PCDH9 · rs17416460
Where this position leads
Condition: Celiac Disease
Strength of the evidence
Its strongest genetic-study result is p = 10−43, with 1 associations in the GWAS Catalog.
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 47,745 European ancestry individuals.
The effect Each copy of the A allele shifted the measure 0.103 higher (95% confidence interval 0.087-0.119); p = 3 × 10−43.
How common The A allele had a frequency of about 16% in the people studied.
Where it sits Chromosome 13, band 13q21.32 — in an intron of PCDH9.
How common each version is
AT
A 7.2% · T 92.8%
A 8.0% · T 92.0%
A 8.7% · T 91.3%
A 8.9% · T 91.0%
A 4.7% · T 95.3%
A 11.7% · T 88.3%
A 11.2% · T 88.8%
A 10.6% · T 89.4%
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.
rs17416460 is a single position in the genome, in or near the PCDH9 gene. Published research associates it with pcdh9 protein levels. A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.
On MyGeneLog this position is linked to Celiac Disease. The research behind each link, and its sources, are set out on that condition page.
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.
GWAS Catalog, Nature genetics 2025, PMID:39789286. Every variant on MyGeneLog comes from public primary sources and is published with its citation and the date it was checked.
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PCDH9 protein levels (rs17416460). MyGeneLog™. https://www.mygenelog.com/variants/rs17416460