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The genotypic and phenotypic spectrum of PIGA deficiency Tarailo-Graovac, Maja; Sinclair, Graham; Stockler-Ipsiroglu, Sylvia; Van Allen, Margot; Rozmus, Jacob; Shyr, Casper; Biancheri, Roberta; Oh, Tracey; Sayson, Bryan; Lafek, Mirafe; Ross, Colin J; Robinson, Wendy P; Wasserman, Wyeth W; Rossi, Andrea; van Karnebeek, Clara D Feb 27, 2015

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RESEARCH Open AccessThe genotypic and phenotypic spectrum ofPIGA deficiencyIDD, treatable seizures and generally a longer lifespan.Tarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 DOI 10.1186/s13023-015-0243-8CanadaFull list of author information is available at the end of the articleKeywords: Intellectual disability, Epileptic encephalopathy, Hypotonia, Dysmorphism, Multi-organ involvement,Genomics, Intramyelin edema, Glycosylphosphatidylinositol, Lipoprotein lipase, Alkaline phosphatase, Iron* Correspondence: cvankarnebeek@cw.bc.ca†Equal contributors1Centre for Molecular Medicine and Therapeutics, Vancouver, Canada3Treatable Intellectual Disability Endeavour in British Columbia, Vancouver,Maja Tarailo-Graovac1,2,3†, Graham Sinclair3,4,6†, Sylvia Stockler-Ipsiroglu3,4,7, Margot Van Allen2,7, Jacob Rozmus5,7,Casper Shyr1,2,3, Roberta Biancheri8, Tracey Oh2,7, Bryan Sayson3,4, Mirafe Lafek3,4, Colin J Ross1,2,3,7,Wendy P Robinson2,7, Wyeth W Wasserman1,2,3,7, Andrea Rossi9 and Clara DM van Karnebeek1,3,4,7*AbstractBackground: Phosphatidylinositol glycan biosynthesis class A protein (PIGA) is one of the enzymes involved in thebiosynthesis of glycosylphosphatidylinositol (GPI) anchor proteins, which function as enzymes, adhesion molecules,complement regulators and co-receptors in signal transduction pathways. Until recently, only somatic PIGA mutationshad been reported in patients with paroxysmal nocturnal hemoglobinuria (PNH), while germline mutations had notbeen observed, and were suspected to result in lethality. However, in just two years, whole exome sequencing (WES)analyses have identified germline PIGA mutations in male patients with XLIDD (X-linked intellectual developmentaldisorder) with a wide spectrum of clinical presentations.Methods and results: Here, we report on a new missense PIGA germline mutation [g.15342986C>T (p.S330N)]identified via WES followed by Sanger sequencing, in a Chinese male infant presenting with developmental arrest,infantile spasms, a pattern of lesion distribution on brain MRI resembling that typical of maple syrup urine disease,contractures, dysmorphism, elevated alkaline phosphatase, mixed hearing loss (a combination of conductive andsensorineural), liver dysfunction, mitochondrial complex I and V deficiency, and therapy-responsive dyslipidemia withconfirmed lipoprotein lipase deficiency. X-inactivation studies showed skewing in the clinically unaffected carriermother, and CD109 surface expression in patient fibroblasts was 57% of that measured in controls; together these datasupport pathogenicity of this mutation. Furthermore, we review all reported germline PIGA mutations (1 nonsense,1 frameshift, 1 in-frame deletion, five missense) in 8 unrelated families.Conclusions: Our case further delineates the heterogeneous phenotype of this condition for which we propose theterm ‘PIGA deficiency’. While the phenotypic spectrum is wide, it could be classified into two types (severe and lesssevere) with shared hallmarks of infantile spasms with hypsarrhythmia on EEG and profound XLIDD. In severePIGA deficiency, as described in our patient, patients also present with dysmorphic facial features, multiple CNSabnormalities, such as thin corpus callosum and delayed myelination, as well as hypotonia and elevated alkalinephosphatase along with liver, renal, and cardiac involvement; its course is often fatal. The less severe form of PIGAdeficiency does not involve facial dysmorphism and multiple CNS abnormalities; instead, patients present with milder© 2015 Tarailo-Graovac et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of theCreative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use,distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons PublicDomain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in thisarticle, unless otherwise stated.Tarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 2 of 13BackgroundGlycosylphosphatidylinositol (GPI) is a glycolipid that issynthesized and transferred to proteins in the membraneof the endoplasmic reticulum [1]. Biogenesis of GPI an-chored proteins is a conserved post-translational mecha-nism in eukaryotes and is important for attaching theseproteins to the cell membrane, for protein sorting,trafficking, and dynamics [1], and plays an essential rolein embryogenesis, neurogenesis, immune responses,and fertilization [2-6]. To date, more than 20 phos-phatidylinositol glycan biosynthesis protein (PIG) sub-classes have been found to be involved in GPI anchorbiosynthesis and remodeling, and more than 150 pro-teins carry GPI anchors [1]. An increasing number ofhuman diseases have been discovered to be due to muta-tions in GPI biosynthesis genes.PIGA (MIM 311770) encodes one of the seven proteinsinvolved in the transfer of N-acetylglucosamine (GlcNAc)from UDP-N-acetylglucosamide (UDP-GlcNAc) to phos-phatidylinositol (PI) to form GlcNac-PI [1]. This is thefirst step of GPI anchor biosynthesis and takes place oncytoplasmic side of the endoplasmic reticulum [1]. Thehuman PIGA gene is located on chromosome Xp22.2. Itspans 162 kb and the longest transcript (NP_002632.1) en-codes for a protein of 484 amino acids expressed in a widevariety of tissues including brain, liver, heart, and bloodcells [7]. Somatic PIGA mutations had been well docu-mented in PNH [MIM 300818], an acquired hemolytic dis-ease that manifests after clonal expansion of hematopoieticcells with somatic PIGA mutations, where loss of CD55and CD59 on erythrocytes causes complement-mediatedlysis [8-12]. Unlike somatic PIGA