Table 1.
Pathogenicity classifications of 33 polyadenylation signal hexamer disease-associated variants in 14 genes.
| Gene | WT Hexamers | Hexamers cDNA Position | GRCh37 Position & Variation | Descriptor | Variant hexamers | CADD score | HGMD ID | Classification | Pathogenicity Criteria |
|---|---|---|---|---|---|---|---|---|---|
| BMP1 | AGTAAA | c.*239_*244 | Chr8:22058957 T > C | NM_001199.4:c.*241 T > C | AGCAAA | 17.97 | CR150372 | Likely Path | PS3_Mod, PS4_Mod, PM3_Sup, PP3, PP4 |
| F9 | AATAAA | c.*1365_*1370 | ChrX:138645597 T > G | NM_000133.4: c.*1367 T > G | AAGAAA | 5.32 | CR2219631 | VUS | PS4_Sup, PM1_Sup, PP4 |
| ChrX:138645598A > G | NM_000133.4: c.*1368A > G | AATGAA | 2.70 | CR005437 | VUS | PS4_Sup, PM1_Sup, PP4, BP4 | |||
| ChrX:138645598A > C | NM_000133.4: c.*1368A > C | AATCAA | 2.37 | CR2219630 | VUS | PM1_Sup, BP4 | |||
| FOXP3 | AATAAA | c.*873_*878 | ChrX:49106919 T > C | NM_014009.4:c.*876A > G | AATGAA | 13.02 | CR014834 | Likely Path | PS4_Mod, PM1_Sup, PP1_Strong, PP3, PP4 |
| ChrX:49106917 T > C | NM_014009.4:c.*878A > G | AATAAG | 12.77 | CR097218 | VUS | PS3_Sup, PS4_Sup, PM1_Sup, PP3, PP4 | |||
| HBA2 | AATAAA | c.*89_*94 | Chr16:223690-223691del | NM_000517.4:c.*91_*92del | AAAAGT | 12.61 | CD2026691 | VUS | PS4_Sup, PM1_Sup, PP3, PP4 |
| Chr16:223691A > G | NM_000517.4:c.*92A > G | AATGAA | 11.73 | CR920785 | Likely Path | PS4_Mod, PM1_Sup, PM3_Sup, PM5_Sup, PP1_Mod, PP3, PP4 | |||
| Chr16:223692-223693del | NM_000517.6:.*93_*94del | AATAGT | 11.84 | CD941949 | Likely Path | PS4_Mod, PM1_Sup, PM3, PM5_Sup, PP3, PP4 | |||
| Chr16:223693A > G | NM_000517.6:c.*94A > G | AATAAG | 12.77 | CR830007 | Pathogenic | PS3_Sup, PS4, PM1_Sup, PM3, PP3, PP4 | |||
| Chr16:223693A > C | NM_000517.6:c.*94A > C | AATAAC | 12.24 | CR106042 | Likely Path | PM1_Sup, PM3, PM5_Sup, PP3, PP4 | |||
| HBB | AATAAA | c.*108_*113 | Chr11:5246720 T > G | NM_000518.5:c.*108A > C | CATAAA | 15.14 | CR016252 | VUS | PS4_Sup, PM1_Sup, PP3 |
| Chr11:5246720 T > C | NM_000518.5: c.*108A > G | GATAAA | 15.27 | CR127145 | VUS | PS4_Mod, PM1_Sup, PP3, PP4 | |||
| Chr11:5246718A > T | NM_000518.5:c.*110 T > A | AAAAAA | 14.07 | CR045224 | VUS | PS4_Sup, PM1_Sup, PM5_Sup, PP3, PP4 | |||
| Chr11:5246718A > G | NM_000518.5:c.*110 T > C | AACAAA | 14.17 | CR850010 | Pathogenic | PS3_Sup, PS4, PM1_Sup, PM3, PM5_Sup, PP1, PP3, PP4 | |||
| Chr11:5246718A > C | NM_000518.5:c.*110 T > G | AAGAAA | 14.03 | CR014260 | VUS | PS4_Sup, PM1_Sup, PM5_Sup, PP3, PP4 | |||
