SPC25 · rs146779637
Where this position leads
Condition: Celiac Disease
Strength of the evidence
Its strongest genetic-study result is p = 10−36, with 2 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 394,642 European ancestry individuals.
The effect Each copy of the T allele shifted the measure 0.242 lower (95% confidence interval 0.2-0.28); p = 2 × 10−36.
How common The T allele had a frequency of about 0% in the people studied.
Where it sits Chromosome 2, band 2q31.1 — a stop-gain change in SPC25.
What ClinVar records
Classification
Uncertain significance for Fasting plasma glucose level quantitative trait locus 1; criteria provided, multiple submitters, no conflicts (2 of 4 stars, 2 submitters), last evaluated 2018-03-05.
ClinVar record 548513 NM_021176.3(G6PC2):c.847C>T (p.Arg283Ter)
Change history MyGeneLog™ keeps a copy of every weekly release from 2026-10-19 and compares them. This position's classification has not changed since.
What this is ClinVar's aggregate record for this position (as of its 2026-10-19 release), not a result about you. A classification describes the variant against the condition named, as laboratories submitted it. Whether a person carries this variant, and what that would mean for them, is a question for a clinical test and a genetic counsellor.
rs146779637 is a single position in the genome, in or near the SPC25 gene. Published research associates it with glucose levels (ukb data field 30740). 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.
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
Glucose levels (UKB data field 30740) (rs146779637). MyGeneLog™. https://www.mygenelog.com/variants/rs146779637