Clinical spectrum and genotype-phenotype correlation of ABCB4 mutations in children: Insights from a North Indian cohort

Table 1 Comparison of clinical, laboratory and genetic parameters between bi-allelic and monoallelic ABCB4 mutations, median (interquartile range)

Parameters	Homozygous/compound HET mutation (n = 16)	HET mutation (n = 10)	P value
General characteristics
Male gender	62.5%	60%	1.00
Median age at symptom onset in months	54 (4, 168)	10.5 (5, 72)	0.40
Median age at presentation in months	60 (4, 172)	18 (11, 126)	0.42
Consanguinity	37.5%	10%	0.19
Positive family history	75%	30%	0.04
Sibling loss	43.8%	33.3%	0.69
Anthropometry
Weight Z-score at admission	-1.09 (-2.03, -0.21)	-1.39 (-2.61, 0.10)	0.97
Height Z-score at admission	-0.91 (-2.72, -0.52)	-2.1 (-3.33, 0.03)	0.57
Weight Z-score at last follow up	-0.42 (-1.29, -0.125)	-0.58 (-1.63, 1.31)	0.90
Height Z-score at last follow up	-0.37(-1.83, 0.33)	-0.76 (-2.23, 0.91)	0.86
Clinical parameters at admission
Jaundice	68.8%	90%	0.35
Pruritus	68.8%	80%	0.66
Ascites	43.2%	0%	0.02
Gastrointestinal bleed	12.5%	0%	0.5
Decompensation at admission	43.8%	0%	0.02
Esophageal varix			0.009
No varix	20%	87.5%
Small varix	40%	12.5%
Large varix	40%	0
Genetics
Missense variants	81.3%	80%	1.00
Recent American College of Medical Genetics class likely pathogenic or pathogenic	100%	30%	< 0.001
Laboratory parameters
First visit
Platelets (× 109/L)	162 (64, 230)	415 (167, 577)	0.007
TB (mg/dL)	2.58 (1.6, 6.7)	3.84 (1.59, 8.27)	0.56
DB (mg/dL)	1.3 (0.71, 4.1)	2.15 (1.08, 4.14)	0.59
AST (U/L)	198 (116, 287)	124.5 (90.75, 238)	0.29
ALT (U/L)	120 (64, 201)	64.5 (37.25, 118.25)	0.06
ALP (U/L)	318 (280, 550)	296 (205.25, 384)	0.15
GGT (U/L)	171 (94, 450)	38 (17, 148.5)	0.007
Prothrombin time	76 (57.5, 100)	100 (88, 100)	0.12
INR	1.27 (1, 1.58)	1.04 (0.97, 1.11)	0.10
Bile acids (µmol/L)	139.5 (33.4, 174.2)	206 (80, 335)	0.24
At last visit
TB (mg/dL)	3.84 (0.94, 15.09)	0.42 (0.28, 2.65)	0.003
DB (mg/dL)	1.87 (0.33, 8.36)	0.09 (0.09, 1.9)	0.007
AST (U/L)	247 (106.7, 462.2)	41 (35.2, 110.2)	0.004
ALT (U/L)	131 (53.5, 140.5)	33 (25.4, 55.5)	0.003
ALP (U/L)	329 (176, 719)	265 (169.5, 461)	0.61
GGT (U/L)	146 (95, 310)	11 (10.25, 13.5)	0.003
INR	1.20 (1.08, 1.69)	1.02 (1, 1.16)	0.01
Total duration of follow up in months	28.5 (3.7, 59)	23 (11.7, 60)	0.61
Outcomes	31.3%	20%	0.66
Progressive disease (death, decompensated disease, uncorrectable coagulopathy at last follow-up)	68.8%	20%	0.01
Mortality	31.3%	20%	0.34

Mann-Whitney U test was applied for non-parametric quantitative variables, and χ²/Fisher's exact test was applied for qualitative variables. ALP: Alkaline phosphatase; AST: Aspartate aminotransferse; ALT: Alanine aminotransferse; DB: Direct bilirubin; GGT: Gamma-glutamyltransferase; HET: Heterozygous; INR: International normalised ratio; TB: Total bilirubin.