mutations, germline mu-tations had not been observed until recently, and based onexperiments in mice [2] and in both murine [13] and hu-man embryonic stem cells [14] it had been proposed thatgermline PIGA mutations were lethal. In 2012, using anX-chromosome exome next-generation sequencing screen,Biesecker and colleagues identified a PIGA germline non-sense mutation in two siblings with an early epileptic en-cephalopathy with hypotonia, brain anomalies (myelinationabnormalities and a thin corpus callosum), cleft palate,cardiac anomalies and early death [15]. Recently, fouradditional clinical reports were published on patients withgermline PIGA mutations depicting a wide spectrumof phenotypes and clinical diagnoses [7,16-18], inclu-ding West syndrome [18], Multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2) [17,18] andFerro-Cerebro-Cutaneous syndrome (FCCS) [16]. Here, wereport a male patient with MRI brain abnormalities that re-semble those of infants with maple syrup urine disease(MSUD), multi-organ involvement, therapy-responsivedyslipidemia, and reductions of mitochondrial respiratorycomplexes I and V on Blue Native Gel (BNG) analysis.Using WES, we identified in this patient a new missensePIGA germline mutation (g.15342986C>T, c.989G>A[NM_002641], [p.S330N]), which will be referred to asc.989G>A (p.S330N). We also review a total of 8 mutationsfrom 9 unrelated families, summarize clinical findings,discuss genotype–phenotype correlations and identify com-mon features that may be used to guide clinical identifica-tion of patients with germline PIGA mutations.MethodsThis study was approved as part of our TIDEX genediscovery project by the Ethics Board of the Faculty ofMedicine of the University of British Columbia (UBCIRB approval H12-00067). Parents provided written in-formed consent for publication of this report.Case reportThe male index (II:2) was the second child (Figure 1) ofnon-consanguineous healthy Chinese parents with unre-markable family history. Prenatal ultrasound showedmacrosomia and increased nuchal thickness. At 31 weeks6 days gestation the biparietal diameter (BPD) was 89 mm(97th centile), head circumference (HC) was 322 mm(91st centile), abdominal circumference (AC) 330 mm(>99th centile), and femur length (FL) was 64 mm (86thcentil) using B.C. Women’s Health Centre standard mea-surements. At 22 weeks 3 days gestation BPD was 59 mm(89th centile), HC was 215 mm (81st centile), AC was213 mm (>99th centile), and FL 42 mm (89th centile).Nuchal fold measurement at 20 weeks 3 days was 6.9 mm.Maternal serum alpha-fetal protein (AFP) at 16 weeks0 days was 49.1 ug/L which is 1.37 multiples of the mean(MoM). Amniotic fluid AFP was 22.0 mg/L which is3.61 MoM (with a risk assessment for open spina bifida of1:11). Acetylcholinesterase electrophoresis appeared to benormal. Prenatal amniocentesis revealed normal malekaryotype (46,XY). The boy was born at 38 weeks by Cae-sarean section due to breech position with Apgar scores 5and 9. His birth weight was 3975 g (>99th centile), lengthwas 51 cm (~75th centile) and head circumference36.0 cm (98th centile). Dysmorphism was noted at birthbut became more apparent at a later age. Phototherapywas administered during one week for unconjugatedhyperbilirubinemia.The onset of epilepsy was 2.4 months; he had intract-able seizures, which were initially classified as infantilespasms (EEG showed modified hypsarrhythmia), evolv-ing one month later to myoclonic seizures (EEG showedsuppression-burst-like pattern). He showed acquiredmicrocephaly at 8.7 months with an occipital frontal cir-cumference (OFC) of 43 cm (~3rd centile). On exa-mination at 14 months (Figure 1A), our patient showedplagio-brachycephaly with the flattening of the right oc-ciput greater than the left and a prominent right side ofthe face, giving the appearance of facial asymmetry.Tarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 3 of 13There was a frontal hair upsweep with unruly scalp hairand poorly defined eyebrows laterally. He had a roundface with flattening of the lateral profile, a broad fore-head with shallow orbital ridges and supraorbital in-dentations, most likely due to poor muscle function inthe temples. There was glabellar fullness, bilateral ptosiswith hypertelorism (intercanthal distance 3.0 cm; +2SD),upslanted short palpebral fissures (palpebral fissure length2.0 cm; −2.0 SD), and an interpupillary distance of4.95 cm (90th centile). The outercanthal distance was7.0 cm (−1 SD), within normal limits the short palpebralfissures correct for the hypertelorism. The nose was short(2.6 cm; −2 SD) with a low bridge, prominent lateral nasalcartilage and anteverted nares. Ears were of normal size,placement and form. Philtrum appeared relatively longFigure 1 Patient images and pedigree of the family. (A) Facial featuresnew c.989G > A germline PIGA mutation. Sanger sequence verification is shconfirmed to be hemizygous for the variant, while mother was confirmedhave a normal copy of the gene. (C) MRI at age 4 months. Upper row, axiacorresponding apparent diffusion coefficient (ADC) maps; bottom row, axiasignal on DWI (arrows) and corresponding low signal on the ADC maps, atpeduncles, ventral midbrain, subthalamus, and inferior striatum. The same rThe abnormalities selectively involve regions that are normally myelinated(measured 1.2 cm) and smooth. There was retrognathia, atented upper lip with thickened alveolar overgrowth givingthe appearance of a high arched palate (intact). He showeddecreased facial expression. Redundant skin at the neckwas noted, along with contractures of the small and largejoints of upper and lower extremities; no pigmentation orother cutaneous abnormalities were noted. From a neuro-logic perspective there was profound global developmen-tal delay with hyperekplexia, axial hypotonia, peripheralhypertonia, rigidity and abnormal cry. There was de-creased range of motion of all major joints including theshoulders, elbows, wrist and fingers, as well as hips, kneesand