IthaID: 2661
Names and Sequences
| Functionality: | Disease modifying mutation | Pathogenicity: | N/A |
|---|---|---|---|
| Common Name: | rs730012 | HGVS Name: | NG_028161.1:g.4653A>C |
Context nucleotide sequence:
TGCCAGGAACAGCCTGGATGGGGAC [A/C] GGGAACAGATAAGGTGGGTGGAGGA (Strand: +)
Also known as:
Comments: SNP associated with stroke risk in pediatric sickle cell disease (SCD) patients acquired from the multicenter Stroke Prevention Trial in Sickle Cell Anemia (STOP) study (49 cases, 49 controls) [PMID: 17600229]. The association was not replicated in an independent study, which enrolled pediatric SCD patients from the Stroke With Transfusion Changing to Hydrxyurea (SWiTCH) trial (130 cases; 103 controls enrolled from the HUSTLE study) [PMID: 21515823].
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: | Stroke [HP:0001297] [OMIM:601367] |
Location
| Chromosome: | 5 |
|---|---|
| Locus: | NG_028161.1 |
| Locus Location: | 4653 |
| Size: | 1 bp |
| Located at: | LTC4S |
| Specific Location: | N/A |
Other details
| Type of Mutation: | Point-Mutation(Substitution) |
|---|---|
| Effect on Gene/Protein Function: | N/A |
| Ethnic Origin: | African American |
| 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
- Hoppe C, Klitz W, D'Harlingue K, Cheng S, Grow M, Steiner L, Noble J, Adams R, Styles L, , Confirmation of an association between the TNF(-308) promoter polymorphism and stroke risk in children with sickle cell anemia., Stroke , 38(8), 2241-6, 2007 PubMed
- Flanagan JM, Frohlich DM, Howard TA, Schultz WH, Driscoll C, Nagasubramanian R, Mortier NA, Kimble AC, Aygun B, Adams RJ, Helms RW, Ware RE, Genetic predictors for stroke in children with sickle cell anemia., Blood , 117(24), 6681-4, 2011 PubMed
Created on 2016-05-10 19:50:59,
Last reviewed on (Show full history)
| A/A | Date | Curator(s) | Comments |
|---|---|---|---|
| 1 | 2016-05-10 19:50:59 | The IthaGenes Curation Team | Created |
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IthaGenes was last updated on 2024-04-18 10:10:45