Mayo Clinic Fatty Liver Discovery: Rare MET Gene Mutation Identified as Direct Cause

The Groundbreaking Mayo Clinic Discovery on Fatty Liver Disease

Mayo Clinic researchers have uncovered a pivotal breakthrough in the understanding of metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as nonalcoholic fatty liver disease (NAFLD). This discovery reveals that a rare germline mutation in the MET gene can act as a direct, monogenic cause of the condition, challenging long-held views that MASLD always stems from a mix of lifestyle and common genetic factors. 89 88

The study, led by Filippo Pinto e Vairo, M.D., Ph.D., from Mayo Clinic's Center for Individualized Medicine, was published in the journal Hepatology in December 2025. It highlights how this single genetic glitch disrupts essential liver functions, leading to fat buildup, inflammation, and progression to severe stages like metabolic dysfunction-associated steatohepatitis (MASH), cirrhosis, and even hepatocellular carcinoma (HCC). 88

This finding emerged from genomic sequencing of a family where both a woman and her father developed MASH without typical risk factors such as diabetes or high cholesterol. The mutation, NM_000245.4:c.3505A>T p.(Ile1169Phe), resides in the MET kinase domain, scrambling instructions for fat processing and liver repair.

What is Metabolic Dysfunction-Associated Steatotic Liver Disease?

MASLD is characterized by excessive fat accumulation in liver cells (hepatocytes) in individuals without significant alcohol consumption. It affects approximately 33% of U.S. adults, with projections estimating a rise to 41% by 2050, making it a leading cause of liver transplants. 59 The condition spans a spectrum: simple steatosis (fat buildup), MASH (with inflammation and cell damage), fibrosis, cirrhosis, and HCC.

Risk factors include obesity, type 2 diabetes, insulin resistance, and dyslipidemia. However, up to 20% of cases occur in lean individuals, suggesting genetic underpinnings. Symptoms are often silent until advanced stages, with fatigue, abdominal pain, or jaundice appearing late. Diagnosis typically involves ultrasound, blood tests (e.g., ALT/AST levels), FibroScan for stiffness, or biopsy for confirmation.

In the U.S., Hispanics face higher prevalence (up to 45%), followed by Whites (33%) and Blacks (24%), per NHANES data. Globally, one-third of adults are affected, underscoring the urgency of this Mayo Clinic finding. 60

The MET Proto-Oncogene: Key Player in Liver Function

The MET gene encodes the MET receptor tyrosine kinase, activated by hepatocyte growth factor (HGF). This signaling pathway is crucial for embryonic development, liver regeneration, wound healing, and fat metabolism. In healthy livers, MET/HGF promotes hepatocyte proliferation, migration, and survival, preventing fat overload. 78

Mutations in MET are known in cancers (e.g., papillary renal carcinoma, HCC), where overactivation drives oncogenesis. Here, the loss-of-function Ile1169Phe variant impairs kinase activity, disrupting HGF signaling. Functional assays showed altered protein dynamics, reduced phosphorylation, and defective downstream pathways like PI3K/AKT and MAPK, leading to impaired lipid handling and increased apoptosis susceptibility. 88

Prior research linked MET to NAFLD protection via Fas antagonism, preventing hepatocyte death. This mutation reverses that, allowing unchecked fat accumulation.

Unraveling the Mutation: Mayo Clinic's Investigative Approach

The journey began with exome sequencing of over 20,000 genes in the proband and her father. The shared ultra-rare variant was absent from public databases like gnomAD, confirming novelty. Protein modeling predicted structural instability in the kinase domain, validated by molecular dynamics simulations showing flexibility loss.

Cell-based assays in hepatocytes demonstrated reduced MET activation, impaired fat oxidation, and heightened steatosis under lipid load. To scale up, researchers mined Mayo's Tapestry dataset—exomes from 100,000+ participants. Among 3,904 with SLD (confirmed via records), 1.1% harbored rare deleterious MET variants; 17.7% targeted the kinase domain, mirroring the proband's. 89

• Sequencing: Whole-exome for family; Tapestry for population.
• Functional validation: CRISPR editing, lipid assays, signaling Western blots.
• Bioinformatics: ACMG classification (pathogenic), CADD scores >30.

Study Results and Population Impact

The Ile1169Phe variant caused severe, early-onset MASLD progressing to MASH despite healthy lifestyles. Tapestry data suggest 1% prevalence among MASLD patients, potentially affecting thousands in the U.S. alone given 100 million+ cases.

This monogenic form explains "lean MASLD" and familial clustering. Unlike polygenic risks (PNPLA3 I148M, TM6SF2 E167K), this single hit suffices. 37

Expert Konstantinos Lazaridis, M.D., notes: "This finding could potentially affect hundreds of thousands... highlighting the profound value of large-scale genomic datasets." 89

Photo by Ekke Krosing on Unsplash

Diagnostic Advances and Genetic Testing Recommendations

Genetic screening for MET variants is now recommended for atypical MASLD cases: young onset, family history, lean patients, rapid progression to HCC. Mayo's Program for Rare and Undiagnosed Diseases has aided 3,200+ patients since 2019 via trio sequencing.

Panel tests including PNPLA3, TM6SF2, HSD17B13, and now MET enable risk stratification. For carriers, lifestyle (Mediterranean diet, exercise) and monitoring (MRI-PDFF, ELF score) are key.Mayo Clinic MASLD management

Treatment Horizons: Targeting MET Pathways

While MET inhibitors (e.g., tepotinib) treat c-Met-driven cancers, repurposing for MASLD requires caution due to regeneration role. HGF mimetics or gene therapy could restore function. Ongoing trials target related pathways; this discovery paves for MET-specific drugs.

Stakeholders like AASLD advocate genomics integration. For researchers, clinical research jobs in hepatology at institutions like Mayo abound.

Familial Cases and Real-World Examples

The index family exemplifies: proband developed MASH in 40s, father cirrhosis requiring transplant. No obesity/diabetes. Similar kinase variants in 8 Tapestry cases suggest underdiagnosis.

Real-world: Undiagnosed MET carriers may receive suboptimal care, mistaking genetic drive for lifestyle failure.

Evolution of Fatty Liver Genetics Research

2008: PNPLA3 rs738409 identified (49% Hispanics carry risk G allele). 38

2014: TM6SF2 E167K impairs VLDL secretion.

2019: HSD17B13 protective.

2025: MET monogenic—first direct cause. 100

• PNPLA3: Alters triglyceride lipase.
• TM6SF2: Lipid droplet regulation.
• MET: Kinase dysfunction—new paradigm.

Future Outlook: Precision Medicine at Mayo Clinic

Mayo's Tapestry (100k+ exomes) accelerates discoveries. Future: CRISPR models, MET agonists, population screening. Impacts higher ed: Boom in genomics training; explore faculty positions in precision medicine.

Filippo Pinto e Vairo: "This opens... potential therapeutic targets." 89

Photo by Google DeepMind on Unsplash

Practical Advice and Calls to Action

For patients: Discuss family history/genetic testing with hepatologists. Lifestyle remains cornerstone: 7-10% weight loss reverses early MASLD.

Professionals: Integrate exome sequencing. Researchers: Join Mayo collaborations. Check higher ed career advice or rate my professor for mentors. For jobs, visit higher ed jobs, clinical research jobs, university jobs.