ankles. He had hand splints for camptodactyly, deeppalmar creases (because of his fisting) and minimal move-ment of his fingers.of the index patient at age 14 months. (B) Pedigree of the family withown next to each member of the family. The deceased index wasto be a carrier; father and two unaffected brothers were confirmed tol diffusion-weighted images (DWI), b = 1000 s/mm2; middle row,l T2-weighted images. There is restricted diffusion, evidenced by highthe level of the ponto-medullary tegmentum, superior cerebellaregions show abnormally elevated signal on the T2-weighted images.at this age and are consistent with intramyelin edema.Tarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 4 of 13Brain MRI at presentation (age 4 months) revealedsignal abnormalities with restricted diffusion at level ofthe brainstem tegmentum, superior cerebellar peduncles,subthalamus, and ventral striatum (Figure 1C), whilefollow-up studies at 10 months and 2.5 years showedprogressive, severe cerebral and cerebellar atrophy asso-ciated with diffuse leukoencephalopathy and thinning ofthe corpus callosum. Serial MR spectroscopy showedinitially mildly elevated lactate peaks, normal on sub-sequent imaging, as well as mild reduction of N-acetylaspartate in the mid brain.His heart was mildly enlarged and ECG and Holter re-vealed right ventricular hypertrophy and arrhythmia (AVblock, Wenckebach type I). He also had moderate hep-atomegaly, apnea, unilateral hydronephrosis with renalcalculi, GI dysmotility which led to aspirations requiringG-tube feeding, visual motor impairment and retinaldystrophy (pale optic disc, flat macula, myopia, atrophicretina; no cherry red spot), moderate conductive andsensorineural hearing loss, stomatocytosis and hypere-choic liver. The child died at the age of 3.4 years of car-diac arrest; autopsy was not performed.TORCH (toxoplasmosis, rubella, cytomegalovirus,herpes simplex, and HIV) screening was negative. Acomprehensive metabolic investigation was initiated butlargely uninformative, with the following exceptions:Plasma lipid profiling revealed markedly elevated tri-glycerides at 85.31 mM (reference 0.4-1.5) and cho-lesterol at 23.4 mM (reference 2.6-5.2), and absentpost-heparin lipoprotein lipase activity suggesting alipoprotein lipase deficiency. The abnormal lipid pro-file normalized quickly with the implementation of amedium-chain triglyceride enriched diet. Persistentlyelevated alkaline phosphatase levels were also noted,ranging from 364–649 U/L (Ref 110–320); calcium,phosphate and vitamin D were within normal limits.BNG Analysis of a muscle biopsy at 10 months showeddecreased amount of complex of I and V (at 30% and 10%of a tissue-matched control sample, respectively). Thesefindings led to the initial clinical suspicion of a mito-chondrial deficiency syndrome (lactates varied betweennormal – 3.8 umol/L) or lipid storage disorder, and inves-tigations were pursued accordingly.Further molecular investigations yielded normal re-sults including array-CGH analysis for copy number var-iations (CNVs), mtDNA genome sequencing, targetedgene sequencing of LPL, MECP2, ARX and a number ofnuclear encoded mitochondrial proteins. Elaborate bio-chemical testing was completed with essentially unre-markable results (ammonia, acylcarnitine profile, plasmaamino acids, very long chain fatty acids, transferrin iso-electric focussing; urine organic acids, purines & pyrimi-dines, mucopolysaccharides, oligosaccharides, bile acids).The following enzymatic analyses yielded normal results:acid phosphatase, sphingomyelinase, arylsulphatase A, hex-osaminidase A&B, biotinidase, chitotriosidase, galactosyl-ceramidase, beta-glucosidase, beta-galactosidase, cathepsinD, palmitoyl protein thio-esterase I, tripeptidyl peptidase I.Filippin staining studies in fibroblasts showed mildly aty-pical peri-nuclear vesicular accumulations of un-esterifiedcholesterol but were considered non-diagnostic. Sphin-gomyelinase enzymology and NPC1 and NPC2 sequen-cing were all unremarkable. Iron staining of muscle wasnegative.Whole exome sequencingWith a profound IDD and an abnormal biochemicalphenotype, this patient met the inclusion requirementsfor our TIDEX (Treatable Intellectual Disability Endea-vour exome sequencing) gene discovery study. We iso-lated genomic DNA samples from the peripheral bloodof the patient as well as parents and two unaffected malesiblings using standard techniques. WES was performedfor the index patient and his unaffected parents usingthe Agilent SureSelect kit and Illumina HiSeq 2000(Perkin-Elmer, Santa Clara, California, USA). An in-house designed bioinformatics pipeline [19] was used toalign the reads to the human reference genome versionhg19 and to identify and assess rare variants for theirpotential to disrupt protein function. The candidate vari-ants were further confirmed using Sanger re-sequencingin all the family members. Deleteriousness of the candi-date variants was assessed using Combined Annotation–Dependent Depletion (CADD) scores [20], PolyPhen-2(http://genetics.bwh.harvard.edu/pph2/) [21] and SIFT(Sorting Intolerant From Tolerant; (http://sift.jcvi.org/)[22]. Protein alignment was generated using T-Coffee(http://www.tcoffee.org/) [23] and analyzed using Gene-Doc http://www.nrbsc.org/gfx/genedoc/gdpaf.htm/). Onlythose variants predicted to be “functional” (missense, non-sense and frameshift changes, as well as in-frame deletionsand splice-site effects) were subsequently screened undera series of inheritance models.X-inactivation studiesX-chromosome inactivation (XCI) was assayed in theunaffected mother using the allelic ratio of methylatedalleles at the Androgen Receptor (AR) locus [24] as de-scribed previously [25]. The degree of allelic bias interms of which X chromosome is inactivated can rangefrom 50% (completely random) to 100% (completelyskewed).Functional analysisTo provide evidence for pathogenicity of the identifiedmutation, patient and control skin fibroblasts wereanalyzed by flow cytometry