Table 2.
Genetic testing results
| Genetic Tests | Gene | Transcript ID | Associated conditions (Inheritance patterns) in OMIM | Variant | Amino-acid change | Hom/Het | Parental origin |
Prediction of pathogenicity |
|||
| Mutation taster | SIFT | Provean | Polyphen2 | ||||||||
| Liver Panel1 | ATP8B1 | NM _005603 | Cholestasis, benign recurrent, intrahepatic (AR); cholestasis, intrahepatic, of pregnancy, 1 (AD); cholestasis, progressive familial intrahepatic 1 (AR) | c.234C> G | p.His78Gln | Het | NA | Polymorphism | Tolerated | Neutral | Benign |
| c.1729A>G | p.Ile577Val | Het | NA | Polymorphism | Tolerated | Neutral | Possibly damaging | ||||
| c.2021T>C | p. Met674Thr | Het | NA | Polymorphism | Tolerated | Neutral | Benign | ||||
| c.3477C>T | Synonymous | Het | NA | Polymorphism | Tolerated | Neutral | NA | ||||
| c.3744C>A | Synonymous | Het | NA | Polymorphism | Tolerated | Neutral | NA | ||||
| Whole exome sequencing | MARS | NM_004990 | Charcot-Marie-Tooth disease, axonal, type 2U (AD); Interstitial lung and liver disease (AR) | c.2158C>T | p.Gln720Stop | Het | Maternal | Disease causing | NA | NA | NA |
| c.893_894insTCG | p.Arg299dup | Het | Paternal | Disease causing | NA | Deleterious | NA | ||||
| ATP8B1 | NM_005603 | Cholestasis, benign recurrent, intrahepatic (AR); cholestasis, intrahepatic, of pregnancy, 1 (AD); cholestasis, progressive familial intrahepatic 1 (AR) | c.2021T>C | p. Met674Thr | Het | Paternal | polymorphism | Tolerated | Neutral | Benign | |
| CPT1A | NM_001876 | CPT deficiency, hepatic, type IA (AR) | c.1163+5G>A | - | Het | Maternal | Disease causing | NA | NA | NA | |
| LRPPRC | NM_133259 | Leigh syndrome, French-Canadian type (AR) | c.2965C>T | p.Arg989Cys | Het | Maternal | Disease causing | Damaging | Deleterious | Probably damaging | |
| FLG | NM_002106 | Ichthyosis vulgaris (AD); (Dermatitis, atopic, susceptibility to, 2) | c.5841G>A | p.Trp1947Stop | Het | Maternal | Disease causing | NA | NA | NA | |
| G6PD | NM_00104251 | Hemolytic anemia, G6PD deficient (favism) (XLD); (Resistance to malaria due to G6PD deficiency) | c.241C>T | p.Arg81Cys | Het | Maternal | Disease causing | Damaging | Deleterious | Benign | |
| POMGNT1 | NM_017739 | Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 (AR); Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 3 (AR); Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 3 (AR); Retinitis pigmentosa 76 (AR) | c.794G>A | p.Arg265His | Het | Maternal | Disease causing | Damaging | Deleterious | Probably damaging | |
| SERPINC1 | NM_000488 | Thrombophilia due to antithrombin III deficiency (AD/AR) | c.719A>G | p.Asn240Ser | Het | Maternal | Polymorphism | Tolerated | Neutral | Benign | |
| TG | NM_003235 | Thyroid dyshormonogenesis 3 (AR); (autoimmune thyroid disease, susceptibility to, 3) | c.5791A>G | p.Ile1931Val | Het | Paternal | Polymorphism | Tolerated | Neutral | Benign | |
| USH2A | NM_206933 | Retinitis pigmentosa 39; Usher syndrome type 2A (AR) | c.8559-2A>G | - | Het | Paternal | Disease causing | NA | NA | NA | |
1
Genes included in liver panel: ATP8B1, ABCB11, ABCB4, TJP2, BAAT, CLDN1, HSD3B7, AKR1D1, CYP7B1, AMACR, CYP27A1, DHCR7, JAG1, NOTCH2, SLC25A13, DGUOK, MPV17, FAH, ABCC2, UGT1A1, NPC1, NPC2, GALT, GALE, ALDOA, ALDOB, KRT18, KRT8, CIRH1A, CFTR, GFDM1, EARS2, HSD17B4, LIPA, PEX1, PEX5, POU1F1, HESX1, SERPINA1, VIPAS39, and VPS33B. NA: Not available.