Table 4 Loss of function variants identified in the five gene candidates.

Phenotype	Gene	Transcript	Protein change	Info	gnomAD AF	G&H AF^	ACMG-AMP	ACMG-AMP criteria	Clinvar
ICP	ABCB4	ENSP00000395716.1:p.Ser99LeufsTer11	S99x	Frameshift	0.00039970	0.00336538	P	PVS1, PM2, PP3
		ENSP00000392983.1:p.Leu759TyrfsTer38	F758x	Frameshift		0.00009610	LP	PVS1, PM2
		ENSP00000392983.1:p.Lys30GlyfsTer7	Lys30Glyfster7	Frameshift	0.00000408	0.00020243	LP	PVS1, PM2
		ENSP00000392983.1:p.Arg595Ter	R595*	Stop-gained	0.00001627	0.00009593	P	PVS1, PM2, PP3, PP5	Pathogenic
Gallstone disease	ABCB11	ENSP00000497931.1:p.Ala1044LeufsTer53	A1044x	Frameshift		0.00009562	P	PVS1, PM2, PP3
		ENST00000263817.7:c.2611-2A > T	c.2611-2A > T	Splice-acceptor-variant	0.00000407	0.00057870	P	PVS1, PM2, PP3
		ENSP00000497931.1:p.Trp239Ter	W239x	Stop-gained		0.00009566	P	PVS1, PM2, PP3
	ATP8B1	ENSP00000283684.4:p.Gln1179GlufsTer56	IQ1178-1179IX	Frameshift_variant & splice_region_variant		0.00193798
		ENSP00000283684.4:p.Pro792HisfsTer8	F791X	frameshift_variant		0.00019069	P	PVS1, PM2, PP3
Gallstone disease		ENST00000283684.9:c.182-4_183del	?-61	Splice_acceptor_variant & coding_sequence_variant & intron_variant		0.00048956
		ENSP00000283684.4:p.Glu20Ter	E20*	Stop_gained		0.00009566	P	PVS1, PM2, PP3
	NR1H4	ENSP00000446760.1:p.Lys4Ter	K4*	Stop_gained		0.00014188	P	PVS1, PM2, PP3
	TJP2	ENSP00000438262.1:p.Glu44Ter	E44*	Stop_gained		0.00009604	LP	PVS1, PM2
	TJP2	ENSP00000345893.4:p.Gly5ArgfsTer26	M1MPVX	Frameshift_variant & start_lost	0.00001343	0.00029768	P	PVS1, PM2, PP3

AF allele frequency, ACMG-AMP American College of Medical Genetics and Genomics and the Association for Molecular Pathology, BP benign supporting, PM pathogenic moderate, PP pathogenic supporting, G&H Genes & Health, LP likely pathogenic, P pathogenic.
^Allele frequency specific to East London Genes & Health cohort.

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