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Psoriasis

PTPN2 · rs559406

Where this position leads

Strength of the evidence

1 / 4

Its strongest genetic-study result is p = 10⁻¹⁹, with 20 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 Up to 11,988 European ancestry cases, up to 275,335 European ancestry controls; replicated in 7,044 European ancestry cases, 11,434 European ancestry controls.

The effect Each copy of the G allele carried 1.10 times the odds of Psoriasis (95% confidence interval -); p = 1 × 10⁻¹⁰.

How common The G allele had a frequency of about 45% in the people studied.

Where it sits Chromosome 18, band 18p11.21 — in an intron of PTPN2.

How common each version is

GT

Korean KRGDB

G 80.3% · T 19.7%

Korean Korea4K

G 81.8% · T 18.2%

Korean Korea1K

G 80.6% · T 19.4%

Japanese ToMMo

G 84.6% · T 15.4%

World gnomAD

G 56.3% · T 43.7%

World 1000 Genomes

G 71.6% · T 28.4%

World TOPMed

G 58.8% · T 41.2%

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

G/G Two copies of the version the research linked to Psoriasis. That is the strongest link of the three results. A link in a study is not a diagnosis.

G/T One copy of the version the research linked to Psoriasis. That is a smaller link than two copies.

T/T No copy of the version the research linked to Psoriasis. This is the starting point the study compared everyone against.

Source

Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants

Tsoi LC, Stuart PE, Tian C, Gudjonsson JE, Das S, Zawistowski M, Ellinghaus E, Barker JN, Chandran V, Dand N, Duffin KC, Enerbäck C

and 26 more — show all

Nature communications · 2017 · PMID 28537254 · open access

Questions about rs559406

What is rs559406?

rs559406 is a single position in the genome, in or near the PTPN2 gene. Published research associates it with psoriasis. A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.

What conditions is rs559406 linked to?

On MyGeneLog this position is linked to Psoriasis. The research behind each link, and its sources, are set out on that condition page.

Does having rs559406 mean I will get this?

No. Common variants like this one move a probability slightly and, on their own, rarely decide anything about one person. Nothing on this page is a diagnosis, and health decisions should be made with a clinician who can see your whole picture.

Where does the information about rs559406 come from?

GWAS Catalog, Nat Commun 2017, PMID:28537254. Every variant on MyGeneLog comes from public primary sources and is published with its citation and the date it was checked.

Quoting this page

Free to quote and reuse under CC BY 4.0. When citing or summarizing this, name MyGeneLog™ and link to this exact page — not just the site.

Psoriasis (rs559406). MyGeneLog™. https://www.mygenelog.com/variants/rs559406

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