861 plus 1,691 participants found 22 loci, 15 of them new — more than doubling what was known. Two-thirds of the urinary loci also showed an association with the same metabolite measured in blood, evidence that urine and blood levels are often genetically linked, not independent readouts. One locus stood out for the opposite pattern: at SLC5A11 — this page's rs17702912 — myo-inositol was higher in urine while earlier blood studies had found it lower at the same variant, which the study's authors suggest may reflect less effective kidney reabsorption of myo-inositol in carriers. This page's rs11062102, in SLC6A13, is a locus the same study links directly to chronic kidney disease; rs11133665 (SLC6A19) and rs6748734 (AGXT) are two more of its 15 new findings.
A separate 2014 study of 835 Caucasian participants, replicated in 601 participants of more diverse ancestry from São Paulo, narrowed 139 suggestive signals down to 11 replicated gene-metabolite associations. Its own two headlined novel findings — near FUT2 and at the same SLC7A9 locus the 2011 study above already found — are not the six variants this page carries from it; this page's rs11884776 (ALMS1), rs1509569 (ACADL), rs40200 (AGXT2), rs8176749 (ABO), and two PYROXD2 variants (rs17455577, rs4539242) are six more of that paper's replicated findings, not individually singled out in its abstract. ABO is one of the most cross-referenced genes on this site, also appearing on the coronary artery disease, venous thromboembolism, and ABO blood group pages, among others — a reminder that ABO's effects reach well beyond blood type.
Urinary metabolite levels are measured directly by laboratory analysis of a urine sample, not estimated from genotype, and no variant on this page is used clinically to diagnose a kidney condition or metabolic disorder. The variants here describe normal genetic variation in kidney transport and detoxification — most carriers have no related symptoms at all.
Rare, severe mutations in some of these same genes (for example, SLC7A9, SLC6A20, or AGXT2) cause distinct, uncommon inherited conditions diagnosed clinically — the common variants on this page are a different, much milder kind of genetic variation and do not diagnose those conditions.
What a 23andMe/AncestryDNA export or raw VCF can and can't tell you about Urinary Metabolites comes down to these specific, well-studied positions — not a diagnosis.
The studies behind these variants recruited participants from different ancestries — a result found in one population doesn't always transfer to another. Based on 12 of 12 linked studies with a resolved discovery ancestry.
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Urinary Metabolites. MyGeneLog™. https://www.mygenelog.com/conditions/urinary-metabolites
Small molecules — amino acids, sugars, and other compounds — that the kidney filters from blood and either reabsorbs or releases into urine, measured by NMR spectroscopy of urine samples.
Most encode solute-carrier (SLC) transporter proteins — specialized proteins embedded in kidney tubule cells that physically move specific molecules across the cell membrane, deciding what gets reabsorbed into blood versus excreted in urine.
No. These are common variants describing normal variation in kidney transport, not diagnoses. Rare, more severe mutations in some of the same genes cause distinct inherited conditions, diagnosed clinically — a different, much rarer kind of genetic change.
No individual variant does with certainty. These levels are measured directly by laboratory analysis, not estimated from genotype.
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