Genetic variant
rs121908120 a variant in the WNT10A gene
rs121908120 is a single-letter difference in the WNT10A gene, on chromosome 2. 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 Odonto-onycho-dermal dysplasia and Tooth agenesis, selective, 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 rs121908120 is the catalogue number of one of them, in the WNT10A gene. Which letters you carry there — one copy from each parent — is your genotype.
WNT10A (Wnt family member 10A): The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is strongly expressed in the cell lines of promyelocytic leukemia and Burkitt's lymphoma.
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
- Odonto-onycho-dermal dysplasia
- Tooth agenesis, selective
- 4
- Inborn genetic diseases
- Hypohidrotic ectodermal dysplasia
- Ectodermal dysplasia
- Schöpf-Schulz-Passarge syndrome
- WNT10A-related disorder
- Ectodermal dysplasia WNT10A related
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 rs121908120, 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
- rs121908120
- Gene
- WNT10A
- Position (GRCh38)
- chr2:218890288
- Variant type
- snv
- Consequence
- missense variant
- ClinVar classification
- Conflicting classifications of pathogenicity
Genome-wide association studies (19)
| Trait | Risk allele | OR / beta | P-value | Study |
|---|---|---|---|---|
| GAL protein levels | A | OR 0.2 | 9E-47 | PubMed |
| Tooth agenesis | A | OR 3.25 | 2E-40 | PubMed |
| Corneal resistance factor | T | OR 0.34 | 1E-34 | PubMed |
| Sebaceous cyst (PheCode 706.2) | T | OR 0.4 | 2E-28 | PubMed |
| Sebaceous cyst (PheCode 706.2) | T | OR 0.4 | 4E-26 | PubMed |
| CST6 protein levels | A | OR 0.14 | 8E-24 | PubMed |
| Number of decayed, missing and filled tooth surfaces or use of dentures | A | β 0.081 | 2E-22 | PubMed |
| Dentures | A | OR 0.16 | 2E-20 | PubMed |
| KLK8 protein levels | A | OR 0.14 | 1E-18 | PubMed |
| ENDOU protein levels | A | OR 0.12 | 5E-18 | PubMed |
| Refractive error | — | — | 2E-17 | PubMed |
| SPINK5 protein levels | A | OR 0.12 | 6E-16 | PubMed |
| PM20D1 protein levels | A | OR 0.11 | 7E-16 | PubMed |
| KLK7 protein levels | A | OR 0.12 | 5E-13 | PubMed |
| Central corneal thickness | A | OR 11.48 | 5E-13 | PubMed |
| KLK13 protein levels | A | OR 0.11 | 6E-13 | PubMed |
| Acne (severe) | T | OR 1.94 | 2E-12 | PubMed |
| Youthful appearance (self-reported) | T | OR 1.09 | 3E-11 | PubMed |
| Central corneal thickness | — | OR 0.39 | 5E-11 | PubMed |
How common the less frequent letter is
- gnomAD ALL
- 97.9%
- 1kG AFR
- 0.2%
- 1kG ALL
- 0.6%
- 1kG AMR
- 98.8%
- 1kG EAS
- 100%
- 1kG EUR
- 98%
- 1kG SAS
- 100%
Sources
- dbSNP: rs121908120 — the reference record
- ClinVar — clinical interpretations submitted by laboratories
- SNPedia — community-written summaries
- NCBI Gene: WNT10A
- Ensembl: WNT10A
- GWAS Catalog — association studies