MCID: GLY032
MIFTS: 36

Glycosylphosphatidylinositol Deficiency

Categories: Genetic diseases, Neuronal diseases, Metabolic diseases, Blood diseases, Rare diseases

Aliases & Classifications for Glycosylphosphatidylinositol Deficiency

MalaCards integrated aliases for Glycosylphosphatidylinositol Deficiency:

Name: Glycosylphosphatidylinositol Deficiency 53 71 28 13 69
Glycosylphosphatidylinositol Biosynthesis Defect 1 53 71
Gpibd1 53 71
Gpid 53 71
Hypercoagulability Syndrome Due to Glycosylphosphatidylinositol Deficiency 55
Congenital Disorder of Glycosylation Due to Pigm Deficiency 55
Glycosylphosphatidylinositol Biosynthesis Defect 1; Gpibd1 53
Pigm-Cdg 55

Characteristics:

Orphanet epidemiological data:

55
hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM:

53
Inheritance:
autosomal recessive

Miscellaneous:
two unrelated families have been reported (last curated may 2014)
onset of thrombosis by age 2 years


HPO:

31
glycosylphosphatidylinositol deficiency:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 53 610293
Orphanet 55 ORPHA83639
UMLS via Orphanet 70 C1853205
ICD10 via Orphanet 33 E88.8
MedGen 39 C1853205
UMLS 69 C1853205

Summaries for Glycosylphosphatidylinositol Deficiency

OMIM : 53 Glycophosphatidylinositol is a glycolipid that anchors more than 150 proteins to the cell surface, and these proteins, termed GPI-anchored proteins (GPI-APs), have various important roles. Reduced surface levels of GPI-APs or abnormal GPI-AP structure can cause various symptoms, mainly including intellectual disability, and sometimes other congenital malformations, seizures, or dysmorphic facial features (summary by Makrythanasis et al., 2016). (610293)

MalaCards based summary : Glycosylphosphatidylinositol Deficiency, also known as glycosylphosphatidylinositol biosynthesis defect 1, is related to hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency and hemolytic anemia, nonspherocytic, due to glucose phosphate isomerase deficiency, and has symptoms including seizures, splenomegaly and hepatomegaly. An important gene associated with Glycosylphosphatidylinositol Deficiency is PIGM (Phosphatidylinositol Glycan Anchor Biosynthesis Class M), and among its related pathways/superpathways are Metabolism and Metabolism of proteins. Affiliated tissues include bone and bone marrow, and related phenotype is Decreased NF-kappaB reporter expression.

UniProtKB/Swiss-Prot : 71 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 Deficiency

Graphical network of the top 20 diseases related to Glycosylphosphatidylinositol Deficiency:



Diseases related to Glycosylphosphatidylinositol Deficiency

Symptoms & Phenotypes for Glycosylphosphatidylinositol Deficiency

Symptoms via clinical synopsis from OMIM:

53
Cardiovascular Vascular:
venous thrombosis
portal hypertension

Abdomen Spleen:
splenomegaly

Hematology:
no hemolysis
no bone marrow abnormalities

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

Neurologic Central Nervous System:
seizures, absence
seizures, atonic

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


Clinical features from OMIM:

610293

Human phenotypes related to Glycosylphosphatidylinositol Deficiency:

31
# 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 portal vein thrombosis 31 HP:0030242

UMLS symptoms related to Glycosylphosphatidylinositol Deficiency:


absence seizures

GenomeRNAi Phenotypes related to Glycosylphosphatidylinositol Deficiency according to GeneCards Suite gene sharing:

25
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased NF-kappaB reporter expression GR00312-A 8.92 ALPL PIGM PIGV PIGW

Drugs & Therapeutics for Glycosylphosphatidylinositol Deficiency

Search Clinical Trials , NIH Clinical Center for Glycosylphosphatidylinositol Deficiency

Genetic Tests for Glycosylphosphatidylinositol Deficiency

Genetic tests related to Glycosylphosphatidylinositol Deficiency:

# Genetic test Affiliating Genes
1 Glycosylphosphatidylinositol Deficiency 28 PIGM

Anatomical Context for Glycosylphosphatidylinositol Deficiency

MalaCards organs/tissues related to Glycosylphosphatidylinositol Deficiency:

38
Bone, Bone Marrow

Publications for Glycosylphosphatidylinositol Deficiency

Articles related to Glycosylphosphatidylinositol Deficiency:

# Title Authors Year
1
A novel mutation in PIGW causes glycosylphosphatidylinositol deficiency without hyperphosphatasia. ( 27626616 )
2016
2
A novel PIGN mutation and prenatal diagnosis of inherited glycosylphosphatidylinositol deficiency. ( 26419326 )
2015
3
Mutations in PIGY: expanding the phenotype of inherited glycosylphosphatidylinositol deficiencies. ( 26293662 )
2015
4
Mechanism for release of alkaline phosphatase caused by glycosylphosphatidylinositol deficiency in patients with hyperphosphatasia mental retardation syndrome. ( 22228761 )
2012
5
Hypomorphic promoter mutation in PIGM causes inherited glycosylphosphatidylinositol deficiency. ( 16767100 )
2006
6
Defective TCR signaling events in glycosylphosphatidylinositol-deficient T cells derived from paroxysmal nocturnal hemoglobinuria patients. ( 10464162 )
1999

Variations for Glycosylphosphatidylinositol Deficiency

ClinVar genetic disease variations for Glycosylphosphatidylinositol Deficiency:

6
# Gene Variation Type Significance SNP ID Assembly Location
1 PIGM NM_145167.2(PIGM): c.-270C> G single nucleotide variant Pathogenic rs587776528 GRCh37 Chromosome 1, 160001799: 160001799

Expression for Glycosylphosphatidylinositol Deficiency

Search GEO for disease gene expression data for Glycosylphosphatidylinositol Deficiency.

Pathways for Glycosylphosphatidylinositol Deficiency

Pathways related to Glycosylphosphatidylinositol Deficiency according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
13.19 ALPL PIGM PIGV PIGW
2
Show member pathways
12.88 ALPL PIGM PIGV PIGW
3
Show member pathways
10.92 ALPL PIGM PIGV PIGW
4
Show member pathways
10.74 PIGM PIGV PIGW

GO Terms for Glycosylphosphatidylinositol Deficiency

Cellular components related to Glycosylphosphatidylinositol Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 endoplasmic reticulum membrane GO:0005789 8.8 PIGM PIGV PIGW

Biological processes related to Glycosylphosphatidylinositol Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 GPI anchor biosynthetic process GO:0006506 9.13 PIGM PIGV PIGW
2 preassembly of GPI anchor in ER membrane GO:0016254 8.8 PIGM PIGV PIGW

Molecular functions related to Glycosylphosphatidylinositol Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 transferase activity GO:0016740 9.13 PIGM PIGV PIGW
2 transferase activity, transferring glycosyl groups GO:0016757 8.62 PIGM PIGV

Sources for Glycosylphosphatidylinositol Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 FMA
27 GO
28 GTR
29 HGMD
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 MedGen
41 MeSH
42 MESH via Orphanet
43 MGI
45 NCI
46 NCIt
47 NDF-RT
50 NINDS
51 Novoseek
53 OMIM
54 OMIM via Orphanet
58 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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