Genetic variant
rs4369876 a variant in the SCN9A gene
rs4369876 is a single-letter difference in the SCN9A gene, on chromosome 2. 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 Paroxysmal extreme pain disorder and Channelopathy-associated congenital insensitivity to pain, autosomal recessive, 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 rs4369876 is the catalogue number of one of them, in the SCN9A gene. Which letters you carry there — one copy from each parent — is your genotype.
SCN9A (sodium voltage-gated channel alpha subunit 9): This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]
Gene description from NCBI Gene
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
- Paroxysmal extreme pain disorder
- Channelopathy-associated congenital insensitivity to pain, autosomal recessive
- Neuropathy
- hereditary sensory and autonomic, type 2A
- Generalized epilepsy with febrile seizures plus, type 7
- Primary erythromelalgia
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 rs4369876, 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
- rs4369876
- Gene
- SCN9A
- Position (GRCh38)
- chr2:166272745
- Variant type
- snv
- Consequence
- missense variant
- ClinVar classification
- Conflicting classifications of pathogenicity
How common the less frequent letter is
- gnomAD ALL
- 99.1%
- 1kG AFR
- 0.3%
- 1kG ALL
- 3.3%
- 1kG AMR
- 87.3%
- 1kG EAS
- 93.9%
- 1kG EUR
- 100%
- 1kG SAS
- 98.7%
Sources
- dbSNP: rs4369876 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: SCN9A
- Ensembl: SCN9A