IthaID: 3579
Names and Sequences
| Functionality: | Disease modifying mutation | Pathogenicity: | N/A |
|---|---|---|---|
| Common Name: | rs3115229 | HGVS Name: | NC_000004.12:g.122088578T>C |
Context nucleotide sequence:
CAGAGGGTGAAGGGCAAGTTTTCCC [T>C] TTGCCCTACAGTAGAAATTAATAAA (Strand: +)
Also known as:
Comments: SNP associated with acute, severe vaso-occlusive pain requiring hospitalization among pediatric patients with SCA (n=1293 participants in the SIT trial and CSSCD). SNP is located 63.7 kb 5' upstream of the KIAA1109 gene.
We follow the HGVS sequence variant nomenclature and IUPAC standards.
External Links
Phenotype
| Allele Phenotype (Cis): | N/A |
|---|---|
| Allele Phenotype (Trans): | N/A |
| Associated Phenotypes: | Vaso-occlusive crisis |
Location
| Chromosome: | 4 |
|---|---|
| Locus: | N/A |
| Locus Location: | N/A |
| Size: | 1 bp |
| Located at: | TRPC3-KIAA1109 |
| Specific Location: | N/A |
Other details
| Type of Mutation: | Point-Mutation(Substitution) |
|---|---|
| Effect on Gene/Protein Function: | N/A |
| Ethnic Origin: | African |
| Molecular mechanism: | N/A |
| Inheritance: | Quantitative trait |
| DNA Sequence Determined: | Yes |
In silico pathogenicity prediction
Note:
The impact thresholds provided in this section are based on the analyses performed in Tamana et.al. For any given tool, the impact thresholds defined for the set of variants with the same effect on function as the variant examined, are preferred over those defined for the full dataset.
Sequence Viewer
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Publications / Origin
- Chaturvedi S, Bhatnagar P, Bean CJ, Steinberg MH, Milton JN, Casella JF, Barron-Casella E, Arking DE, DeBaun MR, Genome-wide association study to identify variants associated with acute severe vaso-occlusive pain in sickle cell anemia., Blood, 130(5), 686-688, 2017 PubMed
Created on 2020-03-25 15:47:40,
Last reviewed on 2020-03-25 20:27:04 (Show full history)
| A/A | Date | Curator(s) | Comments |
|---|---|---|---|
| 1 | 2020-03-25 15:47:40 | The IthaGenes Curation Team | Created |
| 2 | 2020-03-25 15:52:15 | The IthaGenes Curation Team | Reviewed. Link added. |
| 3 | 2020-03-25 20:27:04 | The IthaGenes Curation Team | Reviewed. Gene added. |
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IthaGenes was last updated on 2024-11-20 13:24:07