for surface expression ofCD109, a GPI-anchored protein. Cells were washed withTarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 5 of 13PBS (without Ca2+ or Mg2+) (Gibco), detached using5 mM EDTA (Gibco) in PBS and washed in 2% FBS(Gibco)/PBS. Cells were then stained for 20 minutes at4°C with CD109-PE (BioLegend) and PE mouse IgG1, κisotype control (BioLegend). Data were acquired using aBD™ LSR II flow cytometer and analyzed using FlowJov8.8.4 (Tree Star). Protein expression was determined byWestern blot analysis. Briefly, skin fibroblasts were har-vested and lysed (cell lysis buffer, Cell Signaling) in thepresence of protease inhibitor cocktails (Roche). Equalamounts of protein were separated by SDS-PAGE, trans-ferred to PVDF membrane and blocked with 5% BSA.Protein expression was detected using an anti-PIG-A(clone H-6, Santa Cruz) primary antibody. After wash-ing, bound antibody was detected with HRP-conjugatedanti-mouse secondary antibody and Novex ECL chemi-luminescent substrate (Invitrogen).ResultsNew PIGA germline mutation in our patient withmultisystem diseaseIn the WES data we identified four rare homozygous, fourrare hemizygous and eight rare compound heterozygouscandidates; we did not identify any rare denovo variantsaffecting protein-coding regions. Of those, only three mis-sense variants were considered functional candidates.COX7A2 (encoding the nuclear-coded polypeptide chainsof cytochrome c oxidase, the terminal oxidase in mito-chondrial electron transport (MIM123966)), and C19orf12(associated with neurodegeneration with brain iron accu-mulation 4 (MIM 614298)), and Spastic Paraplegia 43 AR(MIM 615043) phenotypes were subsequently ruled out asSanger sequencing showed the same recessive genotype inboth clinically unaffected brothers. The final candidate,PIGA (g.15342986C>T c.989G>A [NM_002641], [p.S330N])was a novel missense variant not found in more than 250in-house exomes, dbSNP 138, NHLBI Exome SequencingProject or Exome Aggregation Consortium (ExAC). Thevariant is predicted to be the most deleterious of all candi-dates using the CADD scores [20]. It affects a highly con-served amino acid (Figure 2) and is predicted to bedamaging by both PolyPhen-2 [26] and SIFT [22]. TheSanger re-sequencing of the genomic DNA confirmed thatindex II-2 is hemizygous for the C to T transition, motheris the carrier, while the two unaffected brothers do nothave this variant (Figure 1B). Finally, X-inactivation stu-dies showed the pattern of X-inactivation to be 94.5%skewed in the unaffected carrier mother. Together, thegenetic analysis based on WES shows that the c.989G>A(p.S330N) variant is a new variant, it affects an evolution-arily conserved amino acid of PIGA resulting in a deleteri-ous change (Figure 2), and segregates with disease in thefamily (Figure 1B). Functional characterization of the va-riant showed normal expression of PIGA protein in skinfibroblasts (Figure 3A) but there was a 44% reduction inthe surface expression of GPI-anchored CD109 (Figure 3B).The mother of the patient had a normal complete bloodcell count and no evidence of red cell hemolysis on periph-eral blood smear. A standardized flow cytometric methodfor screening PNH measuring CD55 and CD59 expressionon erythrocytes was negative.DiscussionWES revealed a novel, likely pathogenic variant in thePIGA gene in our patient with multisystem disease in-cluding early onset intractable epilepsy, severe IDD, fa-cial dysmorphism, conductive and sensorineural hearingloss and visual impairment, joint contractures and hep-atic and renal involvement.To date, seven germline mutations in PIGA have beendiscovered using WES technologies in eight unrelatedfamilies [7,15-18]. Locations of the pathogenic variants arelisted in Table 1 and highlighted on a multi-sequencealignment of PIGA proteins in Figure 2. PIGA germlinemutations have been found in XLIDD male patients with awide spectrum of clinical diagnoses (Table 1). Mothers ofthe affected males were confirmed to be carriers in all ex-cept for one family (Table 1) where the DNA for themother was unavailable [18].The phenotypic spectrum of PIGA germline mutationshas shown wide variation, as reflected by the range ofclinical diagnoses summarized in Table 1. However, acommon set of characteristic features, shared by our pa-tient, has emerged including infantile spasms with hyp-sarrhythmia on EEG (Table 1) and IDD. Generally, thephenotypic spectrum could be classified into two types(severe and less severe), as proposed by Kato et al. [18],where presence of facial dysmorphism correlates verywell with the more severe spectrum of clinical manifes-tations (Table 1). In addition to early onset infantilespasms with hypsarrhythmia on EEG, IDD and profounddevelopmental delay, the patients with more severe man-ifestations of PIGA germline mutations (patients: IV-2,IV-4 [15], III-1 [17], III-9 [16], 1, 2, and 5 [18], and ourcase [this report]) also present with dysmorphic facialfeatures, multiple CNS abnormalities, such as thin corpuscallosum and delayed myelination, as well as hypotonia(Table 1). Other phenotypes such as polyhydramnios, jointcontractures, hyperreflexia, cardiac anomaly, severe devel-opmental delay and elevated alkaline phosphatase are alsorecurrently seen in these patients, while additional pheno-types appear to be allele-specific (Table 1). Unlike patientswith severe phenotypes, the less severe form of PIGA germ-line mutations (patients: IV-2 [7], 3 and 4 [18]) did not in-volve facial dysmorphism and multiple CNS abnormalities,but did present with early onset of infantile spasms withhypsarrhythmia on EEG (Table 1), and generally longer lifespan marked by IDD, treatable seizures and PDD (Table 1).Figure 3 PIGA expression and surface expression of GPI-AP (CD109) in patient skin fibroblasts. (A) Western Blot showing similar expressionof PIGA in patient versus control fibroblasts; β-actin was used as a loading control. (B) Flow cytometry analysis of patient’s fibroblasts revealed reducedexpression (56%) of GPI-AP (CD109) when compared to control fibroblasts. Isotype controls are included to show specific binding.Figure 2 A multi-sequence alignment of PIGA proteins and distribution of all known germline mutations. The PIGA protein sequenceswere generated using depicted transcript identifiers from: Homo sapiens (human), Mus musculus (mouse), Bos taurus (cow), Gallus gallus (chicken),Danio rerio (zebrafish), Caenorhabditis elegans (worm) and Saccharomyces cerevisiae (yeast). Protein alignment was generated using T-Coffee [23]and analyzed using GeneDoc.Tarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 6 of 13Table 1 Overview of mutations and phenotypes observed in patients with germline PIGA mutations(Johnstonet al. [15])(Johnstonet al. [15])(van derCrabbenet al. [17])(Swobodaet al. [16])(Beletet al. [7])(Katoet al. [18])(Katoet al. [18])(Katoet al. [18])(Katoet al. [18])(Katoet al. [18])Our patientIV-2 IV-4 III-1 III-9 IV-2 1 2 3 4 5MothercarrierYES YES YES YES YES Unknown YES YES YES YES YESMutation c.1234C>T[R412*]c.1234C>T[R412*]c.278C>T[P93L]c.328_330delCCT[L344Del]c.76dupT[Y26Lfs*3]c.1234C>T[R412*]c.616A>T[I206F]c.230G>T[R77L]c.230G>T[R77L]c.355C>T[R119W]c.989G>A[S330N]Polyhydramnios NO YES YES NO NO YES NO NO NO YES NOCurrent age Death at11wkDeath at10wkDeath at2.5 yrsDeath at 7 yrs 24 yrs 6 yrs 10 yrs 8 yrs 18 mo 15 mo Death at3.4 yrsSex M M M M M M M M M M MNeurologyDevelopmentaldelay (severity)Early death Early death Profound Profound Profound Profound Profound Profound Profound Profound ProfoundHypotonia YES YES YES YES YES YES NO NO NO YES YESHyperreflexia YES YES NO YES NR NR NO NO NO YES YESSeizure onset Neonatal Neonatal 8.5 months 7 months 6 months 1 month 3 months 7 months 7 months 3 months 2.4 monthsSeizure types Myoclonic Myoclonic Generalizedclonic(febrile)Febrile,myoclonicMyoclonicepilepticseizuresTonic seizuresfollowed byfrequentmyoclonusMyoclonusor epilepticspasm-likemovementTonic seizures,secondarilygeneralizedseizuresTonic orclonicMyoclonicseizures,tonic spasmsInfantilespasms,myoclonicseizuresEEG findings SuppressionburstSuppressionburstSymptomaticgeneralizedepilepsyPosteriorburstsHyps-arrhythmiaat 7 moSuppressionburst atneonatalperiodHypsarrhythmia,periodic burstsof multifocalepilepticdischargesIrregular spikeand slow waveand multifocalspikes at 2and5 yNormalat 7 moHypsarrhythmiaat 3 mo,suppressionburst at 5 moHypsarrythmiaat 2.4 mos,suppression-burst patternat 3.5 mosSeizureprognosisIntractable Intractable Refractory Intermittent NR Intractable Intractable Seizure-free at3 y with TPMSeizure-freeat 15 moIntractable IntractableThin corpuscallosumYES YES YES NR NO YES YES NO NO YES YESWhite matterimmaturityYES YES YES NR NO YES YES NO NO YES YESSmallcerebellumYES YES YES YES NO NR NR NR NR NR YESCorticalatrophyNR NR NR YES NO YES YES NO NO YES YESRestricteddiffusionbrainstem/cerebellumNR NR NR NR NO YES YES NO NO YES YESTarailo-Graovacetal.OrphanetJournalofRareDiseases (2015) 10:23 Page7of13Table 1 Overview of mutations and phenotypes observed in patients with germline PIGA mutations (Continued)Other organsFacialdysmorphismYES YES YES YES NO YES YES NO NO YES YESJoints(contractures)YES YES NR NR NR YES YES NO NO NO YESCardiac Systolic II–III/VImurmur with afixed split S2,ASDSmall PDA ASD type 2 NR NR NR NR NR NR NR RVH,arrhythmia(grade 1AV block,Wenckebachtype)Liver NR HepaticmicrovesicularsteatosisNR Hepatosplenomegaly NR Hepato-megaly,hepato-blastomaNR NR NR NR Hepatomegaly,hyperechoic liverKidney Vesicoureteralreflux,duplicatedcollectingSystemVesicoureteralrefluxNR NR NR VesicoureteralrefluxNR NR NR NR Lefthydronephrosiswith renal calculiOphthalmologic NR NR NR Blindness NR NR NR NR NR NR Visual motorimpairment,retinaldystrophyHearing loss NR NR NR Deafness NR NR NR NR NR NR Sensorineuralhearing lossDental NR UnderdevelopedgumsAbsenceof teethNR, but III-10microdontia,widely-spaced,delayederuptionNR NR NR NR NR NR Microdontia,widely-spaceddelayed eruptionOther Globulous chestand small nails,broad palmswith shortfingersAbsence ofolfactory bulband tractsAcceleratedlineargrowth,obesityIchthyosis NR Tracheostomy,micropenis,bilateral inguinalherniation,hypotonicquadriplegiaSpasticquadriplegia,bulbar palsywithgastrostomyandtracheostomyNR NR Transversepalmar crease,prominentcalcaneus, leftinguinal hernia,hydroceletesticle,hypotonicquadriplegiaStomatocytesBiochemicalElevatedalkalinephosphataseNR YES YES NR NR NR YES NO NO YES YESMitochondrialabnormalitiesNR NR AbnormalATPproduction(musclebiopsy)DisorganizedmitochondriaNR NR NR NR NR NR Respiratorychain complex Iand V reductions(muscle bluenative gel)Iron storage NO NO NO CNS irondepositionNR NR NR NR NR NR NOTarailo-Graovacetal.OrphanetJournalofRareDiseases (2015) 10:23 Page8of13Table 1 Overview of mutations and phenotypes observed in patients with germline PIGA mutations (Continued)Other Slightly elevatedMCV and RDWand low ionizedcalcium, HgBand RBCSlightlyelevated MCVand RDWNO NR NR NR NR NR NR NR Dyslipidemia(hightriglycerides,hypercholesterolemia,LPL deficiency)ClinicaldiagnosisClinicaldescriptorMCAHS2Bethesda–UtrechtsyndromeMCAHS2Bethesda–Utrecht syndromeMCAHS2Bethesda–UtrechtsyndromeFerro-Cerebro-CutaneoussyndromeMCAHS2-like syndromeX-linkedinfantilespasmsyndrome(Westsyndrome)Ohtaharasyndrome,early myoclonicencephalopathy,Schinzel-GiedionsyndromeWest syndromewithhypomyelinationEarly-onsetepilepticencephalopathyEarly-onsetepilepticencephalopathyWestsyndromePIGA deficiencyCause ofdeathPneumonia Respiratory failure CardiacarrestAspirationpneumoniaNA NA NA NA NA NA Cardiac arrestTarailo-Graovacetal.OrphanetJournalofRareDiseases (2015) 10:23 Page9of13Tarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 10 of 13Early onset infantile spasms appear to be a commonfeature of PIGA mutations, as is seen with many otherdefects in GPI-anchor biosynthesis. Chiyonobu et al.