Table 1. SNP haplotypes, methylation and expression/splicing status of DUSP22 and its paralog.
| DUSP22 (6p25.3) | 16p11.2 paralog | |
|---|---|---|
| SNPs alleles | ||
| rs11242812 | G | A |
| rs1129085 | G and/or A | G |
| rs1046656 | C | T |
| Methylation status (5′ CpG island) | No methylation$($ in normal tissues & tested PTCL cases) | Methylated‡ (‡ if not deleted in the 5′ region) |
| Expression | Expressed in normal tissues& PTCL without 6p25.3 rearrangement Silenced in PTCL with 6p25.3 break | Completely silent or hypomorphic |
| Isoforms | Alternative mRNA splicing | Not detected (expression absent or very weak) |
| Regular splicing, 8 coding exons Protein: 184 a.a. Expressed at the RNA level in PBL Silenced in PTCL with 6p25.3 break | Not detected | |
| Intron 7 not spliced, leading to alternative reading frame, exon 8 then being in the 3′ UTR Predicted protein: 205 a.a., p.A170fs37* Predominant in normal PBL Silenced in PTCL with 6p25.3 break | Not detected | |
| Exon 4 spliced, leading to frameshift Predicted protein: 54 a.a., p.G47fs9* Expressed at the RNA level in PBL Silenced in PTCL with 6p25.3 break Not detected at the protein level | Not detected |
Legends: The SNP haplotypes, methylation and expression status of DUSP22 and its 16p11.2 are summarized here. For isoforms, the splicing events and the predicted consequence at the protein levels (number of amino acids -a. a.- and when there is a alternative reading frame, position of the first amino acid affected by frameshift –fs-, and number of alternative amino acids before the STOP codon -*-). UTR, untranslated region; PTCL, peripheral T-cell lymphomas; PBL, normal peripheral blood lymphocytes.