Hyperphosphatasia with Intellectual Disability via the PIGO Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
2933 PIGO$910.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

In a study of 11 families with elevated alkaline phosphatase levels who tested negative for variants in the PIGV gene, 1 family was found to be compound heterozygous for pathogenic PIGO variants (9%)(Krawitz et al. 2012).

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Clinical Features

Hyperphosphatasia with mental retardation syndrome-2 or Mabry syndrome (HPRMS2) is a neurological condition characterized by developmental delay and seizures. Psychomotor delay is first noticed around 6 months; patients are hypotonic and motor milestones are delayed. Physical features include a broad nasal bridge, tented lip, and hypoplasia of the fingers and or/nails (Kuki et al. 2013, Nakamura et al. 2014). Seizure onset occurs between 1 and 2 years of age, with most patients experiencing refractory tonic-clonic seizures. There has been a report that patients with PIGO variants may respond well to pyridoxine for seizure control (Kuki et al. 2013). EEG reveals slow waves and multifocal spikes (Krawitz et al. 2012; Kuki et al. 2013). MRI is variable with some patients showing hypomyelination and cerebellar atrophy (Kuki et al. 2013). HPRMS2 patients are severely intellectually disabled and do not acquire meaningful speech.

Biochemical indications of HPRMS2 include elevated levels of serum alkaline phosphatase (ALP) and reduced levels of GPI-anchored proteins on the surface of blood granulocytes as assayed via flow cytometry (Kuki et al. 2013).


HPRMS2 is caused by variants in the PIGO gene and is inherited in an autosomal recessive manner. Pathogenic missense, nonsense, splice site, and frameshift variants in PIGO have been reported (Krawitz et al. 2012; Kuki et al. 2013; Nakamura et al. 2014).

 GPIs (glycosylphosphatidylinositol) are glycolipids that are covalently attached to the C-terminus of select proteins and anchor the proteins to the cell surface. Mutations in genes that are part of the GPI-anchor-synthesis pathway result in an array of clinical phenotypes, which are considered to be a subclass of congenital disorders of glycosylation. The PIGO gene encodes GPI ethanolamine phosphate transferase 3, which is required for GPI biosynthesis (Hong et al. 2000). Variants in PIGO lead to defects in GPI biosynthesis, decreased expression of proteins on the cell-surface, and elevated serum levels of alkaline phosphatase (hyperphosphatasia).

Testing Strategy

This test involves bidirectional Sanger sequencing using genomic DNA of all coding exons of the PIGO gene plus ~20 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

PIGO sequencing should be considered in patients with elevated serum alkaline phosphatase levels and symptoms of HPMRS2 or Mabry disease.


Official Gene Symbol OMIM ID
PIGO 614730
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Early Infantile Epileptic Encephalopathy, Recessive Sequencing Panel


Genetic Counselors
  • Hong Y, Maeda Y, Watanabe R, Inoue N, Ohishi K, Kinoshita T. 2000. Requirement of PIG-F and PIG-O for Transferring Phosphoethanolamine to the Third Mannose in Glycosylphosphatidylinositol. Journal of Biological Chemistry 275: 20911–20919. PubMed ID: 10781593
  • Krawitz PM, Murakami Y, Hecht J, Krüger U, Holder SE, Mortier GR, Delle Chiaie B, Baere E De, Thompson MD, Roscioli T, Kielbasa S, Kinoshita T, Mundlos S, Hecht J, Robinson PN, Horn D. 2012. Mutations in PIGO, a Member of the GPI-Anchor-Synthesis Pathway, Cause Hyperphosphatasia with Mental Retardation. The American Journal of Human Genetics 91: 146–151. PubMed ID: 23561847
  • Kuki I, Takahashi Y, Okazaki S, Kawawaki H, Ehara E, Inoue N, Kinoshita T, Murakami Y. 2013. Vitamin B6-responsive epilepsy due to inherited GPI deficiency. Neurology 81: 1467–1469. PubMed ID: 24049131
  • Nakamura K, Osaka H, Murakami Y, Anzai R, Nishiyama K, Kodera H, Nakashima M, Tsurusaki Y, Miyake N, Kinoshita T, Matsumoto N, Saitsu H. 2014. PIGO mutations in intractable epilepsy and severe developmental delay with mild elevation of alkaline phosphatase levels. Epilepsia 55: e13–e17. PubMed ID: 24417746
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  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 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 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 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

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).

Analytical Limitations

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 20 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.

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Ordering Options

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.
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