Table 3.
Significant variants with pathogenicity classification detected using the NEOseq_ACTION panel
| Case No. | Gene symbol | Transcript | Nucleotide change | Amino acid change | Zygosity | Variant classification by MedyPatho | Segregation | Clinical validation | Final classification | ACMG evidences* |
|---|---|---|---|---|---|---|---|---|---|---|
| P2 | GALNS | NM_000512.4 | c.319G >A | p.Ala107Thr | Het | LP | Trans | Serum galactose-6-sulfatase 0.37 nmol/17 hr/mg protein (ref, 18.6–61.8) | LP | PM2, PM3, PP3, PP5 |
| GALNS | NM_000512.4 | c.451C >A | p.Pro151Thr | Het | LP | LP | PM1, PM2, PM5, PP3, PP5 | |||
| P5 | ACADS | NM_000017.2 | c.1031A >G | p.Glu344Gly | Het | LP | Not done | Serum C4 1.995 μmol/L (cut off, 0.41) | LP | PM1, PM2, PP3, PP5 |
| ACADS | NM_000017.2 | c.164C >T | p.Pro55Leu | Het | LP | LP | PS3, PM2, PP5 | |||
| P6 | PCCA | NM_000282.3 | c.1846-2A >G | p? | Het | LP | Trans | Urine propionylglycine 80.0 (ref, not detected) | LP | PVS1, PM2 |
| PCCA | NM_000282.3 | c.938G >C | p.Arg313Pro | Het | VUS† | LP† | PM2, PM3, PM5, PP3 | |||
| P10 | PAH | NM_000277.1 | c.975C >G | p.Tyr325* | Het | P | Not done | Serum phenylalanine 163 μmol/L (ref, 13–91) | P | PVS1, PM2, PP5 |
| PAH | NM_000277.1 | c.158G >A | p.Arg53His | Het | VUS | VUS | BS2, PM5 | |||
| P14 | SLC25A13 | NM_014252.3 | c.852_855delTATG | p.Met285Profs*2 | Het | P | Not done | Serum citrulline 378 μmol/L (ref, 8–36) | P | PVS1, PM2, PP5 |
| SLC25A13 | NM_014252.3 | c.1177+1G >A | p? | Het | P | P | PVS1, PM2, PP5 | |||
| P25 | ACADM | NM_000016.4 | c.1189T >A | p.Try397Asn | Het | LP | Trans | Serum C6 0.145 μmol/L (cut off < 0.1), C8 0.26 μmol/L (cut off < 0.18), C10:1 0.16 μmol/L (cut off < 0.13) | LP | PM2, PM5, PP2, PP3, PP4, PP5 |
| ACADM | NM_000016.4 | c.1231G >T | p.Val411Leu | Het | VUS† | LP† | PM2, PM3, PP2, PP4 | |||
| P36 | ACADM | NM_000016.4 | c.1189T >A | p.Tyr397Asn | Het | LP | Not done | Serum C6 0.64 μmol/L (cut off < 0.1), C8 1.59 μmol/L (cut off < 0.12), C10:1 0.45 μmol/L (cut off < 0.08) | LP | PM2, PM5, PP2, PP3, PP4, PP5 |
| ACADM | NM_000016.4 | c.91C >T | p.Arg31Cys | Het | VUS† | LP† | PM2, PM5, PP2, PP4, PP5 | |||
| P40 | MCCC2 | NM_022132.4 | c.838G >T | p.Asp280Tyr | Het | LP | Not done | Urine 3-hydroxyisovaleric acid 1,731.1 mmol/mol Cr (ref, < 18) | LP | PM2, PP2, PP3, PP4, PP5 |
| MCCC2 | NM_022132.4 | c.1342G >A | p.Gly448Arg | Het | VUS† | LP† | PM2, PP2, PP3, PP4, PP5 | |||
| P41 | PREPL | NM_006036.4 | c.1979_1980del | p.Leu660Glnfs*9 | Het | LP† | Trans | Repetitive nerve stimulation test, insignificant | P† | PVS1, PM2, PM3 |
| PREPL | NM_006036.4 | c.1747-9_1747del | p? | Het | LP† | P† | PVS1, PM2, PM3 | |||
| P45‡ | HBA2 | NM_000517.4 | c.427T >C | p.*143Qext*31 | Hem | LP | Not done | Not done | LP | PM2, PM3, PM4 |
| P46 | PHKA2 | NM_000292.2 | c.1246-2A >G | p? | Hem | LP | Not done | GOT/GPT 59/49 IU/L (ref, 1–40/1–40) | LP | PVS1, PM2 |
| P72 | ACADS | NM_000017.2 | c.164C >T | c.Pro55Leu | Hom | LP | Not done | Serum C4 0.805 μmol/L (ref, < 0.41) | LP | PS3, PM2, PP5 |
| P74 | ACADS | NM_000017.2 | c.1031A >G | p.Glu344Gly | Het | LP | Not done | Serum C4 0.905 μmol/L (ref, < 0.41) | LP | PM1, PM2, PP3, PP5 |
| ACADS | NM_000017.2 | c.1130C >T | p.Pro377Leu | Het | LP | LP | PM1, PM2, PP3, PP5 | |||
| P83 | ACADS | NM_000017.2 | c.1031A >G | p.Glu344Gly | Hom | LP | Not done | Serum C4 1.965 μmol/L (ref, < 0.41) | LP | PM1, PM2, PP3, PP5 |
| P111 | PAH | NM_000277.1 | c.1068C >G | p.Tyr356* | Het | P | Not done | Serum phenylalanine 173 μmol/L (ref, 25–74) | P | PVS1, PM2, PP5 |
| PAH | NM_000277.1 | c.158G >A | p.Arg53His | Het | VUS | VUS | BS2, PM5 |
*All variants were assessed based on the ACMG or Association for Molecular Pathology guidelines [17]; †Initial classification using MedyPatho was changed at final classification; ‡Given the high homology between HBA1 and HBA2 and that common deletions account for 85% of pathogenic variants in alpha thalassemia, Sanger sequencing and multiplex ligation probe amplification were performed to confirm the variant. This patient had a heterozygous common–SEA deletion; thus, the zygosity of the c.427T>C variant was determined to be hemizygous.
Abbreviations: ACMG, American College of Medical Genetics and Genomics; Het, heterozygous; Hem, hemizygous; Hom, homozygous; LP, likely pathogenic; P, pathogenic; VUS, variant of unknown significance; ref, reference range.