Distorted urine sample under a microscope symbolizes unreliable test results.

Mitochondrial DNA Mutation: Why Your Urine Test Results Might Not Be Reliable

Kai Mendoza in Health & Wellness December 2025 • 4 min read.

"New research reveals significant day-to-day variations in urine tests for the m.3243A>G mitochondrial mutation, challenging its use as a prognostic marker."

Mitochondrial DNA (mtDNA) mutations, particularly the m.3243A>G mutation, are a leading cause of mitochondrial disease in adults. This mutation, identified in 1990, affects the MT-TL1 gene responsible for producing tRNALEU(UUR), a crucial component for protein synthesis within mitochondria.

The m.3243A>G mutation is closely linked to MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) syndrome, although it manifests in various other conditions, including maternally inherited diabetes and deafness (MIDD), hypertrophic cardiomyopathy and certain types of macular dystrophy. Its prevalence ranges from 7.59 to 236 per 100,000 individuals.

Clinicians often assess the heteroplasmy levels (the percentage of mutated mtDNA) in different tissues to understand the severity of the mitochondrial disease. While theoretically measurable in most tissues, accessibility and result consistency pose challenges. Urine samples have emerged as a non-invasive alternative to blood or muscle biopsies, but the correlation between mutation load in urine and the actual clinical presentation remains debated. New study challenges the reliability of using urine samples.

Unreliable Urine Test Results: The Day-to-Day Variation Problem

Distorted urine sample under a microscope symbolizes unreliable test results.

A new study reveals a critical issue with using urine samples to assess mitochondrial DNA mutations: significant day-to-day variations in heteroplasmy levels. Researchers collected five urine samples from fifteen individuals carrying the m.3243A>G mutation over a 14-day period. They then measured the percentage of mutated mtDNA in each sample using pyrosequencing technology.

The results showed striking inconsistencies. While six participants had relatively stable heteroplasmy levels (within a 5% margin), five others experienced variations exceeding 20%. The remaining four showed variations between 5% and 20%. These fluctuations raise serious concerns about the reliability of single urine tests for assessing disease severity or predicting outcomes.

Stable Results: Approximately 40% of participants showed consistent heteroplasmy levels in their urine samples.
Significant Variation: A third of participants experienced fluctuations greater than 20%, highlighting the potential for misleading results.
Moderate Fluctuation: The remaining participants had variations between 5% and 20%.

Researchers suggest that the inconsistencies in heteroplasmy levels could stem from variations in the types of epithelial cells present in the urine at different times. They emphasize that a genetic bottleneck effect causes heteroplasmy levels to fluctuate between different tissues and organs. Therefore, urine samples with varying proportions of cells could lead to differing heteroplasmy readings.

What This Means for You: Rethinking Urine Tests for Mitochondrial Mutations

This study highlights that relying solely on urine tests to determine the severity of m.3243A>G mutations might not be reliable due to significant day-to-day variations in heteroplasmy levels. Therefore, these results should be interpreted with caution.

If you are monitoring a mitochondrial DNA mutation, discuss these findings with your doctor. You may need to consider alternative testing methods or repeat urine tests over time to get a more accurate picture of your condition.

The researchers recommend further investigation into more reliable biomarkers for assessing mitochondrial disease progression. They advocate for cautious interpretation of urine heteroplasmy levels, especially in drug intervention studies.

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This article is based on research published under:

DOI-LINK: 10.1002/mgg3.523, Alternate LINK

Title: Intra-Patient Variability Of Heteroplasmy Levels In Urinary Epithelial Cells In Carriers Of The M.3243A≫G Mutation

Subject: Genetics (clinical)

Journal: Molecular Genetics & Genomic Medicine

Publisher: Wiley

Authors: Paul De Laat, Richard J. Rodenburg, Jan A. M. Smeitink, Mirian C. H. Janssen

Published: 2018-12-04

Everything You Need To Know

What is the m.3243A>G mutation and why is it significant?

The m.3243A>G mutation is a specific alteration in the mitochondrial DNA (mtDNA). This mutation affects the MT-TL1 gene, which is responsible for producing tRNALEU(UUR), a crucial component for protein synthesis within the mitochondria. This mutation is significant because it is a leading cause of mitochondrial disease in adults and is linked to conditions like MELAS syndrome, MIDD, and hypertrophic cardiomyopathy.

What are mitochondrial DNA (mtDNA) mutations and why are they important?

Mitochondrial DNA (mtDNA) mutations, such as the m.3243A>G mutation, are alterations in the DNA found within the mitochondria, the powerhouses of cells. The m.3243A>G mutation is particularly associated with mitochondrial diseases because it disrupts the normal function of mitochondria, leading to energy production problems in the body. These issues can lead to various health problems.

What does heteroplasmy mean, and why is it relevant to the m.3243A>G mutation?

Heteroplasmy refers to the percentage of mutated mitochondrial DNA (mtDNA) within a cell or tissue. The m.3243A>G mutation's impact is often assessed by measuring heteroplasmy levels. Measuring heteroplasmy helps clinicians understand how severe the mitochondrial disease might be and potentially predict how the disease may progress. The study showed that heteroplasmy levels can significantly fluctuate in urine samples, which may impact reliability.

How are urine tests used for the m.3243A>G mutation?

A urine test for the m.3243A>G mitochondrial mutation is a non-invasive method to assess the heteroplasmy levels. This involves analyzing a urine sample to determine the percentage of mutated mtDNA present. However, the study found that these levels can vary significantly from day to day. Because of this variation, relying on a single urine test to assess disease severity or predict outcomes might not be reliable.

What did the new study reveal about urine tests for mitochondrial mutations?

The new study revealed that urine tests for the m.3243A>G mutation can show significant day-to-day variations. While some participants had stable heteroplasmy levels, others showed variations exceeding 20%. These fluctuations suggest that a single urine test might not accurately reflect the overall severity of the mitochondrial disease. The study highlights the need for caution when using urine tests to assess mitochondrial DNA mutations due to the potential for misleading results.