Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.
Over 150 different proteins attach to the plasma membrane using glycosylphosphatidylinositol (GPI) anchors. Mutations in 18 genes that encode components of GPI-anchor biogenesis result in a phenotypic spectrum that includes learning disability, epilepsy, microcephaly, congenital malformations and mild dysmorphic features. To determine the incidence of GPI-anchor defects, we analysed the exome data from 4293 parent-child trios recruited to the Deciphering Developmental Disorders (DDD) study. All probands recruited had a neurodevelopmental disorder. We searched for variants in 31 genes linked to GPI-anchor biogenesis and detected rare biallelic variants in PGAP3, PIGN, PIGT (n=2), PIGO and PIGL, providing a likely diagnosis for six families. In five families, the variants were in a compound heterozygous configuration while in a consanguineous Afghani kindred, a homozygous c.709G>C; p.(E237Q) variant in PIGT was identified within 10-12 Mb of autozygosity. Validation and segregation analysis was performed using Sanger sequencing. Across the six families, five siblings were available for testing and in all cases variants co-segregated consistent with them being causative. In four families, abnormal alkaline phosphatase results were observed in the direction expected. FACS analysis of knockout HEK293 cells that had been transfected with wild-type or mutant cDNA constructs demonstrated that the variants in PIGN, PIGT and PIGO all led to reduced activity. Splicing assays, performed using leucocyte RNA, showed that a c.336-2A>G variant in PIGL resulted in exon skipping and p.D113fs*2. Our results strengthen recently reported disease associations, suggest that defective GPI-anchor biogenesis may explain ~0.15% of individuals with developmental disorders and highlight the benefits of data sharing.
National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Alistair T
AT
Pagnamenta
Department of Immunoregulation, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.|World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.
Yoshiko
Y
Murakami
Oxford NHS Regional Molecular Genetics Laboratory, Oxford University Hospitals NHS Trust, Oxford, UK.
John M
JM
Taylor
The Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK.
Consuelo
C
Anzilotti
National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Malcolm F
MF
Howard
Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK.
Venessa
V
Miller
Sheffield Children's Hospital, Western Bank, Sheffield, UK.
Diana S
DS
Johnson
South West Thames Regional Genetics Service, St George's Healthcare NHS Foundation Trust, London, UK.
Shereen
S
Tadros
South West Thames Regional Genetics Service, St George's Healthcare NHS Foundation Trust, London, UK.
Sahar
S
Mansour
Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton and Wessex Clinical Genetics Service, University Hospital NHS Trust, Princess Anne Hospital, Southampton, UK.
I Karen
IK
Temple
Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton and Wessex Clinical Genetics Service, University Hospital NHS Trust, Princess Anne Hospital, Southampton, UK.
Rachel
R
Firth
Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Trust, London, UK.
Elisabeth
E
Rosser
Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK.
Rachel E
RE
Harrison
Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.
Bronwen
B
Kerr
National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Niko
N
Popitsch
Department of Immunoregulation, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.|World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.
Taroh
T
Kinoshita
National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Jenny C
JC
Taylor
Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK.
Usha
U
Kini
D000217:Acyltransferases / Q000235:genetics* / Q000378:metabolism; D000328:Adult; D002265:Carboxylic Ester Hydrolases; D002648:Child; D002658:Developmental Disabilities / Q000235:genetics* / Q000473:pathology; D059472:Exome; D057809:HEK293 Cells; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D017351:N-Acetylglucosaminyltransferases / Q000235:genetics* / Q000378:metabolism; D010375:Pedigree; D010770:Phosphotransferases / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011956:Receptors, Cell Surface / Q000235:genetics / Q000378:metabolism
D008565:Membrane Proteins; C485854:PIGO protein, human; D011956:Receptors, Cell Surface; D000217:Acyltransferases; C081007:COOH-terminal signal transamidase; D017351:N-Acetylglucosaminyltransferases; C561296:PIGN protein, human; D010770:Phosphotransferases; D002265:Carboxylic Ester Hydrolases; C476212:PGAP3 protein, human; C000603519:PIGL protein, human