Inherited Glycosylphosphatidylinositol Biosynthesis Defects (IGDs) Panel

Inherited glycosylphosphatidylinositol (GPI) biosynthesis defects (IGDs) are a group of related conditions that are caused by improperly synthesized GPI anchors and include disorders such as Mabry syndrome, CHIME, hyperphosphatasia with mental retardation syndrome, and multiple congenital anomalies-hypotonia-seizures syndrome. Pathogenic variants within genes responsible for GPI-anchor biosynthesis result in a wide spectrum of clinical phenotypes that can range from mild to severe depending on where the variant occurs in the pathway and the degree to which protein function is impacted (Bellai-Dussault et al. 2019. PubMed ID: 30054924; Ng and Freeze. 2015. PubMed ID: 25164783).

IGDs typically present within the neonatal period and are a rare cause of developmental delay. The incidence of IGDs within a study of 4,000 trios consisting of a proband with a developmental disorder and their unaffected parents was ~0.15% (Pagnamenta et al. 2017. PubMed ID: 28327575). The main/uniting clinical features of IGDs include global developmental delay, intellectual disability, seizures, and hypotonia. Other common features of IGDs can include microcephaly, facial dysmorphism (variable), hyperphoshatasia (variable) and neurological anomalies (tremors, spasticity, rigidity, ataxia, and dystonia). Minor clinical features of IGDs, which are typically associated with specific gene defects, can include the following: hearing impairment, ophthalmological (colobomas, cortical visual impairment, strabismus, nystagmus), cardiac (ventricular septum defects, atrial septal defect, patent ductus arteriousis), urological/renal (ureteral dilation, hydronephrosis, and dysplastic kidney), gastrointestinal (GERD, Hirshsprung disease, anal atresia, anal stenosis, and anteriorly placed anus), nephrocalcinosis, dental (widely spaced teeth, microdontia, abnormal shape, absence of teeth), hand and foot (clinodactyly, oligodactyly, brachytelephalangy, nail hypoplasia) skeletal (scoliosis, osteoporosis, delayed bone age, hip dysplasia), brain (thin corpus callosum, cerebellar and cerebral atrophy, white matter loss, delayed myelination), and polyhydramnios.

Because IGDs are rare with clinical features that are highly variable and often overlap with other developmental disorders, genetic testing is increasingly recognized as an important diagnostic tool (Freeze et al. 2014. PubMed ID: 24507773). Genetic testing can also yield recurrence risks and provide benefit to families for purposes of reproductive planning. Although therapies for IGDs are currently limited, genetic testing and diagnosis may also help to inform treatment options. For example, treatment with sodium phenylbutyrate led to improvement or remission of seizures in individuals with PIGM promoter variants (Almeida et al. 2007. PubMed ID: 17442906; Pode-Shakked et al. 2019. PubMed ID: 31445883). Additionally, a patient with PIGO variants experienced remission of seizures when treated with pyridoxine (B6) (Kuki et al. 2013. PubMed ID: 24049131).

IGDs are mostly inherited in an autosomal recessive manner. One exception to this are IGDs related to variants in PIGA which are inherited through an X-linked recessive manner. Males with pathogenic variants in PIGA present with a severe phenotype while female carriers are unaffected (Johnston et al. 2012. PubMed ID: 22305531; Belet et al. 2014. PubMed ID: 24357517). Somatic variants in PIGA have also been reported in individuals with paroxysmal nocturnal hemoglobinuria (Savoia et al. 1996. PubMed ID: 8557259; Bessler and Hiken. 2008. PubMed ID: 19074066).

The majority of IGD causing-variants are missense, nonsense, and frameshift variants. Splicing variants as well as partial/whole gene duplications and deletions have been reported in a few cases (PIGL: Ng et al. 2012. PubMed ID: 22444671; PIGG: Makrythanasis et al. 2016. PubMed ID: 26996948). De novo variants in IGDs have not been reported.

The GPI anchor is a highly conserved post-translational modification used by over 150 proteins to appropriately traffic within the cell, attach to the outer leaflet of the cell membrane, and partake in a vast array of essential cellular functions including enzymatic activity, cell-cell adhesion, cellular recognition, signaling, transport, and migration. GPI-anchor biosynthesis occurs through a series of steps that can be broken down into three stages. The entire process requires over 30 proteins and takes place in both the endoplasmic reticulum (ER) and the golgi. The first stage begins on the cytoplasmic side of the ER with a complex of proteins (PIGA, PIGC, PIGH, PIGP, PIGQ and PIGY) initiating the attachment of a carbohydrate moiety to a lipid base. After a processing step by PIGL, the GPI-anchor is flipped to the inside of ER. Additional carbohydrate moieties are added and modified through a series of enzymatic steps by PIGW, PIGM, PIGX, PIGV, PIGB, PIGN, PIGF, PIGO, and PIGG. During the second stage of the GPI-anchor biosynthesis pathway, the GPI-anchor is transferred to the C-terminus of a protein by a second complex of proteins (PIGT, PIGK, PIGS, PIGU, and GPAA1). Once the GPI-anchor is attached, the third step of synthesis begins and involves further modification of the GPI-anchor, by PGAP1 and PGAP5. At this point, the protein-GPI-anchor complex is transfered to the lumen of the golgi where further processing is carried out by PGAP3 and PGAP2. After processing is complete, GPI-anchored proteins are sorted into distinct vesicles and are then delivered to the cellular membrane where they typically associate with microdomains or lipid rafts (Zurzolo and Simons. 2016. PubMed ID: 26706096). For comprehensive reviews of this process, see Kinoshita and Fujita. 2016. PubMed ID: 26563290, and Maeda and Kinoshita. 2011. PubMed ID: 21658410.

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

IGDs are rare and many clinical features have variable severity and overlap with other developmental disorders, making it difficult to estimate the clinical sensitivity of this test. Measurement of alkaline phosphatase (AP), a GPI-anchored protein, through blood testing has helped to diagnose certain IGDs that result in elevation of AP (hyperphosphatasia) (Mabry et al. 1970. PubMed ID: 5465362; Chiyonobu et al. 2014. PubMed ID: 24367057). However, hyperphosphatasia is not a hallmark feature of all IGDs and therefore not an ideal test for clinical classification. Additionally, fluorescence-activated cell sorting (FACS) has been used clinically to measure cell surface expression of GPI-anchored proteins through labelling of CD59, CD55, and the GPI-anchor (FLAER) in individuals with IGDs (Knaus et al. 2018. PubMed ID: 29310717; Sutherland et al. 2007. PubMed ID: 17285629). Facial gestalt software may also help to diagnoses individuals with IGDs (Knaus et al. 2018. PubMed ID: 29310717).

Analytical sensitivity should be high as all reported pathogenic variants are detectable by sequencing.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.9% coverage of all coding exons of the genes 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 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).