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Intellectual Disability via the PIGG Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PIGG 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8145PIGG81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks 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.


Genetic Counselors


  • Renee Bend, PhD

Clinical Features and Genetics

Clinical Features

Intellectual Disability (ID) is a heterogeneous group of neurodevelopmental disorders, characterized by congenital limitation in intellectual functioning (intelligence quotient, IQ ≤70) and adaptive behavior. It is diagnosed in ~1–3% of the population before 18 years of age (American Association of Intellectual and Developmental Disabilities, AAIDD).

Glycosylphosphatidylinositol (GPI) is a glycolipid that anchors various proteins to the cell surface. Defects in GPI biosynthesis cause congenital disorders of glycosylation, with clinical features including intellectual disability. PIGG-related GPI deficiency leads to a form of syndromic ID (Mental retardation, autosomal recessive 53, MRT53). The clinical features of MRT53 are variable and may include (but may not be limited to) delayed psychomotor development, intellectual disability, poor/absent speech, early-onset seizures, autistic features, cerebellar hypoplasia, ataxia, cerebral atrophy, hyporeflexia, joint laxity, muscular hypotonia, feeding difficulties, hearing impairment, growth retardation, dysmorphic features including hypertelorism, broad nose, depressed nasal bridge, thin upper lip and abnormalities of the head, neck, skeletal, genitourinary and cardiac systems (Makrythanasis et al. 2016. PubMed ID: 26996948; Zhao et al. 2017. PubMed ID: 28581210). Of note, some patients have been reported with increased serum alkaline phosphatase.


Pathogenic variants in human gene “Phosphatidylinositol glycan anchor biosynthesis class G protein” (PIGG) cause an autosomal recessive form of intellectual disability. PIGG maps to chromosome 4p16.3 and consists of 13 coding exons that translate into a 983 amino acid polypeptide. PIGG (alternatively known as GPI7) is an ER (endoplasmic reticulum)-associated phosphatidyl glycan that forms a complex with PIGF and attaches ethanolamine phosphate (EtNP) to the second mannose of GPI-AP (GPI-anchored protein) backbone, thus impacting the regulation of glycosylphostidylinositol (GPI) biosynthesis (Shishioh et al. 2005. PubMed ID: 15632136; Zhao et al. 2017. PubMed ID: 28581210). To date, missense, nonsense and splice site variants have been reported in human PIGG gene (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

This test is predicted to detect pathogenic variants in <0.1% of individuals with intellectual disability (ID). In this context, it is important to note that although pathological variants over 800 genes have been identified in individuals with ID, a genetic diagnosis is still lacking in most cases due to extreme clinical and genetic heterogeneity of the condition (Vissers et al. 2016. PubMed ID: 26503795). Analytical sensitivity should be high because the majority of pathogenic variants reported within this gene to date are detectable by sequencing. To date, one gross deletion involving PIGG has been reported (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the PIGG gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

This test is primarily implicated for the patients with intellectual disabilities who are negative for any kind of cytogenetic abnormalities, copy number variations, and Fragile-X syndrome and also for the family members of the patients who have PIGG pathogenic variants. Prenatal diagnosis is possible, if the genetic diagnosis has been firmly established in an affected family member. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PIGG.


Official Gene Symbol OMIM ID
PIGG 616918
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Mental Retardation, Autosomal Recessive 53 AR 616917


  • Makrythanasis et al. 2016. PubMed ID: 26996948
  • Shishioh et al. 2005. PubMed ID: 15632136
  • Vissers et al. 2016. PubMed ID: 26503795
  • Zhao et al. 2017. PubMed ID: 28581210


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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

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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