Genetic variant
rs869025580 a variant in the PGAP1 gene
rs869025580 is a single-letter difference in the PGAP1 gene, on chromosome 2. 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 Intellectual disability, autosomal recessive 42 and Cerebral visual impairment and intellectual disability. 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 rs869025580 is the catalogue number of one of them, in the PGAP1 gene. Which letters you carry there — one copy from each parent — is your genotype.
PGAP1 (post-GPI attachment to proteins inositol deacylase 1): The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi.
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
- Intellectual disability, autosomal recessive 42
- Cerebral visual impairment and intellectual disability
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 rs869025580, 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
- rs869025580
- Gene
- PGAP1
- Position
- chr2:196897133
- ClinVar classification
- Pathogenic
Sources
- dbSNP: rs869025580 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: PGAP1
- Ensembl: PGAP1