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Pseudouridine levels

SHROOM3 · rs10029860

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

1 / 4

Its strongest genetic-study result is p = 10−10, with 2 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 8,213 European ancestry individuals.

The effect Each copy of the A allele shifted the measure 0.0917 higher (95% confidence interval 0.064-0.12); p = 1 × 10−10.

How common The A allele had a frequency of about 53% in the people studied.

Where it sits Chromosome 4, band 4q21.1 — in an intron of SHROOM3.

How common each version is

AC
Korean KRGDB
A 33.2% · C 66.8%
Korean Korea4K
A 33.8% · C 66.2%
Korean Korea1K
A 34.1% · C 65.9%
Japanese ToMMo
A 35.6% · C 64.4%
Vietnamese
A 20.4% · C 79.6%
World gnomAD
A 43.5% · C 56.5%
World 1000 Genomes
A 35.7% · C 64.3%
World TOPMed
A 43.3% · C 56.7%

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.

What each result means

A/A Two copies of the version the research linked to Pseudouridine levels. That is the strongest link of the three results. A link in a study is not a diagnosis.
A/C One copy of the version the research linked to Pseudouridine levels. That is a smaller link than two copies.
C/C No copy of the version the research linked to Pseudouridine levels. This is the starting point the study compared everyone against.
Source
Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases
Chen Y, Lu T, Pettersson-Kymmer U, Stewart ID, Butler-Laporte G, Nakanishi T, Cerani A, Liang KYH, Yoshiji S, Willett JDS, Su CY, Raina P
and 7 more — show all
Greenwood CMT, Farjoun Y, Forgetta V, Langenberg C, Zhou S, Ohlsson C, Richards JB
Nature genetics · 2023 · PMID 36635386

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

Pseudouridine levels (rs10029860). MyGeneLog™. https://www.mygenelog.com/variants/rs10029860

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