[27] hypothesized that these seizures are due to intra-cellular pyridoxal phosphate deficiency secondary to theloss of membrane bound alkaline phosphatase, which isrequired to initiate pyridoxal-phosphate for transit of theplasma membrane (after which it is rephosphorylated).Given that GABA synthase requires intracellularpyridoxal-phosphate, it is the intracellular GABA defi-ciency which likely leads to the onset of seizures [27].Additional features are frequently reported in patientswith the severe form of PIGA germline mutations, as pro-posed by [18] including: hypotonia (7/8 patients withavailable data), elevated alkaline phosphatase (5/5 patientswith available data), hyperreflexia (5/5 patients with avail-able data), joint contractures (5/6 patients with availabledata), cardiac anomalies (4/4 patients with available data)and polyhydramnios (4/8 patients with available data) pos-sibly due to dysphagia associated with hypotonia. The pla-giocephaly facial dysmorphism in our and published casesis likely secondary to the hypotonia, causing facial asym-metry and distortion of proportions as well as secondarycontractures. Our patient specifically appears to have ashort nose with anteverted nares and a depressed nasalbridge, seen as the triangular structure at the base of thenose (Figure 1A). This feature appears to be present in themore severely affected published cases [18]. Additionalfeatures such as dental problems (e.g. microdontia, de-layed eruption) [16,17], liver problems [15,16,18] visualimpairment and deafness [16] appear to be recurrent aswell (Table 1). On the other hand some features, such asaccelerated linear growth and obesity [17], CNS irondeposition and ichthyosis [16], dyslipidemia and stoma-tocytosis (in the patient reported here) are reportedonly once. The cause of death in patients with PIGAmutations has been mainly due to cardiac arrest, pneu-monia and respiratory failure (Table 1). Although thelife span of the patients affected with less severe muta-tions is generally longer, there is a great degree ofvariability in life-span even in patients with the samegermline mutation [15,16,18,28].Reports of brain MRI findings in PIGA deficiency de-scribe white matter immaturity with insufficient myelin-ation, cerebral atrophy, thinning of the corpus callosum,and a small cerebellum [7,15,18]. Cerebral atrophy ap-pears to progress rapidly and is associated with abnor-mal white matter myelination, consistent with an earlyneurodegenerative process [18]. Our case showed a simi-larly rapid progression, with an established cerebral atro-phy associated with disrupted subcortical myelination atage 2.5 years. However, the most remarkable finding inthe early stages of the disease was restricted diffusion inthe brainstem tegmentum, superior cerebellar peduncles,subthalamus, and ventral striatum, indicative of intra-myelin edema, involving selectively white matter regionsthat are already physiologically myelinated at birth. Katoet al. [18] also reported three cases showing restricteddiffusion at the brainstem, basal ganglia, thalamus, anddeep white matter. Interestingly, these findings are re-markably similar to those of the classical form of MSUD,an amino aciduria caused by deficiency of branchedchain α-keto acid dehydrogenase enzyme, in which brainMRI of affected newborns or infants studied duringstages of metabolic decompensation shows prominentsignal changes and swelling within myelinated brainareas representing intramyelin edema, caused by a deficitof Na+/K+ ATPase activity as a result of impairment inenergy production secondary to branched chain aminoacids accumulation [29,30]. In particular, the findings ofour case are remarkably similar to those shown in figuresix in the report by Rossi and Biancheri [31], implicatingthat the diagnosis of PIGA deficiency could be suggestedin neonates with similar brain MRI findings and un-remarkable plasma amino acid and urine organic acidprofiles. An explanation for the similarities remainsspeculative; the typical lesions in the newborn withMSUD involve preferentially those structures that arealready myelinated at birth and thus with higher meta-bolic demands and most vulnerable to the energy defi-ciency and toxicity of branched-chain 2-oxo acid(s). InPIGA deficiency, although toxins have not yet been iden-tified, we speculate that mitochondrial and thus energydeficiency could similarly play a role in the etiology ofthe observed intra-myelin edema. Regardless of the im-plicated pathophysiologic mechanism, identification ofsimilarities in the lesion distribution and appearance onMRI represents the foundation of the pattern recogni-tion approach, whereby neuro-imaging can guide thediagnostic process to reduce the number of unnecessarytests and time to diagnosis [32]. PIGA catalyzes the firststep in GPI biosynthesis and it is anticipated that even apartial defect in activity will have a significant impact onthe localization and functionality of a broad range ofGPI-anchored proteins. The elevation in serum alkalinephosphatase reported here as well as in the majority ofother PIGA deficient cases (likely correlated with sever-ity of the disease) (Table 1) as well as other PIG deficien-cies results from the secretion of GPI-deficient alkalinephosphatase (normally membrane-anchored) and mayserve as a diagnostic clue. Normal levels of alkalinephosphatase however, do not rule out the condition, asevidenced by the mild case reported by Belet et al. [7].The hypertriglyceridemia and serum LPL deficiency ob-served in our patient is also likely caused by abnormalGPI biosynthesis. LPL release from endothelial cells in re-sponse to heparin stimulation requires the activity ofGPIHBP1 (GPI-anchored high-density lipoprotein bindingTarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 11 of 13protein 1) and primary genetic defects in this GPI-anchored protein lead to hypertriglyceridemia andnon-detectable serum lipoprotein lipase [33]. The GPIbiosynthesis defect resulting from PIGA mutation likelyleads to a secondary GPIHBP1 deficiency, although fur-ther evaluation is required to confirm this mechanism, asa similar defect has not been