Genetic variant
rs5398 a variant in the SLC2A2 gene
rs5398 is a single-letter difference in the SLC2A2 gene, on chromosome 3. 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 Fanconi-Bickel syndrome and Type 2 diabetes mellitus. 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 rs5398 is the catalogue number of one of them, in the SLC2A2 gene. Which letters you carry there — one copy from each parent — is your genotype.
SLC2A2 (solute carrier family 2 member 2): This gene encodes an integral plasma membrane glycoprotein of the liver, islet beta cells, intestine, and kidney epithelium. The encoded protein mediates facilitated bidirectional glucose transport. Because of its low affinity for glucose, it has been suggested as a glucose sensor.
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
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 rs5398, 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
- rs5398
- Gene
- SLC2A2
- Position (GRCh38)
- chr3:170998040
- Variant type
- snv
- Consequence
- missense variant
- ClinVar classification
- Conflicting classifications of pathogenicity
Genome-wide association studies (7)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| MET protein levels | A | β 0.07 | 1E-37 | PubMed |
| Cholesteryl Esters to Total Lipids in Large HDL percentage | A | β 0.02 | 6E-21 | PubMed |
| Phospholipids to Total Lipids in Small HDL percentage | A | β 0.02 | 1E-20 | PubMed |
| Phospholipids to Total Lipids in Medium HDL percentage | A | β 0.02 | 4E-20 | PubMed |
| Cholesterol to Total Lipids in Large LDL percentage | A | β 0.02 | 1E-16 | PubMed |
| DCBLD2 protein levels | A | β 0.043 | 3E-14 | PubMed |
| Waist circumference | — | — | 2E-8 | PubMed |
How common the less frequent letter is
- gnomAD ALL
- 70.5%
- 1kG AFR
- 63.5%
- 1kG ALL
- 37.3%
- 1kG AMR
- 30.8%
- 1kG EAS
- 24.1%
- 1kG EUR
- 71%
- 1kG SAS
- 28.3%
Sources
- dbSNP: rs5398 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: SLC2A2
- Ensembl: SLC2A2
- GWAS Catalog — association studies