| Chr11:5246717-5256718del | NM_000518.5:c.*110_*111del | AAAAAA | 13.15 | CD951735 | VUS | PS4_Sup, PM1_Sup, PM5_Sup, PP3, PP4 | |||
| Chr11:5246714-5246718del | NM_000518.5:c.*110_*114del | AAAACA | 14.11 | CD920867 | Likely Path | PS3_Sup, PS4_Mod, PM1_Sup, PM3_Sup, PM5_Sup, PP3, PP4 | |||
| Chr11:5246717 T > C | NM_000518.5:c.*111A > G | AATGAA | 14.04 | CR900265 | Pathogenic | PS4, PM1_Sup, PM3, PM5_Sup, PP3, PP4 | |||
| Chr11:5246716 T > C | NM_000518.5:c.*112A > G | AATAGA | 14.73 | CR900266 | Likely Path | PM1_Sup, PM3, PM5_Sup, PP3, PP4 | |||
| Chr11:5246716 T > A | NM_000518.5:c.*112A > T | AATATA | 14.64 | CR057232 | VUS | PS4_Sup, PM1_Sup, PP3, PP4 | |||
| Chr11:5246715 T > C | NM_000518.5:c.*113A > G | AATAAG | 13.23 | CR880076 | Pathogenic | PS3_Sup, PS4, PM1_Sup, PM3, PP3, PP4 | |||
| HBD | AATAAA | c.*106_*111 | Chr11:5254085 T > A | NM_000519.4: c.*109A > T | AATTAA | 13.00 | CR109506 | VUS | PS4_Sup, PM1_Sup, PP3, PP4 |
| IL2RG | AATAAA | c.*303-*308 | ChrX:70327278 T > C | NM_000206.3: c.*308A > G | AATAAG | 15.05 | CR0910465 | VUS | PS3_Sup, PS4_Sup, PM1_Sup, PP3, PP4 |
| INS | AATAAA | Chr11:2181023 T > C | NM_000207.2:c.*59A > G | AATAAG | 12.87 | CR101141 | VUS | PS3_Sup, PS4_Sup, PM1_Sup, PP3 | |
| ITGA2B | AATAAA | c.*163_*168 | Chr17:42449567A > G | NM_000419.5c.*165 T > C | AACAAA | 12.82 | CR153724 | VUS | PS4_Sup, PM1_Sup, PP3 |
| NAA10 | AATAAA | c.*38_*43 | ChrX:153195400 T > C | NM_003491.4:c.*39A > G | AGTAAA | 12.95 | CR1913378 | Likely Path | PS3_Sup, PS4_Sup, PM1_Sup, PP1_Mod, PP3 |
| ChrX:153195401 T > C | NM_003491.4:c.*40A > G | GATAAA | 14.35 | CR1913377 | VUS | PS4_Sup, PM1_Sup, PP3 | |||
| ChrX:153195397 T > C | NM_003491.4:c.*43A > G | AATAGA | 14.18 | CR1913376 | Likely Path | PS3_Sup, PS4_Sup, PM1_Sup, PP1_Strong, PP3 | |||
| RNASEH2C | AATAAA | c.*78_*83 | Chr11:65487176 T > C | NM_032193: c.*78A > G | GATAAA | 16.68 | CR2027419 | VUS | PS4_Sup, PM1_Sup, PP3 |
| STUB1 | AATAAA | c.*238_*243 | Chr16:732729 T > C | NM_005861.3c.*240 T > C | AACAAA | 14.22 | CR1815154 | VUS | PS3_Sup, PS4_Sup, PM1_Sup, PP1, PP3 |
| UROD | AATAAA | c.*57_*62 | Chr1:45481230-45481231del | NM_000374.4:c.*62_*63del | AATAAG | 12.67 | CD122215 | VUS | PS4_Sup, PM1_Sup, PP3 |
| GLA | ATTAAA | c.1272_1277 | ChrX:100652809-810del | NM_000169.2:c.1277_1278del | ATTAGA | 23.7 | CD031841 | VUS | PS3_Sup, PS4_Sup, PM1_Sup, PP3, PP4 |