GPIBD1
MCID: GLY112
MIFTS: 34

Glycosylphosphatidylinositol Biosynthesis Defect 1 (GPIBD1)

Categories: Blood diseases, Bone diseases, Fetal diseases, Genetic diseases, Mental diseases, Metabolic diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Glycosylphosphatidylinositol Biosynthesis Defect 1

MalaCards integrated aliases for Glycosylphosphatidylinositol Biosynthesis Defect 1:

Name: Glycosylphosphatidylinositol Biosynthesis Defect 1 56 73
Glycosylphosphatidylinositol Deficiency 56 73 29 13 6 39
Gpibd1 56 73
Gpid 56 73
Hypercoagulability Syndrome Due to Glycosylphosphatidylinositol Deficiency 58
Congenital Disorder of Glycosylation Due to Pigm Deficiency 58
Portal Hypertension with Seizures and/or Macrocephaly 56
Glycosylphosphatidylinositol Deficiency; Gpid 56
Pigm-Cdg 58

Characteristics:

Orphanet epidemiological data:

58
hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM:

56
Inheritance:
autosomal recessive

Miscellaneous:
onset of thrombosis by age 2 years


HPO:

31
glycosylphosphatidylinositol biosynthesis defect 1:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare neurological diseases
Inborn errors of metabolism
Rare haematological diseases


Summaries for Glycosylphosphatidylinositol Biosynthesis Defect 1

OMIM : 56 Glycosylphosphatidylinositol is a glycolipid that anchors more than 150 proteins to the cell surface, and these proteins, termed GPI-anchored proteins (GPI-APs), perform a variety of functions as enzymes, adhesion molecules, complement regulators, and coreceptors in signal transduction pathways. Reduced surface levels of GPI-APs or abnormal GPI-AP structure can therefore result in variable manifestations. Glycosylphosphatidylinositol biosynthesis defect-1 (GPIBD1) is characterized predominantly by portal hypertension due to portal vein thrombosis. Most patients have absence seizures, cerebral thrombosis, and macrocephaly. Some patients have mildly to moderately impaired intellectual development (summary by Makrythanasis et al., 2016; Pode-Shakked et al., 2019). (610293)

MalaCards based summary : Glycosylphosphatidylinositol Biosynthesis Defect 1, also known as glycosylphosphatidylinositol deficiency, is related to hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency and hemolytic anemia, nonspherocytic, due to glucose phosphate isomerase deficiency, and has symptoms including absence seizures An important gene associated with Glycosylphosphatidylinositol Biosynthesis Defect 1 is PIGM (Phosphatidylinositol Glycan Anchor Biosynthesis Class M), and among its related pathways/superpathways are Post-translational modification- synthesis of GPI-anchored proteins and Glycosylphosphatidylinositol (GPI)-anchor biosynthesis. Affiliated tissues include bone and heart, and related phenotypes are seizures and splenomegaly

UniProtKB/Swiss-Prot : 73 Glycosylphosphatidylinositol deficiency: Autosomal recessive trait that results in a propensity to venous thrombosis and seizures. Deficiency is due to a point mutation in the regulatory sequences of PIGM that disrupts binding of the transcription factor SP1 to its cognate promoter motif, leading to a strong reduction of expression.

Related Diseases for Glycosylphosphatidylinositol Biosynthesis Defect 1

Diseases in the Glycosylphosphatidylinositol Biosynthesis Defect 1 family:

Glycosylphosphatidylinositol Biosynthesis Defect 11 Glycosylphosphatidylinositol Biosynthesis Defect 15
Glycosylphosphatidylinositol Biosynthesis Defect 16 Glycosylphosphatidylinositol Biosynthesis Defect 17
Glycosylphosphatidylinositol Biosynthesis Defect 18 Glycosylphosphatidylinositol Biosynthesis Defect 21

