Unearthing TULP3 Mutation as a Rare Cause of Cryptogenic Cirrhosis: A Case Report and Review of the Literature

Abstract

Whole-exome sequencing may help unearth uncommon monogenic causes of cryptogenic cirrhosis and portal hypertension. Tubby-like protein 3 (TULP3) gene encodes the tubby domain family of proteins, mutations of which is associated with progressive degenerative disease of major organs such as kidney, heart, and liver. Here we report a case of a young male with decompensated cirrhosis who was ultimately identified with homozygous pathogenic splice donor variant c.492+1G > A in intron 5 of TULP3 gene.

Hepatic fibrosis represents a maladaptive response to chronic liver injury leading to accumulation of extracellular matrix proteins, which may ultimately progress to cirrhosis.¹ While the etiology is identifiable in most cases, approximately 5–15% remains unexplained despite comprehensive clinical, laboratory, and histopathological evaluations.² In adults, the majority of such cases of cryptogenic cirrhosis (CC) are possibly attributable to known etiologies like metabolic-associated steatotic liver disease (MASLD) or autoimmune hepatitis with burnt out disease activity. On the other hand, genetic and metabolic disorders are commonly implicated in children, adolescents, and young adults.³ Advanced molecular diagnostic techniques like whole-exome sequencing (WES) and next-generation sequencing (NGS) can be potentially useful in detecting novel genetic causes of CC in adolescents and young adults. Tubby-like protein 3 (TULP3) variants have been recently described as a monogenic cause for unexplained liver, kidney, and heart diseases, collectively referred to as hepatorenocardiac degenerative disease.⁴ Here we present a young male patient with apparent CC who presented with variceal bleeding in whom TULP3-related ciliopathy was subsequently identified as the underlying etiology on WES. The case has been reported in accordance with CARE guidelines.

Case

A 14-year-old male patient presented with multiple episodes of hematemesis and melena over the past 24 h. There was no associated history of clinical jaundice, abdominal distension or pain, retching, and altered sensorium. He was the sole child of a healthy, nonconsanguineous Indian couple and experienced normal growth and developmental milestones. There was no history of liver disease in the family. Physical examination revealed pallor and splenomegaly. Liver was not palpable with no free fluid per abdomen. No additional peripheral stigmata of chronic liver disease were discernible on clinical examination. His vaccination history was completed for his age as per the national immunization schedule (India). Laboratory investigations showed anemia (hemoglobin: 8 g/dL) with thrombocytopenia (70 × 10³/μL) and a normal total leukocyte count (6.9 × 10³/μL). Liver function tests (LFTs) were deranged (total bilirubin: 2.37 mg/dL, aspartate aminotransaminase: 117 IU/L, alanine aminotransferase: 139 IU/L, alkaline phosphatase: 400 IU/L, gamma-glutamyl transferase: 195 U/L), while renal function tests (RFTs) and coagulation profile were normal (International normalized ratio-1.28, aPTT-25 s). After stabilization, an upper gastrointestinal endoscopy was performed that revealed large esophageal varices with red color signs, and endoscopic variceal ligation was done.

Subsequent abdominal ultrasonography showed coarsened echotexture of liver with irregular outline, dilated portal vein (15 mm), and an enlarged spleen (16 cm), which was suggestive of cirrhosis with portal hypertension. Liver stiffness measurement on vibration-controlled transient elastography (VCTE) was 25.3 kPa that was suggestive of cirrhosis with clinically significant portal hypertension. A battery of blood investigations was performed as part of etiological workup including hepatitis B surface antigen, anti-hepatitis B Core total antibody, anti-hepatitis C Virus antibody, antinuclear antibody, anti-smooth muscle antibody, anti-liver-kidney microsomal antibody, anti-soluble liver antigen antibody, anti-liver cytosolic antigen type 1 antibody, anti-mitochondrial antibody, total immunoglobulin G levels (824 mg/dL), ceruloplasmin levels (33 mg/dL), anti-tissue transglutaminase antibody levels, and iron profile. All these results were unremarkable. No Kayser—Fleischer rings were discovered on slit lamp examination. Urine routine microscopy was negative and 24-h urinary copper was within normal limits. A liver biopsy was performed, and histopathology showed thick pauci-inflammatory fibrous septa with mild ductular reaction. Occasional portal tracts were devoid of any interlobular bile ducts and showed branches of unpaired hepatic artery. Accumulation of macrophages (diastase–PAS positive) was noted in the portal tracts that showed an absence of interlobular bile ducts. No ductal plate malformation was seen. The hepatic lobules showed regenerative nodules and sinusoidal dilatation. Focal biliary metaplasia was noted. Immunohistochemistry for multidrug resistance protein 3 immunostaining highlighted retained canalicular positivity in a patchy distribution (<50% area). Overall histological picture was suggestive of advanced fibrosis, but no etiology was discernible Figure 1.

