IthaID: 2940
Names and Sequences
| Functionality: | Disease modifying mutation | Pathogenicity: | N/A |
|---|---|---|---|
| Common Name: | rs2280789 | HGVS Name: | NG_015990.1:g.5375T>C |
Context nucleotide sequence:
ATCTCCTGATCAGTTTTTCTGTCTT [C/T] AAGGTCTACACCCTCAAGGCCTACA (Strand: -)
Also known as: g.In1.+1T>C
Comments: The g.In1.1C variant associated with lower risk of bacterial infection recurrence in children with sickle cell disease (SCD) in Benin and in France (n=115) [PMID: 19425063]. The association was not replicated in an SCD cohort from Tunisia [PMID: 23900864].
We follow the HGVS sequence variant nomenclature and IUPAC standards.
External Links
Phenotype
| Allele Phenotype (Cis): | Decreased expression for CCL5 |
|---|---|
| Allele Phenotype (Trans): | N/A |
| Associated Phenotypes: | Recurrent infections [HP:0002719] |
Location
| Chromosome: | 17 |
|---|---|
| Locus: | NG_015990.1 |
| Locus Location: | 5375 |
| Size: | 1 bp |
| Located at: | CCL5 |
| Specific Location: | Intron 1 |
Other details
| Type of Mutation: | Point-Mutation(Substitution) |
|---|---|
| Effect on Gene/Protein Function: | N/A |
| Ethnic Origin: | Beninese, French |
| 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
- Dossou-Yovo OP, Zaccaria I, Benkerrou M, Hauchecorne M, Alberti C, Rahimy MC, Elion J, Lapoumeroulie C, Effects of RANTES and MBL2 gene polymorphisms in sickle cell disease clinical outcomes: association of the g.In1.1T>C RANTES variant with protection against infections., Am. J. Hematol. , 84(6), 378-80, 2009 PubMed
- Kalai M, Chaouch L, Mansour IB, Hafsia R, Ghanem A, Abbes S, Frequency of three polymorphisms of the CCL5 gene (rs2107538, rs2280788 and rs2280789) and their implications for the phenotypic expression of sickle cell anemia in Tunisia., Pol J Pathol , 64(2), 84-9, 2013 PubMed
Created on 2016-08-09 11:07:12,
Last reviewed on 2019-07-03 22:19:50 (Show full history)
| A/A | Date | Curator(s) | Comments |
|---|---|---|---|
| 1 | 2016-08-09 11:07:12 | The IthaGenes Curation Team | Created |
| 2 | 2016-08-09 11:08:32 | The IthaGenes Curation Team | Reviewed. |
| 3 | 2016-08-09 11:17:12 | The IthaGenes Curation Team | Reviewed. |
| 4 | 2016-08-09 11:27:14 | The IthaGenes Curation Team | Reviewed. |
| 5 | 2016-08-26 12:11:37 | The IthaGenes Curation Team | Reviewed. Location corrected. |
| 6 | 2019-07-03 22:19:50 | The IthaGenes Curation Team | Reviewed. Phenotype added. |
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IthaGenes was last updated on 2024-12-03 11:48:06