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Depression

SPPL3 · rs3213572

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 = 10−19, with 6 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 118,811 European ancestry cases, 327,427 European ancestry controls, 127,552 cases, 233,763 controls; replicated in 414,055 European ancestry cases, 892,299 European ancestry controls.

The effect Each copy of the A allele carried 1.02 times the odds of Depression (95% confidence interval 1.016-1.024); p = 6 × 10−20.

How common The A allele had a frequency of about 47% in the people studied.

Where it sits Chromosome 12, band 12q24.31 — in an intron of SPPL3.

How common each version is

AG
Korean KRGDB
A 54.4% · G 45.6%
Korean Korea4K
A 54.4% · G 45.6%
Korean Korea1K
A 54.6% · G 45.4%
Japanese ToMMo
A 51.0% · G 49.0%
Vietnamese
A 45.3% · G 54.7%
World gnomAD
A 40.5% · G 59.5%
World 1000 Genomes
A 38.6% · G 61.4%
World TOPMed
A 40.2% · G 59.8%

By ancestry gnomAD

East Asian
A 44.0% · G 56.0%
European (non-Finnish)
A 47.3% · G 52.7%
African / African American
A 18.9% · G 81.0%
South Asian
A 47.4% · G 52.6%
Admixed American (Latino)
A 56.2% · G 43.8%
Middle Eastern
A 56.1% · G 43.9%
Finnish
A 47.5% · G 52.5%
Ashkenazi Jewish
A 58.8% · G 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. The ancestry rows are gnomAD's own groups (via Ensembl), as the survey defines them, not races.

What each result means

A/A Two copies of the version the research linked to Depression. That is the strongest link of the three results. A link in a study is not a diagnosis.
A/G One copy of the version the research linked to Depression. That is a smaller link than two copies.
G/G No copy of the version the research linked to Depression. This is the starting point the study compared everyone against.
Source
Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions
Howard DM, Adams MJ, Clarke TK, Hafferty JD, Gibson J, Shirali M, Coleman JRI, Hagenaars SP, Ward J, Wigmore EM, Alloza C, Shen X
and 26 more — show all
Barbu MC, Xu EY, Whalley HC, Marioni RE, Porteous DJ, Davies G, Deary IJ, Hemani G, Berger K, Teismann H, Rawal R, Arolt V, Baune BT, Dannlowski U, Domschke K, Tian C, Hinds DA, Trzaskowski M, Byrne EM, Ripke S, Smith DJ, Sullivan PF, Wray NR, Breen G, Lewis CM, McIntosh AM
23andMe Research Team · Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium
Nature neuroscience · 2019 · PMID 30718901

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

Depression (rs3213572). MyGeneLog™. https://www.mygenelog.com/variants/rs3213572

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