Table 2.
mtDNA variants identified by NGS in p.E99K-ACTC1 isogenic lines used for HCM modeling (WT, healthy; het, heterozygous). In silico pathogenicity prediction algorithms used: § MitoTIP; * Polyphen-2; † CAROL; ‡ APOGEE. Phenotypically severe hPSC-CM line is highlighted in red and less severe ones in green.
| Isogenic hPSC-CM Set(s) | Locus | mtDNA Mutation | Percent Heteroplasmy (WT-Het) | In silico Prediction (Score) | Potential HCM Effect |
|---|---|---|---|---|---|
| E99K1 | MT-HV2, MT-OHR | m.152T > C | 99.3–99.9 | N/A (non-coding) |
Aggravator (present only in E99K1) |
| E99K1 | MT-HV2, MT-OHR, MT-CSB2 | m.309_310insCT | 15.3–25.3 | N/A (non-coding) |
Aggravator (present only in E99K1) |
| E99K1 | MT-HV2, MT-OHR, MT-CSB2 | m.309_310insCCT | 18.8–9.3 | N/A (non-coding) |
Aggravator (present only in E99K1) |
| E99K1 + NC-EDIT-E99K + E99K2 | MT-HV2, MT-OHR, MT-CSB2 | m.310T > C |
E99K1: 60.6–59.9 NC-EDIT-E99K: 17.0–16.3 E99K2: 17.5–16.4 |
N/A (non-coding) |
Aggravator (more prevalent in E99K1) |
| E99K1 + NC-EDIT-E99K + E99K2 | MT-HV2, MT-OHR, MT-CSB2 | m.310_311insC |
E99K1: 26.6–27.2 NC-EDIT-E99K: 61.6–62.7 E99K2: 63.6–61.7 |
N/A (non-coding) |
Protective (less prevalent in E99K1) |
| E99K1 + NC-EDIT-E99K + E99K2 | MT-TA | m.5597A > C |
E99K1: 9.6–9.6 NC-EDIT-E99K: 7.5–6.9 E99K2: 10.2–7.1 |
Possibly pathogenic (73.80%) § | None (present in all lines) |
| NC-EDIT-E99K + E99K2 | MT-ATP6 | m.8952T > C |
NC-EDIT-E99K: 99.9–99.9 E99K2:100–99.9 |
N/A (redundant) |
Protective (absent in E99K1); |
| E99K1 | MT-ATP6 | m.9116T > C | 100–99.5 | Benign (0.000) * Neutral (0.8) † Neutral (0.42) ‡ |
None (benign mutation) |
| E99K1 | MT-ND4 | m.11176G > A | 99.9–99.2 | N/A (redundant) |
Aggravator (only present in E99K1) |
| NC-EDIT-E99K + E99K2 | MT-ND5 | m.12715A > G |
NC-EDIT-E99K: 99.8–99.8 E99K2: 99.9–99.7 |
Benign (0.1) * Neutral (0.47) † Neutral (0.28) ‡ |
Protective (absent in E99K1) |