Figure 1.

Histopathology of the liver showing (a) thick fibrous septa (thick white arrow)[200μ], (b) lack of inflammation and ductular reaction in the septa [50μ], (c) absence of interlobular bile ducts from a few portal tracts with unpaired branches of hepatic artery (thin black arrows) and accumulation of macrophages (thin white arrow) [20μ], (d) focal presence of canalicular expression of MDR3 [20μ], and (e) focal absence of canalicular expression of MDR3 [20μ].

WES was planned to identify potential genetic variants causing CC in this adolescent male. It was performed from the patient’s blood sample using Illumina SBS chemistry on NextSeq 2000 sequencer platform with variant coverage of 100x. This revealed a homozygous pathogenic variant, c.492+1G > A in intron 5 of TULP3 gene (chr12:g.3039512G > A; rs145289428). Thus, a diagnosis of TULP3-related ciliopathy with cirrhosis and portal hypertension was made. To look for associated cardiac renal abnormalities, renal ultrasound and 2D echocardiography were performed which were unremarkable. The patient was initiated on nonselective beta blockers along with endoscopic variceal ligation as secondary prophylaxis for variceal bleed and is under close follow-up for any abnormal renal or cardiac manifestations in the future.

Both parents were investigated for liver, renal, and cardiac diseases. LFTs, RFTs, abdominal ultrasonography, VCTE, and 2D echocardiography were within normal limits in both the parents. They were provided genetic counseling. Genetic testing was advised to the parents, but they declined the same as they were asymptomatic.

Discussion

As a cell organelle, the cilium is vital for cell signaling. Ciliopathies affecting the liver usually manifest as cystic liver disease often in association with polycystic kidney disease.⁵ TULP3 mutation, a novel autosomal recessive ciliopathy causing hepatorenocardiac degenerative fibrosis, was first described in 15 patients in 8 families in a seminal paper by Devane et al. in 2022(4). Unlike other well-established ciliopathies, TULP3 does not affect ciliogenesis per se. TULP3 gene encodes tubby-like protein 3, a 442-amino acid protein essential for intraflagellar transport through its interaction with complex A. This protein plays a crucial role in cilium maintenance and cell signaling. Mutated TULP3 genes disrupt protein transport to cilia, contributing to increased fibrosis in organs such as the liver, kidneys, and heart. These deleterious variants result in significant dysregulation of profibrotic pathways, including the transforming growth factor beta, Sonic hedgehog, and Wnt signaling pathways, thereby promoting the progression of fibrosis.⁶ Our patient was homozygous for c.492+1G > A in intron 5 of TULP3. This variant is a splice donor variant that is predicted to cause loss of protein function either through protein truncation or nonsense-mediated mRNA decay.⁴ In silico analysis with SpliceAI revealed a score of 0.99 for donor loss thereby corroborating its pathogenicity. The variant was categorized as pathogenic as per the American College of Medical Genetics and Genomics (ACMG) classification.⁷ To the best of our knowledge, this is the second report of TULP3 mutation causing liver disease from India. The various reported cases in the literature have been summarized in Table 1.

Table 1.

Reported Cases of TULP3 Gene Mutations Throughout the World.

