GALNT3-Related Disorders via the GALNT3 Gene
- Summary and Pricing
- Clinical Features and Genetics
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For ordering targeted known variants, please proceed to our Targeted Variants landing page.
The great majority of tests are completed within 18 days.
Clinical sensitivity of this test is expected to be high as, to date, all reported patients have been found to be homozygous or compound heterozygous for two pathogenic variants detectable via direct sequencing, suggesting a clinical sensitivity near 100% (Finer et al. 2014; Rafaelsen et al. 2014; Demellawy et al. 2015; Masi et al. 2015; Viera et al. 2015).
Hyperphosphatemic Familial Tumoral Calcinosis (HFTC) and Hyperphosphatemic Hyperostosis Syndrome (HHS) are rare, allelic disorders associated with defects in the GALNT3 gene (Frishberg et al. 2005; Rafaelsen et al. 2014). HFTC patients develop periarticular and other ectopic calcifications that can be debilitating. These calcified masses often develop in areas around the hips, elbows, shoulders and knees, although they can develop in other locations. Surgical removal of the masses may be the only viable treatment. These patients may also develop secondary skin and bone infections, painful skin ulcerations, scarring and incapacitating mutilation. Dental abnormalities are also occasionally reported (Topaz et al. 2004; Ichikawa et al. 2005; Campagnoli et al. 2006; Rafaelsen et al. 2014). In contrast, HHS patients do not develop such calcifications, and skin findings are rarely reported in these individuals. Clinically, HHS patients present with recurrent, transient painful swelling of long bones, which may be mistaken for osteosarcoma or other bone malignancies. These patients have been found to have periosteal reactions, diaphysitis, and cortical hyperostosis upon radiological exam (Frishberg et al. 2005).
Although the clinical manifestations are different, the biochemical hallmarks of HFTC and HHS are quite similar. These patients present with persistent hyperphosphatemia with normal serum calcium levels, normal or only slightly elevated levels of 1,25-dihydroxyvitamin D and low or low normal parathyroid hormone levels (Joseph et al. 2010).
Some patients have presented with a combined HFTC + HHS phenotype. In addition, the same GALNT3 variant(s) may lead to HHS in one family member, but HFTC in another (Topaz et al. 2004; Frishberg et al. 2005). Onset of these disorders ranges from childhood to adulthood (Rafaelsen et al. 2014).
Both HFTC and HHS are autosomal recessive disorders. Pathogenic variants in the GALNT3 gene are the most common cause of HFTC and HHS, although variants in the FGF23 and KL genes are also associated with HFTC (Rafaelsen et al. 2014). To date, nearly 30 different causative variants have been reported in the GALNT3 gene. The majority of reported variants are nonsense, splicing or missense variants, although a few small deletions or insertions have also been reported (Human Gene Mutation Database). The variants are spread throughout the gene, and no variants have been reported to be common across multiple ethnic groups.
The GALNT3 gene encodes the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3) enzyme. This enzyme is required for the glycosylation of the protein fibroblast growth factor 23 (FGF23), which is involved in regulating phosphate levels. Pathogenic variants that lead to defective GalNAc-T3 are thought to prevent the glycosylation of FGF23, thereby allowing its breakdown and inactivation (Garringer et al. 2006; Rafaelsen et al. 2014).
This test involves bidirectional Sanger sequencing using genomic DNA of all coding exons of the GALNT3 gene plus ~10 bp of flanking non-coding DNA on each side. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
Patients with clinical and/or biochemical features of Hyperphosphatemic Familial Tumoral Calcinosis (HFTC) and/or Hyperphosphatemic Hyperostosis Syndrome (HHS) are candidates for this test. Family members of patients known to have GALNT3 variants are also good candidates, and we will also sequence the GALNT3 gene to determine carrier status.
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- Genetic Counselor Team - firstname.lastname@example.org
- McKenna Kyriss, PhD - email@example.com
- Campagnoli M.F. et al. 2006. Journal of Clinical Pathology. 59: 440-2. PubMed ID: 16567474
- Demellawy D.E. et al. 2015. Scandinavian Journal of Rheumatology. 44: 170-2. PubMed ID: 25351881
- Finer G. et al. 2014. American Journal of Medical Genetics. Part A. 164A: 1545-9. PubMed ID: 24668887
- Frishberg Y. et al. 2005. Journal of Molecular Medicine. 83: 33-8. PubMed ID: 15599692
- Garringer H.J. et al. 2006. The Journal of Clinical Endocrinology and Metabolism. 91: 4037-42. PubMed ID: 16868048
- Human Gene Mutation Database (Bio-base).
- Ichikawa S. et al. 2005. The Journal of Clinical Endocrinology and Metabolism. 90: 2420-3. PubMed ID: 15687324
- Joseph L. et al. 2010. Skeletal Radiology. 39: 63-8. PubMed ID: 19830424
- Masi L. et al. 2015. Calcified Tissue International. 96: 438-52. PubMed ID: 25899975
- Rafaelsen S. et al. 2014. Bmc Genetics. 15: 98. PubMed ID: 25249269
- Topaz O. et al. 2004. Nature Genetics. 36: 579-81. PubMed ID: 15133511
- Vieira A.R. et al. 2015. Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology. 120: e235-9. PubMed ID: 26337219
Bi-Directional Sanger Sequencing
Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org). As required, DNA is extracted from the patient specimen. PCR is used to amplify the indicated exons plus additional flanking non-coding sequence. After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions. In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.
As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.
Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).
In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.
Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.
In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.
In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.
Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.
Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.
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.
- 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.
(Delivery accepted Monday - Saturday)
- Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
- For small babies, we require a minimum of 1 ml of blood.
- Only one blood tube is required for multiple tests.
- Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
- During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
- In cold weather, include an unfrozen ice pack in the shipping container as insulation.
- At room temperature, blood specimen is stable for up to 48 hours.
- If refrigerated, blood specimen is stable for up to one week.
- Label the tube with the patient name, date of birth and/or ID number.
(Delivery accepted Monday - Saturday)
- Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
- For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
- DNA may be shipped at room temperature.
- Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
- We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.
(Delivery preferred Monday - Thursday)
- PreventionGenetics should be notified in advance of arrival of a cell culture.
- Culture and send at least two T25 flasks of confluent cells.
- Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
- Send specimens in insulated, shatterproof container overnight.
- Cell cultures may be shipped at room temperature or refrigerated.
- Label the flasks with the patient name, date of birth, and/or ID number.
- We strongly recommend maintaining a local back-up culture. We do not culture cells.