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Table 2 ‘Pathogenic’ or ‘Likely pathogenic’ genomic variations identified in Indian patients with PFIC syndrome

From: Spectrum of genomic variations in Indian patients with progressive familial intrahepatic cholestasis

Gene showing sequence variation Subject ID History of consanguinity Nature of variation Nucleotide change Type of mutation AA change In silico prediction Inclusion in databasesa Population frequency (in ExAC)
‘Pathogenic’/ likely pathogenic variations  
ATP8B1 PF05 Yes Homozygous c.[589_592inv;592_593insA]
GGAG CTCCA
Frame-shift; truncation after 205 amino acids p.Gly197LeufsTer10 Deleterious Novelb  
PF20 No Homozygous c.1587_1589delCTT
CTT  -
In-frame deletion of one amino acid p.Phe529del Deleterious rs756395915, 18:55351308 CAAG/C 8.24 × 10− 6
PF19 Yes Homozygous c.1660G > A Mis-sense (GATAAT) p.Asp554Asn Deleterious rs121909101, CM004386
ClinVar:7269
 
PF18 No Homozygous c.2941G > A Mis-sense (GAGAAG) p.Glu981Lys Deleterious CM096608  
ABCB11 PF03 Yes Homozygous c.548 T > C Mis-sense (ATG  ACG) p.Met183Thr Deleterious CM103530  
PF13 Yes Homozygous c.1360delG Truncation after 453 amino acids p.Val454* Deleterious Novel  
ABCB4 PF25 Yes Homozygous c.431G > A Mis-sense (CGA  CAA) p.Arg144Gln Likely deleterious rs863225299,
ClinVar:217883
3.3 × 10− 5
Variation of ‘uncertain significance’  
ABCB11 PF21 No Heterozygousc c.784 + 1 G > C Splice site variation Possible abnormal splicing Deleterious Novel  
ABCB4 PF09 No Heterozygous c.475C > T Truncation after 474 amino acids (CGA  TGA) p.Arg159* Deleterious rs377160065,
CM075939, 7:87082321 G/A
3.2 × 10− 5
  1. aThis column shows identification details of the particular sequence variant in large-scale human mutation databases, i.e. dbSNP, ExAC, HGMD and ClinVar
  2. bThis variation found in our cohort has also been reported as a single case report previously [16]
  3. cThis patient also had homozygous p.Val444Ala variation in ABCB11 gene
  4. None of the nine variations shown in this table was found in 1000 genome database