Diseases related to Glycosylphosphatidylinositol Biosynthesis Defect 1 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 32)
# Related Disease Score Top Affiliating Genes
1 hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency 12.5
2 hemolytic anemia, nonspherocytic, due to glucose phosphate isomerase deficiency 11.3
3 glucose phosphate isomerase deficiency 11.2
4 hyperphosphatasia with mental retardation syndrome 1 11.1
5 coloboma, congenital heart disease, ichthyosiform dermatosis, mental retardation, and ear anomalies syndrome 11.1
6 multiple congenital anomalies-hypotonia-seizures syndrome 2 11.1
7 multiple congenital anomalies-hypotonia-seizures syndrome 1 11.1
8 hyperphosphatasia with mental retardation syndrome 3 11.1
9 hyperphosphatasia with mental retardation syndrome 2 11.1
10 multiple congenital anomalies-hypotonia-seizures syndrome 3 11.1
11 hyperphosphatasia with mental retardation syndrome 4 11.1
12 mental retardation, autosomal recessive 42 11.1
13 glycosylphosphatidylinositol biosynthesis defect 11 11.1
14 hyperphosphatasia with mental retardation syndrome 6 11.1
15 mental retardation, autosomal recessive 53 11.1
16 glycosylphosphatidylinositol biosynthesis defect 15 11.1
17 glycosylphosphatidylinositol biosynthesis defect 17 11.1
18 glycosylphosphatidylinositol biosynthesis defect 18 11.1
19 epileptic encephalopathy, early infantile, 77 11.1
20 epileptic encephalopathy, early infantile, 80 11.1
21 glycosylphosphatidylinositol biosynthesis defect 21 11.1
22 paroxysmal nocturnal hemoglobinuria 10.1
23 hemoglobinuria 10.1
24 hyperphosphatasia-intellectual disability syndrome 10.1
25 thrombophilia due to thrombin defect 9.9
26 autosomal recessive disease 9.9
27 microcephaly 9.9
28 cataract 9.9
29 congenital disorders of n-linked glycosylation and multiple pathway 9.9
30 hypotonia 9.9
31 multiple congenital anomalies-hypotonia-seizures syndrome 9.4 PIGW PIGM
32 anterior segment dysgenesis 4 9.2 PIGW PIGM

Graphical network of the top 20 diseases related to Glycosylphosphatidylinositol Biosynthesis Defect 1:



Diseases related to Glycosylphosphatidylinositol Biosynthesis Defect 1

Symptoms & Phenotypes for Glycosylphosphatidylinositol Biosynthesis Defect 1

Human phenotypes related to Glycosylphosphatidylinositol Biosynthesis Defect 1:

31 (show all 10)
# Description HPO Frequency HPO Source Accession
1 seizures 31 HP:0001250
2 splenomegaly 31 HP:0001744
3 hepatomegaly 31 HP:0002240
4 portal hypertension 31 HP:0001409
5 venous thrombosis 31 HP:0004936
6 absence seizure 31 HP:0002121
7 atonic seizures 31 HP:0010819
8 portal vein thrombosis 31 HP:0030242
9 hepatic vein thrombosis 31 HP:0030243
10 reduced granulocyte cd59 level 31 HP:0031555

Symptoms via clinical synopsis from OMIM:

56
Abdomen Spleen:
splenomegaly

Cardiovascular Vascular:
portal hypertension
venous thrombosis
dilated superficial facial and abdominal veins (in some patients)

Neurologic Central Nervous System:
cerebellar atrophy (in some patients)
seizures, absence
seizures, atonic
cerebral atrophy (in some patients)
cerebral infarcts (in some patients)

Laboratory Abnormalities:
decreased expression of glycosylphosphatidylinositol-linked proteins (e.g., cd59 ) on hematopoietic cells

Abdomen Liver:
hepatomegaly
portal hypertension
portal vein thrombosis
hepatic venous thrombosis

Hematology:
thrombocytopenia

Head And Neck Head:
macrocephaly (in some patients)

Clinical features from OMIM:

610293

UMLS symptoms related to Glycosylphosphatidylinositol Biosynthesis Defect 1:


absence seizures

Drugs & Therapeutics for Glycosylphosphatidylinositol Biosynthesis Defect 1

Search Clinical Trials , NIH Clinical Center for Glycosylphosphatidylinositol Biosynthesis Defect 1