S. no	Author/Country/Year	Age/Sex	TULP3 nucleotide/amino acid change	Clinical/biochemical features	Liver histopathology findings	Kidney phenotype	Cardiac phenotype
1	Devane et al., Germany, 2022	68/M	c.(41þ1_42_1)_(696þ1_697_1)del	HSM, portal HTN, elevated liver enzymes, cirrhosis	Probably cirrhosis, mild pericellular fibrosis, steatosis-5%, minimal portal inflammation, moderate ductular reaction, atypical ductal plate-possible	Cystic kidneys	HOCM
2		65/M	c.612T > G (p.Cys204Trp)	Elevated liver enzymes, HSM, portal HTN, variceal banding, HE, cirrhosis,	Architectural distortion probably cirrhosis, mild pericellular fibrosis, steatosis-5%, minimal portal inflammation, moderate ductular reaction, atypical ductal plate-possible	Cystic kidneys	HOCM
3		68/F	c.1223G > A (p.Arg408His)	Cholestasis/jaundice, portal HTN, GI bleeding, portovenous shunt, LTx done	Biliary cirrhosis, mild pericellular fibrosis, minimal cholangitis, mild portal inflammation, moderate ductular reaction, atypical ductal plate-possible	Cystic and enlarged kidneys	Normal
4		57/M	c.1023þ1G > A	Elevated liver enzymes, portal HTN, esophageal bleeding, portacaval shunt, HE, and death due to liver failure	–	–	–
5		53/F	c.1023þ1G > A	Elevated liver enzymes, HSM, thrombocytopenia, bridging fibrosis	Bridging portal fibrosis, mild pericellular fibrosis, minimal cholangitis, minimal portal inflammation, moderate ductular reaction, atypical ductal plate-possible	eGFR:52, normal-sized kidneys, reduced CMD	HOCM
6		18/M	c.544delC (p.Leu182TrpfsTer4)	Elevated liver enzymes, HSM, portal HTN, variceal banding, increased elastography values	–	Normal	Normal
7		16/F	c.544delC (p.Leu182TrpfsTer4)	Abdominal pain, HSM, portal HTN, variceal banding	–	Normal	Normal
8		34/F	c.492þ1G > A	Cholestasis, portal HTN, bridging fibrosis	–	eGFR: 50, normal Kidney USG	Normal
9		21/M	c.1023þ1G > A	Elevated liver enzymes, HSM, ascites, cirrhosis, LTx at 21 years, deceased at 21 years	Bridging portal fibrosis, mild pericellular fibrosis, mild cholangitis, hepatocellular and canalicular cholestasis, minimal to mild portal inflammation, mild lobular inflammation, moderate ductular reaction, atypical ductal plate-possible	Normal-sized hyperechogenic kidneys, reduced CMD	Normal
10		26/M	c.70C > T (p.Arg24Ter)	Elevated liver enzymes, HSM, cirrhosis	Probably cirrhosis, mild pericellular fibrosis, minimal portal inflammation, mild to moderate ductular reaction, atypical ductal plate-possible	Enlarged hyperechogenic kidneys, eGFR >90; biopsy—diffuse Interstitial fibrosis, Corticomedullary scarring, Tubular dilatations	Normal
11		24/M	c.70C > T (p.Arg24Ter)	Elevated liver enzymes, HSM, bridging fibrosis	Bridging portal fibrosis, mild pericellular fibrosis, minimal portal inflammation, moderate ductular reaction, atypical ductal plate-possible	Enlarged hyperechogenic Kidneys, eGFR >90	Normal
12		22/F	c.70C > T (p.Arg24Ter)	Elevated liver enzymes, HSM, esophageal variceal bleeding (TIPS), bridging fibrosis	Bridging portal fibrosis with architectural distortion, mild pericellular fibrosis, minimal portal inflammation, mild lobular inflammation, moderate ductular reaction, atypical ductal plate-possible	Renal parenchymal hyperechogenicity, Reduced CMD, small right kidney	Normal
13		29/F	c.925_1G > A	Elevated liver enzymes, portal HTN with esophageal varices, cirrhosis, LTx at 27 years	–	Non-enlarged cystic kidneys, eGFR >90	Normal
14		26/M	c.925_1G > A	Elevated liver enzymes, decompensated portal HTN, TIPS, cirrhosis, LTx at 21 years	–	Enlarged kidneys, eGFR >60	Normal
15		16/M	c.544delC (p.Leu182TrpfsTer4)	Cholestasis and jaundice, portal HTN, bridging fibrosis	Bridging portal fibrosis with architectural distortion, mild pericellular fibrosis, minimal portal inflammation, mild lobular inflammation, moderate ductular reaction, atypical ductal plate-possible	Non-enlarged kidneys with cortical and medullary microcysts, increased cortical echogenicity, eGFR: 86	Normal
16	HJ Khamirani et al., Iran, 2022,	12/F	c.1144C > T, p.Arg382Trp	Elevated liver enzymes, cirrhosis,	Bridging fibrosis, nodule formation, distorted lobular and vascular architecture, ballooning degeneration	Enlarged cystic kidneys, diffuse global glomerulosclerosis and tubular atrophy, kidney Tx at 5 years	Normal
17		-/F	c.1144C > T, p.Arg382Trp	–	Bridging fibrosis, nodule formation, distorted lobular and vascular architecture, ballooning degeneration	–	Normal
18	Jiang C et al., China, 2024	50/F	c.253þ1G > A	Portal HTN, esophageal varices	Swollen hepatocytes in lobules, occasional punctate necrosis, mild dilatation of hepatic sinusoids, mild portal lymphocytic inflammation, periportal and portal–portal septa, ductular reaction	Normal	LVH
19	Kumar P et al., India, 2024	29/M	c.492+1G > A (chr12:g.2930346G > A)	Deranged liver function tests, large esophageal varices	Portal fibrosis and porto-portal bridging with thick bands of fibrous tissue incorporating islands of hepatic lobules, marked nonspecific bile duct proliferation, fibrous intimal thickening of portal venules, and normal arterioles, moderate increase in copper-associated proteins	Normal	Normal
20	Index case, India, 2025	14/M	c.492+1G > A (chr12:g.3039512G > A)	Esophageal variceal bleed, elevated liver enzymes	Thick pauci-inflammatory fibrous septa with mild ductular reaction, occasional portal tracts devoid of interlobular bile ducts, accumulation of macrophages (diastase–PAS positive), regenerative nodules and sinusoidal dilatation, focal biliary metaplasia, IHC for MDR3-retained canalicular positivity in patchy distribution (<50% area), no DPM	Normal	Normal

