Genetic variant
rs2403254 a variant in the HPS5 gene
rs2403254 is a single-letter difference in the HPS5 gene, on chromosome 11. ClinVar, the public archive of variant interpretations, lists it as association: seen more often in people with a condition, which is not the same as causing it. It has been reported in connection with decreased blood alpha-hydroxyisovalerate levels. 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 rs2403254 is the catalogue number of one of them, in the HPS5 gene. Which letters you carry there — one copy from each parent — is your genotype.
HPS5 (HPS5 biogenesis of lysosomal organelles complex 2 subunit 2): This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 6 protein and may interact with the cytoplasmic domain of integrin, alpha-3. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 5.
Gene description from NCBI Gene
Why might it matter?
ClinVar records this variant as association, meaning seen more often in people with a condition, which is not the same as causing it. 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
- decreased blood alpha-hydroxyisovalerate levels
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 rs2403254, 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
- rs2403254
- Gene
- HPS5
- Position (GRCh38)
- chr11:18303598
- Variant type
- snv
- Consequence
- intron variant
- ClinVar classification
- association
Genome-wide association studies (3)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| Alpha-hydroxyisovalerate levels | T | β 0.041 | 1E-30 | PubMed |
| Metabolic traits | T | OR 0.11 | 1E-20 | PubMed |
| Serum metabolite levels | — | β 0.052 | 3E-16 | PubMed |
How common the less frequent letter is
- 1kG AFR
- 91.1%
- 1kG ALL
- 41.9%
- 1kG AMR
- 49.1%
- 1kG EAS
- 40.6%
- 1kG EUR
- 53.6%
- 1kG SAS
- 50.1%
Sources
- dbSNP: rs2403254 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: HPS5
- Ensembl: HPS5
- GWAS Catalog — association studies