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Updated: Dec 13, 2025

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A founder noncoding GALT variant interfering with splicing causes galactosemia.

Kumarie Latchman1, Jeanette Brown2, Claire J Sineni2

  • 1Division of Clinical and Translational Genetics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Journal of Inherited Metabolic Disease
|August 5, 2020
PubMed
Summary

A rare genetic disorder, galactosemia, can be caused by a deep intronic GALT gene variant. This specific mutation disrupts splicing, leading to reduced enzyme activity and a biochemical variant form of the disease.

Keywords:
GALTMayagalactosemiagenome sequencingnewborn screeningpseudoexon

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Area of Science:

  • Biochemistry
  • Genetics
  • Metabolic Disorders

Background:

  • Galactosemia is a rare, hereditary carbohydrate metabolism disorder.
  • Newborn screening programs identify cases, but some present with decreased GALT enzyme activity despite lacking detectable GALT variants.
  • The etiology of such cases requires further investigation.

Purpose of the Study:

  • To investigate the cause of decreased galactose-1-phosphate uridyltransferase (GALT) enzyme activity in newborns without detectable GALT variants.
  • To identify novel genetic factors contributing to galactosemia.

Main Methods:

  • Genome sequencing was performed on affected individuals.
  • Sanger sequencing was used for confirmation.
  • Segregation analysis within families was conducted.

Main Results:

  • Six individuals from four families of Guatemalan heritage with GALT enzyme activity between 20-34% of normal were identified.
  • All affected individuals were homozygous for a deep intronic GALT variant (c.1059+390A>G).
  • This variant disrupts splicing, causes premature termination, and is linked to a specific haplotype, suggesting a founder effect.

Conclusions:

  • A deep intronic GALT variant (c.1059+390A>G) causes a biochemical variant form of galactosemia.
  • This variant can lead to decreased GALT enzyme activity and may be missed by standard molecular testing.
  • Targeted molecular testing is necessary for diagnosing this specific galactosemia variant.