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Urinary metabolites (H-NMR features)

AGXT2 · rs40200

Stands on its own. Nothing else here links to this position yet — but the page above is the point: what the research found, what each genotype means, and where it came from, in language you can read. Links to conditions, drugs and the senses appear automatically if we write them.

Strength of the evidence

2 / 4

Its strongest genetic-study result is p = 10−36, with 3 associations in the GWAS Catalog.

How this is scored

4: ClinVar disease-causing, reviewed by an expert panel or a guideline (3–4 stars). 3: ClinVar, several labs agreeing (2 stars), or a genetic study at p ≤ 10−50. 2: ClinVar from one lab (1 star), or p ≤ 10−20. 1: ClinVar submitted without criteria (0 stars), or genome-wide significance (p ≤ 5×10−8). The higher of the two counts. It says how solid the evidence is, not whether it matters for a particular person.

What the study found

Who was studied 835 European ancestry individuals; replicated in 601 Brazilian individuals.

The effect Each copy of the G allele shifted the measure 0.67 higher; p = 9 × 10−37.

How common The G allele had a frequency of about 9% in the people studied.

Where it sits Chromosome 5, band 5p13.2 — in an intron of AGXT2.

How common each version is

AG
Korean KRGDB
A 43.8% · G 56.2%
Korean Korea4K
A 44.5% · G 55.5%
Korean Korea1K
A 44.3% · G 55.7%
Japanese ToMMo
A 45.1% · G 54.9%
Vietnamese
A 46.3% · G 53.7%
World gnomAD
A 15.7% · G 84.3%
World 1000 Genomes
A 24.2% · G 75.8%
World TOPMed
A 17.4% · G 82.6%

By ancestry gnomAD

East Asian
A 45.1% · G 54.9%
European (non-Finnish)
A 10.0% · G 90.0%
African / African American
A 20.3% · G 79.7%
South Asian
A 16.8% · G 83.2%
Admixed American (Latino)
A 23.4% · G 76.5%
Middle Eastern
A 8.8% · G 91.2%
Finnish
A 10.0% · G 90.0%
Ashkenazi Jewish
A 12.6% · G 87.4%

The share of all copies of this position that are each version. Source: the population studies published in dbSNP (US NCBI); each row names its study. The ancestry rows are gnomAD's own groups (via Ensembl), as the survey defines them, not races.

What each result means

A/A No copy of the version the research linked to Urinary metabolites (H-NMR features). This is the starting point the study compared everyone against.
A/G One copy of the version the research linked to Urinary metabolites (H-NMR features). That is a smaller link than two copies.
G/G Two copies of the version the research linked to Urinary metabolites (H-NMR features). That is the strongest link of the three results. A link in a study is not a diagnosis.
Source
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links
Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S
and 10 more — show all
Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z
PLoS genetics · 2014 · PMID 24586186 · open access

Quoting this page

Licensed CC BY-NC 4.0: free to read, share and adapt for non-commercial use, naming MyGeneLog™ and linking the exact page. Commercial use, including training or serving a commercial AI system, needs a licence — https://www.mygenelog.com/license

Urinary metabolites (H-NMR features) (rs40200). MyGeneLog™. https://www.mygenelog.com/variants/rs40200

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