described or investigated inother individuals with PIGA defects.The germline mutational spectrum for PIGA com-prises various mutation types including one nonsensemutation [15,18], one frameshift mutation that results inproduction of 36 amino acids shorter PIGA protein [7],one small in-frame deletion [16], and four missensemutations [17,18] (Figure 2). PIGA protein is well con-served from yeast to human (Figure 2), and all of thereported mutations, except for c.76dupT, occurred atevolutionarily conserved or semi-conserved amino acids(Figure 2). The c.76dupT frameshift mutation occurs inthe non-conserved part of the protein but results intranslation of the PIGA protein using a cryptic start siteat amino acid position 37 producing shorter PIGAprotein with the majority of the conserved amino acidsintact [7]. One mutation, c.1234C>T, was recurrent(Table 1) [15,18].Studies in mice revealed that complete disruption ofthe PIGA gene results in early embryonic lethality inmales, while in carrier female mice late embryonic le-thality is observed [3]. Based on these studies, it isbelieved that complete loss of PIGA function is lethal inhumans. A number of studies suggest that the humanmutations identified to date result in reduced, but notabsent, PIGA activity and using the flow cytometry ofblood granulocytes method, Kato et al. [18] showed thatthe phenotype severity of the PIGA germline mutationsappeared to correlate with genotype and the residual func-tional activity of the PIGA protein [18]. Functional studieson the truncating c.1234C>T mutation (p.R412X) suggestthat small amounts of full length PIGA protein were gen-erated by the read through of the premature terminationcodon (PTC) [15,18]. During two stages of eukaryotictranslation (elongation and termination), aminoacyl-tRNAs and termination factors compete for codon bin-ding. When aminoacyl-tRNAs supersedes, read through ofthe termination codon occurs, which allows the gener-ation of the full-length polypeptide. Depending on theamino acid inserted during the read through, the resultingprotein may have normal or partial activity. Studies on baselevel of read through reveal 10 fold higher frequency atPTCs (<1%) [34,35] when compared to naturally occurringstop codons (<0.1%) [36,37]. In addition to c.1234C>T(p.R412X), studies on the c.328_330delCCT (p.L344Del)mutation revealed reduced GPI-anchored proteins on thepatient’s granulocytes, while normal levels were observedon the red blood cells and monocytes, suggesting reducedbut not absent PIGA activity [16]. Complementation assaysusing the c.76dupT frameshift mutation confirmed partialfunction of the shorter PIGA protein, which was sufficientto rescue surface expression of CD59 in a PIGA null cellline [7]. Consistent with previous findings, our patient’smutation also led to reduced surface expression of theGPI-anchored protein CD109 on skin fibroblasts, despitenormal levels of protein expression.Patients with PIGA germline mutations share key pheno-typic features with patients carrying mutations in genes en-coding various PIG family members, including IDD,seizures, hypotonia, growth defects, congenital abnorma-lities, heart defects, and abnormal metabolic profiles. Forexample, inherited glycosylphophatidylinositol deficiency(MIM 610293) resulting in portal- and hepatic-vein throm-bosis and absence seizures was found to be due to muta-tions in PIGM gene (MIM610273) [5]. HyperphosphatasiaMental Retardation syndrome (HPMRS, MIM 239300,MIM 214749, and MIM 614207), also known as Mabrysyndrome, was found to be associated with PIGV (MIM610274), PIGO (MIM 614730),PGAP2 (MIM 615187) andPGAP3 (MIM 611801) mutations [38-42]. HPMRS ischaracterized by elevated alkaline phosphatase levels, IDD,seizures, hypotonia, and facial dysmorphic features [38].CHIME syndrome (MIM 280000), also known as ZunichNeuro-Ectodermal syndrome was found to be due to mu-tations in PIGL (MIM 605947). Individuals with CHIMEsyndrome present with colobomas, congenital heart de-fects, early onset migratory ichthyosiform dermatosis, IDD,and ear anomalies, including conductive and sensori-neural hearing loss [43]. PIGT mutations cause congenitalanomalies-seizures-hypotonia type 3, with hypophosphata-sia as key feature [44,45]. The wide spectrum of humanconditions associated with mutations in PIG genes reflectstheir role in multiple developmental processes and resem-bles the diversity of clinical features associated with glyco-sylation pathways deficiencies [43].A variety of clinical case descriptors have been appliedto individuals with germline PIGA mutations (Table 1).However, given the varied clinical spectrum reported todate, it appears that the multi-system roles of GPI-anchored proteins and private nature of most of thePIGA mutations identified will preclude the definition ofa common feature set. To unify further reports on thisintriguing condition, we advocate for the use of ‘PIGAdeficiency’.Careful patient phenotyping will continue to shed lighton the (patho-) physiologic roles of PIGA deficiency; forexample, its relation with mitochondrial structure andfunction. We are the first to report severely reducedamount of mitochondrial complexes (specifically I andV), but other mitochondrial defects have been reportedin PIGA mutations: e.g. ‘disorganized mitochondria’ inFCC syndrome [16] and ‘abnormal ATP production’ in aTarailo-Graovac et al. Orphanet Journal of Rare Diseases  (2015) 10:23 Page 12 of 13patient with accelerated linear growth and obesity [17].In fact, recent publications show that several mitochon-drial membrane proteins are either modified with GPIanchor addition or associated with GPI anchored pro-teins, a process required for their proper function [46].Therefore, it is of great interest to test patients with thePIGA mutations for mitochondrial defects and viceversa, to test the patients with unexplained mitochon-drial phenotypes for potential PIGA mutations, espe-cially in the presence of features described here.ConclusionsBased on the