Clinical, genetic and functional perspectives on ATP-binding cassette subfamily B member 4 variants in five cholestasis adults

Table 1 Clinical features of five patients and the corresponding ATP-binding cassette subfamily B member 4 mutations

No.	Gender	Age at first presentation	Clinical manifestation	Biochemical examination, (maximal value)	Abdominal enhanced, CT scan	MRCP	Pathological features1	Pathological score	CK7	IHC5	Therapy	Outcome on 2024
1	M	24	Haematemesis, Hematochezia, Cholelithiasis	TB 175, ALT 512, ALP 883, GGT 713, TBA 54	Liver cirrhosis, Megalosplenia, ascites	Cholecystitis, Cholelithiasis, Choledocholithiasis	Ductopenia, cholestasis, hepatic fibrosis	G1S4	(+)	Normal	UDCA, transmetil, glycyrrhein	Died
2	M	21	Scleral icterus, Hepatic dysfunction	TB 29, ALT 159, ALP 346, GGT 1016, TBA 59	Cholecystitis, splenomegaly	Intrahepatic bile duct dilatation	Bile duct hyperplasia	G2S2	(-)	Normal	UDCA, transmetil, Fenofibrate, glycyrrhein	Alive
3	M	18	Hepatic dysfunction, Pruritus, Cholestasis	TB 26, ALT 117, ALP 163, GGT 321, TBA 48	Cholangiectasis	Cholangiectasis	Bridging fibrosis, Ductopenia	G1S3	(+)	Decrease	UDCA, transmetil, glycyrrhein	Alive
4	M	31	Hepatic dysfunction, abdominal distention, jaundice	TB 7, ALT 80, ALP 139, GGT 309	Hepatic cyst, splenomegaly	/	/	/	/	/	UDCA, transmetil, glycyrrhein	Alive
5	F	38	Hepatic dysfunction, abdominal distention, edema	TB 72, ALT 52, ALP 528, GGT 233, TBA 257	Splenectomy, Esophageal and gastric varices, liver cirrhosis	Mild dilation of bile duct	Ductopenia, portal inflammation	G2S4	(+)	Decrease	UDCA, Transmetil, glycyrrhein	Alive

¹It represents the hematoxylin-eosin staining characteristics of liver biopsy.

Reference value: Total bilirubin 3-19 μmol/L, glutamic pyruvic transaminase: 5-40 U/L, aspartate aminotransferase: 5-40 U/L, alkaline phosphatase: 35-135 U/L, GGT: 0-50 U/L, TBA: 0-13 μmol/L. The pathological diagnosis was based on the Scheuer score. ALP: Alkaline phosphatase; ALT: Glutamic pyruvic transaminase; GGT: Glutamyl transpeptidase; TB: Total bilirubin; TBA: Total bile acids; CK7: Cytokeratin 7; IHC: Immunohistochemistry; UDCA: Ursodeoxycholic acid; CT: Computed tomography; MRCP: Magnetic resonance cholangiopancreatography; M: Male; F: Female; /: No data.

Table 2 Analysis of ATP-binding cassette subfamily B member 4 variants and corresponding pathogenicity in five patients

No.	Zygosity of variant	Nucleotide change	Amino acid change	Reference sequence	Location	Domin	Minor allele frequency	SIFT	PolyPhen-2 (HumDiv)	MutPred-2	NNSplice	Mutation Taster	VASOR	Classification according to ACMG
1	Composite heterozygosity	c.2362C>T, c.2777C>T	p.R788W, p.P926 L	NM_000443.3	Exon20, Exon22	IC4, IC5	2.48e-6, -	0.00, 0.01	1, 0.961	0.904, 0.617	-, -	-, -	0.851, 0.876	Uncertain significance (PS3 + PP3), Uncertain significance (PM2 + PP3)
2	Heterozygosity	c.2362C>T, c.537-32G>T	p.R788W, -	NM_000443.3	Exon20, Intron6	IC4, NA	2.48e-6, -	0.00, -	1, -	0.904, -	-, splicing donor loss	-, Pathogenic	0.851, -	Uncertain significance (PS3 + PP3), Uncertain significance (PM2 + PP3)
3	Heterozygosity	c.1865G>A	p.G622E	NM_000443.3	Exon15	IC3	1.24e-6	0.00	0.921	0.83	-	-	0.915	Uncertain significance (PP3)
4	Heterozygosity	c.1757T>A	p.V586E	NM_000443.3	Exon15	NBD1	-	0.02	0.999	0.873	-	-	0.757	Uncertain significance (PM2 + PP3)
5	Heterozygosity	c.3250C>T, c.C504T	p.R1084W, p.N168N	NM_000443.3	Exon25, Exon6	NBD2, Cytoplasmic	3.10e-6, 0.475	0.00, -	1, -	0.807, -	-, -	-, polymorphism	0.857, -	Uncertain significance (PM2 + PP3), Benign (BA1 + BP4 + BP7)

Minor allele frequency is sourced from gnomAD Database, with samples from at least 25 different countries/regions, mainly from Europe and South Asia. SIFT: A predicted score of less than or equal to 0.05 indicates that the mutation will affect protein function, while a score greater than 0.05 indicates that the effect on the protein is tolerable. PolyPhen-2: The range of predicted values is from 0 to 1. If > 0.5, the mutation is predicted to be harmful, and if < 0.5, it is predicted to be benign. MutPred-2: The general score indicates the pathogenicity of a given variant, ranging from 0 to 1. The higher the score, the greater the pathogenicity tendency. Generally, a score greater than 0.5 is considered a pathogenic mutation. “-”does not affect amino acids or the software is not suitable for this type of mutation. Vasor: It gives out a probability of pathogenicity, which can range from 0 (likely benign) to 1 (likely pathogenic). NBD1: Nucleotide binding domain; TMD: Transmembrane domain; IC: Intracytoplasmic.