Table 2 Clinical characteristics of patients with biallelic ABCB4 mutations (n = 16)

Patient	Gender	Age at symptom onset (months)	Age at first presentation (months)	Consanguinity	Family history	Anthropometry (weight/height)	Clinical features	Disease status at presentation	Esophageal varix	Type of ABCB4 mutation	Disease status at last follow-up	Issues at last follow up	Final outcome at last follow-up
P1	Male	22	24	Yes	Yes	-0.34Z, -0.55Z	HSM	C	Small varix	Homozygous	S	PH	Alive
P2 (sibling of P1)	Male	6	60	Yes	Yes	0.21Z, -0.52Z	J, P, HSM	C	Large varix	Homozygous	S	PH	Alive
P3	Male	6	9	No	Yes	NA	HSM, P	C	No varix	Homozygous	W	PH, INR > 1.5	Alive
P4	Male	6	24	No	No	-1.42Z, -0.87Z	P, HSM	C	No varix	Homozygous	S		Alive
P5	Male	96	96	No	Yes	-0.17Z, 0.09Z	A, HSM	D	Large varix	Homozygous	S	PH, recurrent acute kidney injury and nephrotic range proteinuria	Alive
P6 (sibling of P5)	Female	168	172	No	Yes	-0.75Z, -1.11Z	J, P, A, HSM, E, B	D	Large varix	Homozygous	W	PH, INR > 1.5	Expired post LT (primary graft non-function)
P7	Male	120	120	Yes	Yes	-3.59Z, -2.70Z	J, P, A, HSM	C	Large varix	Homozygous	W	PH, INR > 1.5, E	Expired after 3 years of (LT (acute rejection)
P8	Female	58	60	No	No	0.06Z, -0.72Z	J, P, HSM, A, B	D	Small varix	Homozygous	W	INR > 1.5	Alive
P9	Female	6	48	No	Yes	-2.9Z, -2.72Z	J, P, HSM	C	Small varix	Homozygous	W	PH, E	Expired
P10 (sibling of P9)	Male	12	34	No	Yes	-2.5Z, -3.14Z	J, P, HSM	C	Large varix	Homozygous	W	PH	Alive
P11	Female	84	108	Yes	Yes	-0.02Z, -0.91Z	J, P, A, HSM	D	Small varix	Homozygous	W	PH, INR > 1.5, MRCP-sclerosing cholangitis	Expired
P12	Female	120	144	No	Yes	NA	J, HSM	C	Small varix	Homozygous	W	PH, B, INR > 1.5	Alive
P13	Male	60	60	Yes	Yes	-1.36Z, -3.46Z	J, A, HSM	D	Small varix	Homozygous	S		Alive
P14	Male	80	83	No	No	-0.77, 0.35	J, P	C	Large varix	Homozygous	W	PH, INR > 1.5	Alive
P15	Male	4	4	No	Yes	NA	J, HSM	C	Not done	Compound HET	W	PH, INR > 1.5, E, acute-on-chronic liver failure	Expired
P16	Male	50	52	No	No	-1.94Z, -3.07Z	P, HSM, A	D	No varix	Compound HET	S	Nephrotic range proteinuria (carries additional X-linked FLNA mutation)	Alive

Small and large varix as per Baveno VI guidelines. P3: Progression of portal hypertension (gastric varix), international normalised ratio > 1.5. P8, P13 and P15: Short follow-up (< 6 months). A: Ascites; B: Gastrointestinal bleed; C: Compensated; D: Decompensated; E: Encephalopathy; H: Hepatomegaly; HET: Heterozygous; HSM: Hepatosplenomegaly; INR: International normalised ratio; J: Jaundice; LT: Liver transplantation; NA: Not available; P: Pruritis; PH: Portal Hypertension; S: Stable; W: Worsened.

Table 3 ABCB4 variants in biallelic mutation and their pathogenicity (n = 16)