patient descriptions published to date, in-tractable, infantile onset epilepsy with suppression burstand/or hypsarrhythmia in patients with X-linked IDD ofunknown etiology should prompt clinicians to considergermline mutations in the PIGA, particularly in a patientwith elevated serum alkaline phosphatase. The additionalpresence of dysmorphic facial features, CNS abnorma-lities, hypotonia, heart defects, dyslipidemia/lipoproteinlipase deficiency, or signs of intra-myelin edema on brainMRI, may increase the likelihood of mutations in PIGAspecifically, and PIG family members in general. Flow cy-tometry of blood granulocytes has also proven a usefultest for levels of GPI-anchored proteins expression in pa-tients with PIGA mutations [7,15,16,18].AbbreviationsPIGA: Phosphatidylinositol glycan biosynthesis class A protein;GPI: Glycosylphosphatidylinositol; PIG: Phosphatidylinositol glycan biosynthesisprotein; PI: Phosphatidylinositol; PNH: Paroxysmal nocturnal hemoglobinuria;GlcNAc: N-acetylglucosamine; UDP-GlcNAc: UDP-N-acetylglucosamide;WES: Whole Exome Sequencing; MSUD: Maple syrup urine disease;MCAHS2: Multiple congenital anomalies-hypotonia-seizures syndrome 2;FCCS: Ferro-Cerebro-Cutaneous syndrome; BNG: Blue Native Gel; OFC: Occipitalfrontal circumference; NAA: N-Acetylaspartic acid; TORCH: Toxoplasmosis,rubella, cytomegalovirus, herpes simplex, and HIV; IDD: Intellectualdevelopmental disorder; TIDEX: Treatable Intellectual Disability EndeavoureXome sequencing; CNV: Copy number variation; CADD: CombinedAnnotation–Dependent Depletion; SIFT: Sorting Intolerant From Tolerant;AR: Androgen Receptor; XCI: X-Chromosome inactivation; XLIDD: X-linkedintellectual developmental disability; GPIHBP1: GPI-anchored high-densitylipoprotein binding protein 1; HPMRS: Hyperphosphatasia Mental Retardationsyndrome; PTC: Premature termination codon.Competing interestsThe authors declare that they have no competing interests.Authors’ contributionsMTG: performed bioinformatics analysis and identified PIGA mutation;reviewed and summarized the literature, and drafted the manuscriptl:GS: participated in data analysis and interpretation as well as drafting andrevision of the manuscript: SS: clinical case description, clinical diagnosticmanagement, enrolment in WES research project, critical editing and revisionof the manuscript: MVA: described the dysmorphologic exam, performeddiagnostic investigations and contributed to the drafting and critical edits ofthe manuscripts: JR: designed and performed the functional analyses(CD109 measurements and Western Blot on fibroblasts): CS: contributed tothe bio-informatic analysis: RB: contributed to the phenotypic description ofthe case, with focus on epilepsy and neuro-imaging results: TO: providedgenetic counselling to the family, contributed to data collection andprovided critical manuscript edits: ML: collected phenotypical and testingdata, contributed to the case description and extracted qualitative data fromprinted and electronic records: BS: contributed to the case description andprovided manuscript edits and revisions: CJR: performed targeted Sangersequencing for all candidate variants identified via WES in this family,provided critical edits to the manuscript: WR: performed and interpretedX-inactivation studies, contributed to the manuscript with subsequent criticaledits: WW: Supervised the bio-informatic analysis and pipeline creation:AR: interpretation and description of ten euro-imaging findings, preparationfigures, critical editing and revision of the manuscript: CvK: spearheaded theconception and design of the study, acquisition of data, and coordinateddata analysis and interpretation, as well as drafting and revision of themanuscript. All authors read and approved the final manuscript.AcknowledgmentsWe are indebted to the patient and his family for participation in this study;Dr. S. Miller, Dr. S. Mahmutoglu and Dr. P. Louie for their contributions toclinical management of the patient; Dr. Maria Penaherrera and Ms. RubyJiang for X-inactivation studies; Mrs. X. Han for Sanger sequencing; Dr. M.Thomas for consenting and data management; Mrs. M. Higginson for DNAextraction and sample handling; Mr. D. Arenillas and Mr. M. Hatas for systemssupport, and Mrs. D. Pak for research management support (University ofBritish Columbia). Dr. R. Hegele (University of Western Ontario, Canada) forLPL molecular analysis. We are also grateful to the anonymous reviewers;their thoughtful comments and suggestions helped us strengthen themanuscript.This work was supported by funding from the B.C. Children’s HospitalFoundation as “1st Collaborative Area of Innovation” (www.tidebc.org);Genome BC (SOF-195 grant); BC Clinical Genomics Network (#00032 grant),and the Canadian Institutes of Health Research (#301221 grant). Informaticsinfrastructure supported by Genome BC and Genome Canada (ABC4DEProject). Dr. C. van Karnebeek is a recipient of the Michael Smith Foundationfor Health Research Scholar Award.Author details1Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.2Department of Medical Genetics, University of British Columbia, Vancouver,Canada. 3Treatable Intellectual Disability Endeavour in British Columbia,Vancouver, Canada. 4Division of Biochemical Diseases, Department ofPediatrics, BC Children’s Hospital, University of British Columbia, Vancouver,Canada. 5Division of Hematology, Oncology & BMT, Department of Pediatrics,BC Children’s Hospital, University of British Columbia, Vancouver, Canada.6Biochemical Genetics Laboratory, Department of Pathology, BC Children’sHospital, University of British Columbia, Vancouver, Canada. 7Child & FamilyResearch Institute, Vancouver, BC, Canada. 8Department of PaediatricNeurology, Children’s Hospital Oxford, John Radcliffe Hospital, Oxford, UK.9Department of Neuroradiology, Istituto Giannina Gaslini, Via GerolamoGaslini 5, I-16147 Genoa, Italy.Received: 17 December 2014 Accepted: 18 February 2015References1. 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