IthaID: 3898
Names and Sequences
| Functionality: | Disease modifying mutation | Pathogenicity: | N/A |
|---|---|---|---|
| Common Name: | rs1409419 | HGVS Name: | NC_000001.11:g.100717840T>C |
Context nucleotide sequence:
AAGTAGAAAATATAGGCATATTAA [T>C] CAGTAAATGCAGAATGATAAATGCT (Strand: +)
Also known as:
Comments: 2KB Upstream Variant - T allele showed a positive association with overt ischemic stroke and high time averaged mean velocity (TAMMV) values obtained during transcranial Doppler (TCD) screening in pediatric patients with sickle cell anemia of sub-Saharan African ancestry in Portugal.
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: | 1 |
|---|---|
| Locus: | NG_023034.2 |
| Locus Location: | 3100 |
| Size: | 1 bp |
| Located at: | VCAM1 |
| Specific Location: | N/A |
Other details
| Type of Mutation: | Point-Mutation(Substitution) |
|---|---|
| Effect on Gene/Protein Function: | N/A |
| Ethnic Origin: | sub-Saharan 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
- Silva M, Vargas S, Coelho A, Ferreira E, Mendonça J, Vieira L, Maia R, Dias A, Ferreira T, Morais A, Soares IM, Lavinha J, Silva R, Kjöllerström P, Faustino P, Biomarkers and genetic modulators of cerebral vasculopathy in sub-Saharan ancestry children with sickle cell anemia., Blood Cells Mol Dis, 83(0), 102436, 2020 PubMed
Created on 2022-03-23 18:03:29,
Last reviewed on 2022-03-24 11:46:16 (Show full history)
| A/A | Date | Curator(s) | Comments |
|---|---|---|---|
| 1 | 2022-03-23 18:03:29 | The IthaGenes Curation Team | Created |
| 2 | 2022-03-24 11:45:33 | The IthaGenes Curation Team | Reviewed. Ethnic origin. |
| 3 | 2022-03-24 11:46:16 | The IthaGenes Curation Team | Reviewed. Ethnic origin. |
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IthaGenes was last updated on 2024-04-18 10:10:45