Genetic variant
rs200521449 a variant in the LHX3 gene
rs200521449 is a single-letter difference in the LHX3 gene, on chromosome 9. 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 Non-acquired combined pituitary hormone deficiency with spine abnormalities and Combined pituitary hormone deficiencies, genetic form. 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 rs200521449 is the catalogue number of one of them, in the LHX3 gene. Which letters you carry there — one copy from each parent — is your genotype.
LHX3 (LIM homeobox 3): This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms.
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
- Non-acquired combined pituitary hormone deficiency with spine abnormalities
- Combined pituitary hormone deficiencies, genetic form
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 rs200521449, 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
- rs200521449
- Gene
- LHX3
- Position
- chr9:136199691
- ClinVar classification
- Conflicting classifications of pathogenicity
Sources
- dbSNP: rs200521449 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: LHX3
- Ensembl: LHX3