Genetic variant
rs3087456 a variant in the CIITA gene
rs3087456 is a single-letter difference in the CIITA gene, on chromosome 16. ClinVar, the public archive of variant interpretations, lists it as risk factor: linked to a somewhat higher chance of a condition, not a cause on its own. It has been reported in connection with Rheumatoid arthritis. Carrying it does not, on its own, mean you have or will develop any condition.
What is this?
Your DNA is a long sequence of four letters. At a few million positions, people commonly differ by a single letter; each of those positions is called a SNP (“snip”), and rs3087456 is the catalogue number of one of them, in the CIITA gene. Which letters you carry there — one copy from each parent — is your genotype.
CIITA (class II major histocompatibility complex transactivator): This gene encodes a protein with an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the "master control factor" for the expression of these genes.
Gene description from NCBI Gene
This SNP has been linked to increased risk of adrenal insufficiency However. there is mixed informat...
From SNPedia
Why might it matter?
ClinVar records this variant as risk factor, meaning linked to a somewhat higher chance of a condition, not a cause on its own. A classification describes the variant, not you: what it means for one person depends on their genotype, their family history and often on other genes and circumstances.
Conditions it has been reported with
Listed in ClinVar submissions for this variant. Being listed is a report of an association, not a statement that the variant causes the condition in any given person.
Do I have this variant?
If you have taken a consumer DNA test (23andMe, AncestryDNA and similar), you can download its raw data file and check. Create a free account, upload the file, and this page will show the letters you carry at rs3087456, if your test read this position.
Connect this with your blood results
A gene is a fixed instruction; a blood test shows what your body is doing now. CheckMyBloods reads the two side by side, so a variant can be set against the markers it could plausibly affect.
Blood markers do not diagnose a genetic condition, and a variant does not explain a blood result on its own. Together, with symptoms and family history, they give a clinician context.
What should I do next?
- Find out whether you carry it. Reading about a variant says nothing about you until you know your genotype.
- Put it in context. Add your blood results, so the variant can be read against what your body is doing.
- Ask questions. Dr. Hemsworth, our AI assistant, can explain this variant and your results in plain English.
- Take anything that worries you to a professional. A GP or genetic counsellor can order a confirmatory test and interpret it with your history.
This page is general information drawn from public research databases. It cannot diagnose anything, and it is not a substitute for advice from a doctor or genetic counsellor who knows your history.
Technical details
- dbSNP ID
- rs3087456
- Gene
- CIITA
- Position (GRCh38)
- chr16:10877044
- Variant type
- snv
- Consequence
- intron variant
- ClinVar classification
- risk factor
Genome-wide association studies (8)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| HLA DR+ T cell%T cell | A | OR 0.46 | 3E-70 | PubMed |
| HLA DR+ T cell%lymphocyte | A | OR 0.47 | 7E-69 | PubMed |
| HLA DR+ CD8+ T cell %T cell | A | OR 0.45 | 1E-62 | PubMed |
| HLA DR+ CD8+ T cell %lymphocyte | A | OR 0.45 | 9E-61 | PubMed |
| HLA DR+ T cell Absolute Count | A | OR 0.44 | 4E-55 | PubMed |
| HLA DR+ CD8+ T cell Absolute Count | A | OR 0.43 | 6E-52 | PubMed |
| HLA DR+ CD4+ T cell %lymphocyte | A | OR 0.31 | 1E-33 | PubMed |
| HLA DR+ CD4+ T cell Absolute Count | A | OR 0.29 | 1E-25 | PubMed |
How common the less frequent letter is
- 1kG AFR
- 91.1%
- 1kG ALL
- 62.6%
- 1kG AMR
- 55.9%
- 1kG EAS
- 88.3%
- 1kG EUR
- 76.1%
- 1kG SAS
- 42%
Sources
- dbSNP: rs3087456 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: CIITA
- Ensembl: CIITA
- GWAS Catalog — association studies