Galactosemia Type I (Classic and Variant Galactosemia) via the GALT Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
9613 GALT 81406 81406,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9613GALT81406 81406(x1), 81479(x1) $890 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Galactosemia is a defect in the metabolism of galactose resulting in elevated levels of galactose and derivatives such as galactose-1-phosphate and galactitol. Severity of this disorder is quite variable, though it is generally categorized into three groups based on patient phenotype (Berry 2014). The first is the most severe “classic” form with onset in early infancy, and is characterized by feeding difficulties, vomiting, diarrhea, jaundice, cataracts, hypotonia, hepatomegaly and sepsis. If the amount of lactose in the diet is not reduced in the first days of life, these symptoms progress to death. Even in surviving patients, ovarian failure and lifelong speech and cognitive disabilities are expected (Berry 2014; Fridovich-Keil and Walter 2014). The second phenotypic category is termed "clinical variant" galactosemia, which also presents early in infancy and is more common in African Americans and native Africans in South Africa (Crushell et al. 2009; Berry 2014; Fridovich-Keil and Walter 2014). These patients tend to present with feeding difficulties, which may include failure to thrive, and hepatocellular damage, such as cirrhosis and bleeding. In these patients, if a lactose-restricted diet is implemented within the first days of life, the severe neonatal complications are typically prevented and the patients do not appear to be at risk for long-term complications (Berry 2014). The third phenotypic category is termed "biochemical variant galactosemia", the most common form of which is "Duarte variant galactosemia". Biochemical variant galactosemia is currently not thought to result in clinical disease in most patients (Berry 2014; Fridovich-Keil et al. 2014).

Today in wealthy nations, nearly all cases of classic galactosemia are detected through routine neonatal screening. However, it may be more difficult to detect patients with clinical and biochemical variant galactosemias because the galactose level in such patients is not as high as in classic galactosemia patients, and results of breath testing may be normal (Berry 2014). In situations where the activity of the GALT enzyme is always tested or the patient is fed enough lactose, clinical and biochemical variant galactosemias should be detectable (Berry 2014; Fridovich-Keil et al. 2014).

Genetics

Galactosemia is an autosomal recessive disorder. Pathogenic variants in the GALT gene are the primary genetic cause of galactosemia. Relatively small numbers of cases are caused by pathogenic variants in the GALK1 (galactokinase) and GALE (UDPgalactose-4’-epimerase) genes. GALT encodes the enzyme galactose-1-phosphate uridyltransferase. Over 300 causative GALT variants have been reported to date (Human Gene Mutation Database; ARUP GALT Database at http://arup.utah.edu/database/GALT/GALT_display.php). Roughly 70% of these variants are missense, although frameshift, nonsense, splicing, small insertions and deletion variants and gross deletions have all been reported. The Gln188Arg variant is the most common cause of classic galactosemia, comprising up to 50% of all causative alleles in U.S. classic galactosemia patients and higher fractions among patients with western European ancestry (Berry 2014). Other common variants associated with classic galactosemia are the Lys285Asn and Leu195Pro missense variants, and a 5.5 kb complex deletion common in individuals of Ashkenazi Jewish descent. The Ser135Leu variant is particularly common among patients with African ancestry and is associated with clinical variant galactosemia (Suzuki et al. 2001; Crushell et al. 2009), whereas a 4-bp deletion in the GALT promoter, termed c.-119_-116delGTCA or D2 allele, is currently considered to be the main cause of Duarte variant galactosemia (Berry 2014). The Asn314Asp missense variant is usually found on the D2 allele together with the c.-119_-116delGTCA promoter variant, but as this missense variant also occurs on functionally normal GALT alleles, it is no longer considered to be a contributing factor to Duarte variant galactosemia (Berry 2014).

Testing for the 5.5 kb GALT deletion is available separately.

Clinical Sensitivity - Sequencing with CNV PGxome

Using DNA sequencing, Bosch et al. (2005) reported detection of 91% of causative variants in 106 consecutive galactosemia patients. Similarly, Kozák et al. (2000) reported detection of 96% of causative variants in 37 patients. More recently, Boutron et al. (2012) reported detection of 99% of causative variants in a cohort of 210 French families using direct sequencing.

While the great majority of GALT variants are expected to be detected via gene sequencing, several exonic or whole-gene deletions have been reported (Human Gene Mutation Database). In general, these deletions have been observed in a single patient, although a ~5.5 kb complex deletion is common in those of Ashkenazi Jewish descent (Barbouth et al. 2006; Coffee et al. 2006; Berry 2014). If desired, the specific Ashkenazi Jewish ~5.5 kb deletion can also be detected by our PCR-based deletion test.

Testing Strategy

This test provides full coverage of all coding exons of the GALT gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Our test covers the 4 bp deletion in the promoter region upstream of exon 1 (c.-119_-116 delGTCA) that has been shown to decrease enzyme activity in the Duarte allele (Elsas et al. 2001; Berry 2014).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

All patients with reduced galactose-1-phosphate uridyltransferase activity are candidates for this test. We will also sequence the GALT gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
GALT 606999
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Galactosemia AR 230400

Related Tests

Name
Galactosemia Type I (Classic and Variant Galactosemia) via the GALT Gene, 5.5 kb Common Deletion
Premature Ovarian Failure (POF) Panel

Citations

  • Barbouth D. et al. 2006. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 8: 178-82. PubMed ID: 16540753
  • Berry GT. 2014. Classic Galactosemia and Clinical Variant Galactosemia. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301691
  • Bosch A.M. et al. 2005. Human Mutation. 25: 502. PubMed ID: 15841485
  • Boutron et al. 2012. Molecular Genetics and Metabolism. 107:438-447 PubMed ID: 22944367
  • Coffee B. et al. 2006. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 8: 635-40. PubMed ID: 17079880
  • Crushell E. et al. 2009. Journal of Inherited Metabolic Disease. 32:412-5. PubMed ID: 19418241
  • Elsas L.J. et al. 2001. Molecular Genetics and Metabolism. 72: 297-305. PubMed ID: 11286503
  • Fridovich-Kei J.L. et al. 2014. Duarte Variant Galactosemia. In: Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 25473725
  • Fridovich-Keil J.L., Walter J.H. 2014. Galactosemia. In: Valle D, Beaudet A.L., Vogelstein B, et al., editors. New York, NY: McGraw-Hill. OMMBID.
  • Kozák L. et al. 2000. Human Mutation. 15: 206. PubMed ID: 10649501
  • Suzuki M. et al. 2001. Human Genetics. 109: 210-5. PubMed ID: 11511927

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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