Genetic Tests for Glycosylphosphatidylinositol Biosynthesis Defect 1

Genetic tests related to Glycosylphosphatidylinositol Biosynthesis Defect 1:

# Genetic test Affiliating Genes
1 Glycosylphosphatidylinositol Deficiency 29 PIGM

Anatomical Context for Glycosylphosphatidylinositol Biosynthesis Defect 1

MalaCards organs/tissues related to Glycosylphosphatidylinositol Biosynthesis Defect 1:

40
Bone, Heart

Publications for Glycosylphosphatidylinositol Biosynthesis Defect 1

Articles related to Glycosylphosphatidylinositol Biosynthesis Defect 1:

# Title Authors PMID Year
1
Hypomorphic promoter mutation in PIGM causes inherited glycosylphosphatidylinositol deficiency. 61 56 6
16767100 2006
2
Cerebral and portal vein thrombosis, macrocephaly and atypical absence seizures in Glycosylphosphatidyl inositol deficiency due to a PIGM promoter mutation. 56 6
31445883 2019
3
Targeted therapy for inherited GPI deficiency. 56 6
17442906 2007
4
Pathogenic Variants in PIGG Cause Intellectual Disability with Seizures and Hypotonia. 56
26996948 2016
5
Cell-type-specific transcriptional regulation of PIGM underpins the divergent hematologic phenotype in inherited GPl deficiency. 6
25293775 2014
6
Clinical variability in inherited glycosylphosphatidylinositol deficiency disorders. 61
30054924 2019
7
A novel mutation in PIGW causes glycosylphosphatidylinositol deficiency without hyperphosphatasia. 61
27626616 2016
8
A novel PIGN mutation and prenatal diagnosis of inherited glycosylphosphatidylinositol deficiency. 61
26419326 2016
9
Mechanism for release of alkaline phosphatase caused by glycosylphosphatidylinositol deficiency in patients with hyperphosphatasia mental retardation syndrome. 61
22228761 2012

Variations for Glycosylphosphatidylinositol Biosynthesis Defect 1

ClinVar genetic disease variations for Glycosylphosphatidylinositol Biosynthesis Defect 1:

6 ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 PIGM NM_145167.2(PIGM):c.-270C>GSNV Pathogenic 1288 rs587776528 1:160001799-160001799 1:160032009-160032009
2 PIGW NM_001346754.2(PIGW):c.608T>G (p.Leu203Trp)SNV Uncertain significance 634642 rs12952744 17:34893558-34893558 17:36537709-36537709
3 PIGM NM_145167.3(PIGM):c.950G>A (p.Cys317Tyr)SNV Uncertain significance 640196 1:160000580-160000580 1:160030790-160030790
4 PIGM NM_145167.3(PIGM):c.238C>G (p.Leu80Val)SNV Uncertain significance 665365 1:160001292-160001292 1:160031502-160031502
5 PIGM NC_000001.10:g.(?_160000238)_(160001799_?)deldeletion Uncertain significance 641554 1:160000238-160001799 1:160030448-160032009

Expression for Glycosylphosphatidylinositol Biosynthesis Defect 1

Search GEO for disease gene expression data for Glycosylphosphatidylinositol Biosynthesis Defect 1.

Pathways for Glycosylphosphatidylinositol Biosynthesis Defect 1

Pathways related to Glycosylphosphatidylinositol Biosynthesis Defect 1 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
10.95 PIGW PIGM
2
Show member pathways
10.24 PIGW PIGM

GO Terms for Glycosylphosphatidylinositol Biosynthesis Defect 1

Cellular components related to Glycosylphosphatidylinositol Biosynthesis Defect 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 endoplasmic reticulum membrane GO:0005789 8.62 PIGW PIGM

Biological processes related to Glycosylphosphatidylinositol Biosynthesis Defect 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 GPI anchor biosynthetic process GO:0006506 8.96 PIGW PIGM
2 preassembly of GPI anchor in ER membrane GO:0016254 8.62 PIGW PIGM

Sources for Glycosylphosphatidylinositol Biosynthesis Defect 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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