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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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Related Experiment Video

Updated: Jul 23, 2025

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Synonymous Variants of Uncertain Silence.

Christopher J Giacoletto1,2,3, Jerome I Rotter2,4, Wayne W Grody5,6,7

  • 1Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA.

International Journal of Molecular Sciences
|July 14, 2023
PubMed
Summary
This summary is machine-generated.

Synonymous variants are not always silent. Many synonymous variants show significant functional deviations, challenging their traditional classification and necessitating careful interpretation in genetic testing.

Keywords:
sequencesilent variantsynonymous variantvariant interpretation

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Synonymous variants, or "silent mutations," traditionally do not alter protein sequences.
  • Emerging evidence suggests some synonymous variants can impact protein function, challenging this long-held assumption.
  • Understanding the functional impact of these variants is crucial for accurate genetic interpretation.

Purpose of the Study:

  • To investigate the functional activity of synonymous variants.
  • To challenge the notion that synonymous variants are functionally inert.
  • To propose a new classification for functionally relevant synonymous variants.

Main Methods:

  • Analysis of 70 synonymous variants within the HIV Tat transcription factor.
  • Assessment of variant activity compared to wild-type.
  • Review of existing literature on synonymous variant function.

Main Results:

  • 50% of analyzed synonymous variants exhibited significant deviations from wild-type activity.
  • Findings support previous research indicating functional roles for certain synonymous variants.
  • The study highlights the potential for non-silent synonymous variants in human genes.

Conclusions:

  • Synonymous variants can possess significant functional impact, contrary to traditional views.
  • The authors propose classifying these variants as "synonymous variants of uncertain silence" (sVUS).
  • This classification underscores the need for cautious interpretation and further research in clinical and genetic settings.