Patient	Zygosity	Exon number	Mutation	Predicted effect	Domain	Type of mutation	Polyphen	SIFT	Mutation taster	GnomAD1	Updated ACMG class	ACMG criteria
P1	Ho	23	c.2908T>C	p.Phe970Leu	NBD2	MISSENSE	B	D	DC	0	LP	PM1, PM2, PP2
P2 (sibling of P1)	Ho	23	c.2908T>C	p.Phe970Leu	NBD2	MISSENSE	B	D	DC	0	LP	PM1, PM2, PP2
P3	Ho	23	c.2908T>C	p.Phe970Leu	NBD2	MISSENSE	B	D	DC	0	LP	PM1, PM2, PP2
P4	Ho	23	c.2908T>C	p.Phe970Leu	NBD2	MISSENSE	B	D	DC	0	LP	PM1, PM2, PP2
P5	Ho	23	c.2860G>A	p.Gly954Ser	Linker (NBD2 adjacent)	MISSENSE	PossD	D	DC	0	LP	PM1, PM2, PM5, PP2, PP3, PP5
P6 (sibling of P5)	Ho	23	c.2860G>A	p.Gly954Ser	Linker (NBD2 adjacent)	MISSENSE	PossD	D	DC	0	LP	PM1, PM2, PM5, PP2, PP3, PP5
P7	Ho	23	c.2860G>A	p.Gly954Ser	Linker (NBD2 adjacent)	MISSENSE	PossD	D	DC	0	LP	PM1, PM2, PM5, PP2, PP3, PP5
P8	Ho	23	c.2860G>A	p.Gly954Ser	Linker (NBD2 adjacent)	MISSENSE	PossD	D	DC	0	LP	PM1, PM2, PM5, PP2, PP3, PP5
P9	Ho	4	c.139C>T	p.Arg47Ter	TMD1	NONSENSE	-	-	DC	0	P	PVS1, PS4, PM2
P10 (sibling of P9)	Ho	4	c.139C>T	p.Arg47Ter	TMD1	NONSENSE	-	-	DC	0	P	PVS1, PS4, PM2
P11	Ho	25	c.3230C>T	p.Thr1077Met	NBD2	MISSENSE	ProbD	D	DC	0.005	LP	PP2, PP3, PM3
P12	Ho	28	c.3760G>A	p.Gly1254Ser	NBD2	MISSENSE	ProbD	D	DC	0	LP	PP2, PP3, PM3
P13	Ho	15	c.1783C>T	p.Arg595Ter	NBD2 start	NONSENSE	D	D	DC	0.001	P	PVS1, PM2, PP5
P14	Ho	6	c.431G>A	p.Arg144Gln	-	MISSENSE	ProbD	D	DC	0.0007	LP	PM1, PM2, PP2, PP3
P15	Co HET	10	c.1031C>G	p.Ala344Gly	NBD1	MISSENSE	PossD	D	DC	0	LP	PM2, PP2
		19	c.2362C>T	p.Arg788Trp	NBD2	MISSENSE	PossD	D	DC	0.016	LP	PM2, PP2
P16	Co HET	15	c.1783C>T	p.Arg595Ter	NBD2 start	NONSENSE	D	D	DC	0.001	P	PVS1, PM2, PP5
		23	c.2906G>A	p.Arg969His	NBD2	MISSENSE	B	-	Polymorphism	0.0001	LP	PM2, PP2

¹Allele frequency: (1) 0: Strengthens pathogenicity; (2) 0.0001: May support pathogenicity; (3) 0.001: Considered rare; (4) 1%-5%: Unlikely pathogenic; and (5) > 5%: Too common to cause rare disease.

ACMG: American College of Medical Genetics; B: Benign; Co HET: Compound heterozygous; D: Damaging; DC: Mutation taster 1 disease causing; Ho: Homozygous; LP: Likely pathogenic; NBD: Nucleotide binding domain 1; P: Pathogenic; ProbD: Probably damaging; PossD: Possibly damaging; TMD: Transmembrane domain.

Table 4 Clinical characteristics of patients with monoallelic ABCB4 mutations (n = 10)

Patient	Gender	Age at symptom onset (months)	Age at first presentation (months)	Consanguinity	Family history	Anthropometry (weight/height)	Clinical features	Disease status at presentation	Esophageal varix	Disease status at last follow-up	Issues at last follow up/salient features	Final outcome at last follow- up
P17 (sibling of P3)	Female	180	180	No	Yes	0.73Z, 0.87Z	H	C	No	S	Screening detected	Alive
P18 (sibling of P15)	Female	5	17	No	Yes	-0.46Z	J, P, H	C	Not done	I	Infantile onset, self-limiting course	Alive
P19	Male	5	19	No	Yes	-2.33Z, -4.06Z	J, P, HSM	C	No varix	I	Infantile onset, self-limiting course	Alive
P20	Female	48	72	No	No	0.1Z, 0.1Z	J, P, H	C	No varix	I	Recurrent jaundice	Alive
P21	Male	1	3	No	No	-3.43Z, -2.15Z	J, P, HSM	C	No varix	I	Infantile onset, self-limiting course	Alive
P22	Male	8	8	No	No	-3.2Z, -2.54Z	J, P, HSM	C	No varix	I	Infantile onset, self-limiting course	Alive
P23	Male	144	192	No	No	-2.42Z, -3.33Z	J, P, HSM	C	Large varix	W	PH, B, A, E, MRCP-sclerosing cholangitis	Expired
P24	Female	48	108	No	No	-2.39Z, -3.34Z	J, P, HSM	C	Small varix	W	PH, E, SNHL, additional heterozygous mutations in GJB6 and SPTB (both autosomal dominant)	Expired
P25	Male	11	13	No	No	-0.34Z, -1.63Z	J, P, H	C	Not done	I	Infantile onset, self-limiting course	Alive
P26	Male	10	12	No	No	0.11Z, -0.04Z	J, P, HSM	C	No varix	I	Infantile onset, self-limiting course	Alive

