Novel methionyl-tRNA synthetase gene variants/phenotypes in interstitial lung and liver disease: A case report and review of literature

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

¹Genes 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.