Genetic variant
rs2479409 a variant in the PCSK9 gene
rs2479409 is a single-letter difference in the PCSK9 gene, on chromosome 1. ClinVar, the public archive of variant interpretations, lists it as conflicting interpretations: laboratories that have assessed it do not agree on whether it matters. It has been reported in connection with Hypercholesterolemia, familial and 1, autosomal dominant, among others. 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 rs2479409 is the catalogue number of one of them, in the PCSK9 gene. Which letters you carry there — one copy from each parent — is your genotype.
PCSK9 (proprotein convertase subtilisin/kexin type 9): This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway.
Gene description from NCBI Gene
Molecular population genetics of PCSK9: a signature of recent positive selection. [OMIM:?] [GWAS:No...
From SNPedia
Why might it matter?
ClinVar records this variant as conflicting interpretations, meaning laboratories that have assessed it do not agree on whether it matters. 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
- Hypercholesterolemia, familial
- 1, autosomal dominant
- 3
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 rs2479409, 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
- rs2479409
- Gene
- PCSK9
- Position (GRCh38)
- chr1:55038976
- Variant type
- snv
- Consequence
- intergenic variant
- ClinVar classification
- Conflicting classifications of pathogenicity
Genome-wide association studies (11)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| LDL cholesterol | G | β 0.064 | 3E-50 | PubMed |
| LDL cholesterol levels | A | β 0.064 | 3E-42 | PubMed |
| Cholesterol, total | G | β 0.054 | 2E-39 | PubMed |
| Total cholesterol levels | A | β 0.054 | 1E-32 | PubMed |
| LDL cholesterol | G | OR 2.01 | 2E-28 | PubMed |
| Cholesterol, total | G | OR 1.96 | 4E-24 | PubMed |
| LDL x depression interaction (2df test) | A | OR 1.47 | 1E-22 | PubMed |
| Low density lipoprotein cholesterol levels | G | β 0.053 | 3E-20 | PubMed |
| Total cholesterol levels | G | β 0.05 | 9E-19 | PubMed |
| LDL cholesterol levels | A | OR 1.45 | 6E-16 | PubMed |
| Plasma proprotein convertase subtilisin/kexin type 9 levels in stable coronary artery disease | A | β 0.057 | 3E-7 | PubMed |
How common the less frequent letter is
- 1kG AFR
- 25.2%
- 1kG ALL
- 60.1%
- 1kG AMR
- 56.8%
- 1kG EAS
- 33.1%
- 1kG EUR
- 68%
- 1kG SAS
- 27.9%
Sources
- dbSNP: rs2479409 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: PCSK9
- Ensembl: PCSK9
- GWAS Catalog — association studies