Galactosemia Type II (Galactokinase Deficiency) via the GALK1 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
9609 GALK1 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9609GALK181479 81479(x2) $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 Type II is caused by a defect in galactose metabolism, resulting in an elevated level of total galactose and derivative metabolites. In the vast majority of affected patients, the only clinical and biochemical findings are bilateral cataracts, galactosemia and increased urinary galactitol. However, a few patients have been reported with intellectual disability or pseudotumor cerebri. The onset of symptoms is usually within the first weeks or months of life. This disorder is treated by restricting dietary intake of galactose and lactose, and if treatment is started early, symptoms are preventable or reversible. However, in cases where treatment is not begun until after cataracts have already formed, the damage may not be reversible by dietary restriction and surgery may be required (Fridovich-Keil and Walter 2014).

In countries where newborn screening programs operate, such programs typically identify galactosemic individuals shortly after birth. However, in cases where the first round of screening is based on GALT enzyme activity alone, individuals with galactosemia type II rather than GALT-deficient classical galactosemia may be missed (Berry 2014; Fridovich-Keil and Walter 2014).

Genetics

Galactosemia Type II is an autosomal recessive disorder, and GALK1 is the only gene in which defects are known to cause galactokinase deficiency (Fridovich-Keil and Walter 2014). To date, over 35 causative variants have been reported in the GALK1 gene (Kalaydjieva et al. 1999; Kolosha et al. 2000; Okano et al. 2001; Park et al. 2007; Stambolian et al. 1995; Human Gene Mutation Database). Roughly two-thirds are missense variants, although nonsense, frameshift and small insertion and deletion variants have also been reported. The variants are spread throughout the coding regions of GALK1, although they tend to be somewhat clustered near conserved functional regions in exons 1, 3 and 7 (Fridovich-Keil and Walter 2014). The Pro28Thr variant has been reported to be a founder mutation in individuals of Romani and southeastern European descent (Kalaydjieva et al. 1999). The relatively mild Ala198Val variant has been found to be common in Japanese and Korean patients and has been termed the Osaka variant (Okano et al. 2001). The Gln382* variant has been reported to be common in patients from Costa Rica (Kolosha et al. 2000). No other pathogenic variants have been reported to be particularly common.

Galactosemia Type II is caused by defects in the galactokinase protein, which is encoded by the GALK1 gene. This enzyme is part of the galactose metabolism pathway in many organisms and performs the first step in the Leloir pathway, converting galactose to galactose-1-phosphate. While the phosphorylation reaction performed by galactokinase is reversible, the reaction equilibrium leans heavily in favor of galactose-1-phosphate formation (Berry 2014; Fridovich-Keil and Walter 2014). In the absence of galactokinase activity, galactose builds up and is converted to other metabolites, including galactitol, at a higher rate than normal. Excess galactitol accumulation in the lens of the eye leads to osmotic irregularities, which is thought to be the cause of cataract formation (Okano et al. 2001; Fridovich-Keil and Walter 2014).

Clinical Sensitivity - Sequencing with CNV PGxome

Using DNA sequencing, Kolosha et al. (2000) analyzed the GALK1 gene from thirteen probands with low levels of erythrocyte galactokinase activity. Causative variants were found in the homozygous or compound heterozygous state in all thirteen probands (100%). Additionally, Kalaydjieva et al. (1999) used DNA sequencing to analyze the GALK1 gene in eight galactokinase deficient Romani children, and found the same variant (c.82C>A, p.Pro28Thr) in the homozygous state in all eight (100%). Additionally, this same variant was identified in the heterozygous state in all unaffected family members.Overall, the analytical sensitivity of this test is expected to be high because all pathogenic variants in the GALK1 gene reported to date are detectable via DNA sequencing.

To date, there have been no reported gross deletions or duplications in the GALK1 gene (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the GALK1 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).

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

Patients identified as galactosemic via newborn screening or other biochemical testing, especially individuals with elevated total galactose, elevated urinary galactitol, normal GALT enzyme activity levels and decreased GALK enzyme activity levels, are good candidates for this test. Infants with bilateral cataracts that develop within the first weeks or months of life are also good candidates for this test (Berry 2014; Fridovich-Keil and Walter 2014). Lastly, family members of patients who have known GALK1 variants are candidates. We will also sequence the GALK1 gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
GALK1 604313
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Deficiency Of Galactokinase AR 230200

Related Tests

Name
Congenital Cataracts Panel
Epimerase Deficiency Galactosemia via the GALE Gene
Galactosemia Type I (Classic and Variant Galactosemia) via the GALT Gene, 5.5 kb Common Deletion

Citations

  • 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
  • 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.
  • Human Gene Mutation Database (Bio-base).
  • Kalaydjieva L, Perez-Lezaun A, Angelicheva D, Onengut S, Dye D, Bosshard NU, Jordanova A, Savov A, Yanakiev P, Kremensky I, Radeva B, Hallmayer J, Markov A, Nedkova V, Tournev I, Aneva L, Gitzelmann R. 1999. A founder mutation in the GK1 gene is responsible for galactokinase deficiency in Roma (Gypsies). Am. J. Hum. Genet. 65: 1299–1307. PubMed ID: 10521295
  • Kolosha V, Anoia E, Cespedes C de, Gitzelmann R, Shih L, Casco T, Saborio M, Trejos R, Buist N, Tedesco T, Skach W, Mitelmann O, Ledee D, Huang K, Stambolian D. 2000. Novel mutations in 13 probands with galactokinase deficiency. Hum. Mutat. 15: 447–453. PubMed ID: 10790206
  • Okano Y, Asada M, Fujimoto A, Ohtake A, Murayama K, Hsiao K-J, Choeh K, Yang Y, Cao Q, Reichardt JKV, Niihira S, Imamura T, Yamano T. 2001. A Genetic Factor for Age-Related Cataract: Identification and Characterization of a Novel Galactokinase Variant, “Osaka,” in Asians. Am J Hum Genet 68: 1036–1042. PubMed ID: 11231902
  • Park H-D, Bang Y-L, Park KU, Kim JQ, Jeong B-H, Kim Y-S, Song Y-H, Song J. 2007. Molecular and biochemical characterization of the GALK1 gene in Korean patients with galactokinase deficiency. Mol. Genet. Metab. 91: 234–238. PubMed ID: 17517531
  • Stambolian D, Ai Y, Sidjanin D, Nesburn K, Sathe G, Rosenberg M, Bergsma DJ. 1995. Cloning of the galactokinase cDNA and identification of mutations in two families with cataracts. Nat. Genet. 10: 307–312. PubMed ID: 7670469

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

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1) Select Test Method (Backbone)


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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.
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