Small and large varix as per Baveno VI guidelines. A: Ascites; B: Gastrointestinal bleed; C: Compensated; E: Encephalopathy; H: Hepatomegaly; HSM: Hepatosplenomegaly; I: Improved; J: Jaundice; P: Pruritis; PH: Portal Hypertension; S: Stable; SNHL: Sensorineural Hearing Loss; W: Worsened.

Table 5 ABCB4 variants in monoallelic mutations and their pathogenicity (n = 10)

Patient	Zygosity	Exon Number	Mutation	Predicted effect	Domain	Type of mutation	Polyphen	SIFT	Mutation taster	GnomAD1	Updated ACMG class	ACMG criteria
P17 (sibling of P3)	HET	23	c.2908T>C	p.Phe970Leu	NBD2	MISSENSE	B	D	DC	0	VUS	PM1, PM2, PP2
P18 (sibling of P15)	HET	19	c.2362C>T	p.Arg788Trp	NBD2	MISSENSE	ProbD	D	DC	0.016	VUS	PM2, PP2
P19	HET	8	c.808G>C	p.Gly270Arg	TMD1/NBD1 boundary	MISSENSE	ProbD	D	DC	0.189 (THRESHOLD:0.1)	VUS	PS1, PP2, PP3, BS1
P20	HET	8	c.808G>C	p.Gly270Arg	TMD1/NBD1 boundary	MISSENSE	ProbD	D	DC	0.189 (THRESHOLD:0.1)	VUS	PS1, PP2, PP3, BS1
P21	HET	16	c.1963C>G	p.Pro655Ala	NBD2	MISSENSE	B	-	Polymorphism	0	VUS	PP2
P22	HET	14	c.1571C>A	p.Thr524Asn	TMD2	MISSENSE	ProbD	D	DC	0	LP	PS4, PM2, PP3, PP2
P23	HET	9	c.928G>A	p.Ala310Thr	NBD1	MISSENSE	PossD	-	-	-	VUS	-
P24	HET	13	c.1558C>T	p.Gln520Ter	Linker before TMD2	NONSENSE	-	-	-	0.0001	LP	PVS1, PM2
P25	HET	15	c.1650C>A	p.Asn550Lys	TMD2	MISSENSE	PossD	D	-	0.0004	VUS	PM1, PM2, PP2
P26	HET	15	c.1783C>T	p.Arg595Ter	NBD2 start	NONSENSE	-	-	DC	0.001	Pathogenic	PVS1, PM2, PP5

¹Allele frequency: (1) 0: Strengthens pathogenicity; (2) 0.0001: May support pathogenicity; (3) 0.001: Considered rare; (4) 1%-5%: Unlikely pathogenic; and (5) > 5%: Too common to cause rare disease.

ACMG: American College of Medical Genetics; B: Benign; D: Damaging; DC: Mutation taster 1 disease causing; HET: Heterozygous; LP: Likely pathogenic; NBD: Nucleotide binding domain 1; ProbD: Probably damaging; PossD: Possibly damaging; TMD: Transmembrane domain 1; VUS: Variant of unknown significance.

Table 6 Phenotypic, genetic and laboratory characteristics of various pediatric studies with biallelic ABCB4 mutation

Ref.	Year/country	Number of patients	Median age at onset of symptoms (months)	Median Age at presentation (years)	Pruritus (%)	Jaundice (%)	Hepatomegaly (%)	Splenomegaly (%)	Variants with missense mutation (%)	Laboratory parameters
										Gamma-glutamyltransferase (IU/L)	Alanine aminotransferse (IU/L)	Aspartate aminotransferse (IU/L)	Total bilirubin (mg/dL)
Schatz et al[12]	2018/Germany	26	5	4.8	100	61.5	84.6	96.1	77.1	320	212
Chen et al[13]	2022/China	13	36	-	30.7	53.8	100	77	61.5	197		130	1.1
Al-Hussaini et al[14]	2021/Saudi Arabia	25	10	2	92	12	80	-	81.4	202		149	1.27
Gonzales et al[15]	2023/France	38	11	3.3	79	29	82	68	71	150		-	0.73
Index study	2025/India	16	54	5	68.8	68.8	100	81.2	81.3	171	120.5	198	2.58