CMD, corticomedullary differentiation; DPM, ductal plate malformation; GFR, glomerular filtration rate; GI bleeding, gastrointestinal bleeding; HE, hepatic encephalopathy; HOCM, hypertrophic obstructive cardiomyopathy; HSM, hepatosplenomegaly; Portal HTN, portal hypertension; LTx, liver transplantation; MDR3, multidrug resistance protein 3; PAS, periodic acid Schiff; portal TIPS, transhepatic intrajugular portosystemic shunt.

The age of presentation varies from infancy to the sixth decade of life. Individuals often exhibit abnormal liver function tests, particularly elevated cholestatic markers or portal hypertension. Although patients with portal hypertension may have underlying cirrhosis as in our case, the condition may also closely mimic noncirrhotic congenital hepatic fibrosis. Histopathology typically reveals paucicellular fibrosis with minimal portal inflammation. Nonspecific bile ductular reaction and biliary type fibrosis may also occur. However, ductal plate malformation is conspicuously absent.⁴ Needless to say, as in other etiologies, fibrosis can progress to cirrhosis as seen in our case.

The liver biopsy in the index case showed thick bland fibrous septa, ductular reaction, occasional absence of interlobular bile duct, focal biliary metaplasia, and regenerative nodule formation in the absence of any ductal plate malformation. These histological features expand the histological spectrum of TULP3 mutation-associated liver disease as many of the aforementioned features were not described in the literature. The histomorphology, clinical, and biochemical features may be occasionally seen in ABCB4 mutation-associated liver disease. Hence, MDR3 immunostaining (product of ABCB4 gene) was performed highlighting a heterogeneous expression of the canalicular protein. The relation between TULP3 gene mutation and MDR3 expression had not been previously depicted in the literature and thus, the reason for the reduced/patchy expression of MDR3 is not clear. The biopsy in the index case was not sufficient to diagnose a definite reason for the cirrhosis and a genetic evaluation was suggested. The whole-exome sequencing revealed a homozygous pathogenic variant in the TULP3 gene, thereby clinching the diagnosis.

Of note, our patient did not have any renal or cardiac manifestations. As such, kidney disease manifesting as fibrocystic renal disease and hypertrophic obstructive cardiomyopathy usually become apparent later in life, usually in the sixth or seventh decade Table 1.

In the absence of antifibrotic therapies, management of this condition as of now entails portal pressures lowering interventions like nonselective beta-blocker therapy or transjugular intrahepatic portosystemic shunt. Liver transplantation may be required in end-stage liver disease and has been shown to be feasible in four patients in the literature Table 1.⁴ Periodic comprehensive assessments, especially of the heart and kidneys, are also prudent for holistic management of these patients.

Our case also highlights the role of advanced molecular techniques like WES for unearthing uncommon monogenic causes of apparently cryptogenic liver diseases. Such techniques should be particularly considered for CC or unexplained intrahepatic cholestasis in children, adolescents, and young adults even when the family history is absent. While targeted genetic panels are suitable when the clinical phenotype and other organ involvements suggest a particular syndromic diagnosis. In other cases, WES is usually required for unearthing the culprit variant. The variant identified should be categorized as per ACMG classification to determine its pathogenic role. Depending on the clinical phenotype, type of mutation identified, and the existing literature, this categorization may require additional aids including in silico analysis and segregation studies. In our patient, WES was performed as a gamut of investigations including liver biopsy that did not provide a clue about the etiology of cirrhosis in this young boy of 14 years. Of note, the boy did not have a family history of liver disease, which is possible as TULP3 ciliopathy is an autosomal recessive disease. Thus, it is probable that both the parents are carriers. A second possibility is that the mutation arose de novo in the index case. Differentiation between these two scenarios requires parenteral screening which was refused by the family.

In conclusion, TULP3 gene mutation is a pathophysiologically distinct cause that may progress to cirrhosis and portal hypertension. It should be particularly suspected in a young patient with no apparent etiology. Early diagnosis and genetic counseling may enhance clinical outcomes and facilitate timely management decisions.

Informed consent

Written informed consent for patient information and images to be published was taken from the patient.

Credit authorship contribution statement

AS contributed to manuscript writing; SB contributed to data collection and manuscript writing; AD contributed to data collection and review of the literature; SM contributed to histology analysis; AD: contributed to manuscript writing, data collection, and critical review.

Funding

None.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.