IthaID: 2604
Names and Sequences
| Functionality: | Disease modifying mutation | Pathogenicity: | N/A |
|---|---|---|---|
| Common Name: | rs1019856 | HGVS Name: | NG_007490.1:g.53823T>C |
Context nucleotide sequence:
CTTGTGGTGTGATATGTAGGTATCC [A/G] AATGCTCAGTTTATGCACCACAGTC (Strand: -)
Also known as:
Comments: SNP associated with osteonecrosis (442 cases; 455 controls) and leg ulcers (243 cases; 516 controls) in the Cooperative Study of Sickle Cell Disease (CSSCD). Associated with risk of stroke in individuals with sickle cell disease.
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: |
Leg ulcers [OMIM:150590] Osteonecrosis/Avascular necrosis [HP:0010885] [OMIM:608805] Stroke [HP:0001297] [OMIM:601367] |
Location
| Chromosome: | 3 |
|---|---|
| Locus: | NG_007490.1 |
| Locus Location: | 53823 |
| Size: | 1 bp |
| Located at: | TGFBR2 |
| Specific Location: | Intron 4 |
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
- Baldwin C, Nolan VG, Wyszynski DF, Ma QL, Sebastiani P, Embury SH, Bisbee A, Farrell J, Farrer L, Steinberg MH, Association of klotho, bone morphogenic protein 6, and annexin A2 polymorphisms with sickle cell osteonecrosis., Blood , 106(1), 372-5, 2005 PubMed
- Nolan VG, Adewoye A, Baldwin C, Wang L, Ma Q, Wyszynski DF, Farrell JJ, Sebastiani P, Farrer LA, Steinberg MH, Sickle cell leg ulcers: associations with haemolysis and SNPs in Klotho, TEK and genes of the TGF-beta/BMP pathway., Br. J. Haematol. , 133(5), 570-8, 2006 PubMed
- Fertrin KY, Costa FF, Genomic polymorphisms in sickle cell disease: implications for clinical diversity and treatment., Expert Rev Hematol , 3(4), 443-58, 2010 PubMed
Created on 2016-05-09 17:26:25,
Last reviewed on 2016-06-03 09:29:45 (Show full history)
| A/A | Date | Curator(s) | Comments |
|---|---|---|---|
| 1 | 2016-05-09 17:26:25 | The IthaGenes Curation Team | Created |
| 2 | 2016-05-16 10:40:23 | The IthaGenes Curation Team | Reviewed. |
| 3 | 2016-06-03 09:29:45 | The IthaGenes Curation Team | Reviewed. |
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IthaGenes was last updated on 2024-11-20 13:24:07