Whole-exome sequencing result of the variants of ABC transporters’ genes in 151 ICP samples
Totally ABC transporters covering 44 genes went through targeted WES to identify variants in a cohort of 151 patients with ICP disease. Overall, we identified 2953 genetic variants, including 1254 mutations in 12 ABCA genes which consisted of ABCA1 -ABCA10 ,ABCA12 -ABCA13 , 479 variants in ABCB1 ,ABCB4 -ABCB11 , 812 genetic variants in eleven genes covering ABCC1 -ABCC6 , ABCC8 -ABCC12 , 408 variants in ABCD-ABCG series genes. These types of variants covered 2057 intron, 297 synonymous, 76 splice, 13 stop gained /start lost, 36 3’ primer UTR, 21 5’ primer UTR, 10 downstream gene, 32 upstream gene, 3 structural interaction and 408 missense. The percentage of these types of variants is shown in Figure S1A (See Supplementary material). After quality control (MAF < 0.01 in all databases), 42 out of 320 variants were detected which was first reported, including 17 out of 146 variants in ABCA genes, 10 out of 59 in ABCB, 9 out of 71 in ABCC and 6 out of 44 in ABCD-ABCG genes (See Supplementary material, Figure S1B).
For these 42 novel mutations, we classified these mutations as four echelons (damaging, probable damaging, possible damaging and neutral) according to prediction results (Table 1). Damaging group have fifteen mutation, which contained 7 mutations in three known functional genes associated with ICP disease, such as ABCB4 Trp708Ter, Gly527Glu and Lys386Glu, ABCB11 Gln1194Ter, Gln605Pro and Leu589Met, andABCC2 Ser1342Tyr (Data has shown in our previous ). Besides, 8 functional mutations in other ABC genes, i.e. ABCA4 Phe754Ser,ABCA12 Cys2440Tyr, ABCA13 Ser3286Ter, ABCB1Pro693Ser, ABCB5 Ser925Ile, ABCC3 Ile1147Thr, ABCC9Ala456Thr and ABCG2 Leu646Met. The frequency of these mutations in 151 ICP samples reached 10.60% (16/151). Moreover, they are absent in 1029 local healthy women. Therefore, significantly difference in frequency between cases and control groups (P = 1.10E-14).
Twenty-one mutations were assigned to the second tier (probable damaging), including 9 in ABCA genes (ABCA2 Asp1108Glu and Ala583Val, ABCA5 Val997Ala, ABCA7 Pro449His, ABCA8Val8Ala, ABCA10 Leu260Ser, ABCA12 Ile1022Thr,ABCA13 Leu4624Val and Thr4912Ala), Glu386Lys and Ile339Val in all in ABCB9 gene, 6 in ABCC series genes (ABCC1 Ser497Gly,ABCC3 Leu137Phe, ABCC5 Gln851Pro, ABCC6 His1043Gln,ABCC9 Glu1034Val and ABCC12 Pro37Ser), ABCD4Ser395Phe and Thr385Ala, ABCF2 Gly47Ser and ABCG1Ile273Val in ABCD-ABCG series genes. These mutations were also absent in controls. The MAF in these mutations between cases and controls showed a significant difference (P = 2.20E-16).
We identified five possible potential pathogenic mutations associated with ICP disease, including ABCA3 Ser593Gly, ABCA10Leu823Val, ABCA12 Asn2492Ser, ABCA13 Ser3111Asn andABCG1 Thr378Ile. Only one mutation was divided into neutral group. 42 mutations in all were absent in the databases, including 1000 Genome Project, ExAC, dbSNP, ChinaMAP and 1029 local controls.