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Can changes in noncoding DNA affect health and development?
Reviewed by Medicinsk Expert•Last updated: 2026-10-22•Mutationsanddisorders

Can changes in noncoding DNA affect health and development?

While noncoding DNA does not contain genes, variants in these regions can disrupt gene regulation and protein production, leading to various health conditions.

The Role of Noncoding DNA

Scientists have determined that changes in regions of DNA that do not contain genes—known as noncoding DNA—can lead to disease. Many of these regions control gene activity, determining when and where genes are turned on or off, or are involved in protein assembly.

A variant in noncoding DNA can disrupt these processes by:

  • Turning on a gene in the wrong place or at the wrong time.
  • Reducing or eliminating the production of an important protein.

Regulatory Elements and Disease

Variants in noncoding DNA can disrupt several types of regulatory elements:

  • Enhancers: Attach proteins that help turn on particular genes. Alterations here are linked to conditions like isolated Pierre Robin sequence, which involves the SOX9 gene.
  • Promoters: Where proteins that turn on genes attach.
  • Insulators: Where proteins that help shape gene activity attach.
  • Silencers: Where proteins that turn off genes attach.

Additionally, some noncoding DNA provides instructions for RNA molecules (such as transfer RNAs, microRNAs, or long noncoding RNAs) that regulate gene activity or assemble proteins. Interrupting these molecules has also been implicated in disease.

Types of Genetic Changes

The same types of genetic changes that affect genes—such as substitution variants, insertions, deletions, duplications, and translocations—can affect health when they occur in noncoding DNA. These variants can be inherited or acquired during a person’s life. Because much is still unknown about the function of noncoding regions, linking these genetic changes to specific health conditions remains a growing and complex area of research.

Frequently Asked Questions

Most standard clinical diagnostic tools, such as whole exome sequencing (WES), analyze only the protein-coding exons, which represent roughly 1 to 2 percent of the human genome. Identifying changes in noncoding regulatory regions usually requires whole genome sequencing (WGS) or targeted chromosomal microarrays, which analyze the remaining 98 percent of the genetic code.
Noncoding DNA contains crucial regulatory switches, including enhancers and promoters, that signal genes when and where to activate during embryonic development. If an enhancer that guides tissue formation is mutated or deleted—such as enhancers controlling the SOX9 gene—the target gene fails to turn on at the exact developmental window required, resulting in structural anomalies like cleft palate or isolated Pierre Robin sequence.
variant of uncertain significance (VUS) means a genetic change was detected, but scientists currently lack adequate functional or population data to classify it as either harmless or disease-causing. Because noncoding regions do not follow a predictable triplet-codon protein code, determining whether a specific noncoding change disrupts transcription factors or RNA structures is challenging, resulting in frequent VUS classifications.
Noncoding variations can be both inherited (germline) and acquired (somatic). Somatic noncoding variants develop over a person's lifetime due to cellular division errors or environmental damage like ultraviolet radiation and chemical carcinogens. For example, acquired mutations in the noncoding promoter region of the TERT gene are common driver mutations in several cancers, causing telomerase to remain abnormally active.
Source: MedlinePlus, National Library of Medicine

MedlinePlus brings together authoritative health information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), and other government agencies and health-related organizations.

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