Genetic variant
rs11558538 a variant in the HNMT gene
rs11558538 is a single-letter difference in the HNMT gene, on chromosome 2. ClinVar, the public archive of variant interpretations, lists it as benign: not known to cause disease. It has been reported in connection with Inherited susceptibility to asthma and HNMT-related disorder. 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 rs11558538 is the catalogue number of one of them, in the HNMT gene. Which letters you carry there — one copy from each parent — is your genotype.
HNMT (histamine N-methyltransferase): In mammals, histamine is metabolized by two major pathways: N(tau)-methylation via histamine N-methyltransferase and oxidative deamination via diamine oxidase. This gene encodes the first enzyme which is found in the cytosol and uses S-adenosyl-L-methionine as the methyl donor.
Gene description from NCBI Gene
Why might it matter?
ClinVar records this variant as benign, meaning not known to cause disease. 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
- Inherited susceptibility to asthma
- HNMT-related disorder
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 rs11558538, 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
- rs11558538
- Gene
- HNMT
- Position
- chr2:138002079
- ClinVar classification
- Benign; risk factor
Genome-wide association studies (1)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| Histamine N-methyltransferase levels | T | OR 0.69 | 2E-62 | PubMed |
Sources
- dbSNP: rs11558538 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: HNMT
- Ensembl: HNMT
- GWAS Catalog — association studies