Genetic variant
rs2139964469 a variant in the GNPNAT1 gene
rs2139964469 is a single-letter difference in the GNPNAT1 gene, on chromosome 14. ClinVar, the public archive of variant interpretations, lists it as pathogenic: able to cause or contribute to disease. It has been reported in connection with Rhizomelic dysplasia and Ain-Naz type. 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 rs2139964469 is the catalogue number of one of them, in the GNPNAT1 gene. Which letters you carry there — one copy from each parent — is your genotype.
GNPNAT1 (glucosamine-phosphate N-acetyltransferase 1): Enables identical protein binding activity. Predicted to be involved in UDP-N-acetylglucosamine biosynthetic process. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in endoplasmic reticulum-Golgi intermediate compartment and late endosome. [provided by Alliance of Genome Resources, Apr 2025]
Gene description from NCBI Gene
Why might it matter?
ClinVar records this variant as pathogenic, meaning able to cause or contribute to 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
- Rhizomelic dysplasia
- Ain-Naz type
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 rs2139964469, 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
- rs2139964469
- Gene
- GNPNAT1
- Position
- chr14:52781903
- ClinVar classification
- Pathogenic
Sources
- dbSNP: rs2139964469 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: GNPNAT1
- Ensembl: GNPNAT1