Table 9 Top RNA-editing SNVs in breast
Gene | Locus (Chr:bp) | Variant | Type | Class | Description |
|---|---|---|---|---|---|
NEIL1 | 15:75646087 | A →G | exonic | ER+ | A DNA repair protein in which polymorphisms and RNA-editing sites have been reported in several cancers [65] |
ZNF552 | 19:58321691 | T →C | intronic | ER+ | Zinc finger protein [68] |
ABHD2 | chr15:89744476 | G →T | 3’ UTR | ER+ | Upregulation is associated with colorectal cancer [84] |
RAB11FIP3 | chr16:548088 | A →G | intronic | ER+ | Rab11-binding protein that regulates breast cancer cell motility [34] |
SMIM11 | chr21:35761073 | G →T | 3’ UTR | TR- | Uncharacterized small integral membrane protein [34] |
PSMB2 | chr1:36068370 | T →C | 3’ UTR | TR- | A SNP, rs6661896, within this gene is associated with chronic myelogenous leukemia [11] |
TPM4 | chr19:161915020 | A →G | intronic | TR- | Upregulated in primary breast tumors compared to metastatic lesions [59] |
NOM1 | chr7:156762883 | A →G | 3’ UTR | TR- | Nucleolar Protein with MIF4G domain, involved with protein translation [68] |
NEAT1 | chr11:65208856 | A →G | intergenic | TR- | A lncRNA whose overexpression is associated with poor prognosis in squamous cell carcinoma patients [19] |
SEPT2 | chr2:242266408 | A →G | intronic | TR- | Expression is associated with hepatocellular cancer growth [16] |
LANCL2&VOPP1 | chr7:55525773 | T →C | intergenic | TR- | LANCL2 is a regulator of the oncogene AKT1[86] |
PLB2&SDS | chr12:113828961 | A →G | intergenic | TR- | Uncharacterized locus |