Genetic variant
rs3829241 a variant in the TPCN2 gene
rs3829241 is a single-letter difference in the TPCN2 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 Skin/hair/eye pigmentation and Variation in, among others. 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 rs3829241 is the catalogue number of one of them, in the TPCN2 gene. Which letters you carry there — one copy from each parent — is your genotype.
TPCN2 (two pore segment channel 2): This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney.
Gene description from NCBI Gene
This SNP influences appearance and is located in the TPCN2 gene. A study of 5130 Icelanders (with fu...
From SNPedia
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
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 rs3829241, 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
- rs3829241
- Gene
- TPCN2
- Position (GRCh38)
- chr11:69087894
- Variant type
- snv
- Consequence
- missense variant
- ClinVar classification
- association
Genome-wide association studies (11)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| Blond vs. brown/black hair color | A | OR 1.27 | 5E-188 | PubMed |
| Sex hormone-binding globulin levels and heel estimated bone mineral density | — | — | 5E-77 | PubMed |
| Sex hormone-binding globulin levels adjusted for BMI and heel estimated bone mineral density | — | — | 5E-73 | PubMed |
| Heel bone mineral density | — | — | 3E-63 | PubMed |
| Heel bone mineral density | G | β 0.031 | 8E-62 | PubMed |
| Heel bone mineral density | — | β 0.03 | 9E-51 | PubMed |
| CTSS protein levels | A | β 0.041 | 2E-18 | PubMed |
| Height | A | β 0.022 | 4E-14 | PubMed |
| Heel bone mineral density | G | β 0.032 | 6E-13 | PubMed |
| Bone density (confirmatory factor analysis Factor 19) | — | — | 1E-12 | PubMed |
| Hip circumference adjusted for BMI | A | β 0.018 | 1E-8 | PubMed |
How common the less frequent letter is
- gnomAD ALL
- 64.2%
- 1kG AFR
- 3.9%
- 1kG ALL
- 82.4%
- 1kG AMR
- 22%
- 1kG EAS
- 20.6%
- 1kG EUR
- 61.8%
- 1kG SAS
- 91.1%
Sources
- dbSNP: rs3829241 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: TPCN2
- Ensembl: TPCN2
- GWAS Catalog — association studies