PIGA phosphatidylinositol glycan anchor biosynthesis, class A [Homo sapiens (human)] - Gene

Summary

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Official Symbol: PIGAprovided by HGNC
Official Full Name: phosphatidylinositol glycan anchor biosynthesis, class Aprovided by HGNC
Primary source: HGNC:8957
See related: Ensembl:ENSG00000165195; HPRD:02410; MIM:311770; Vega:OTTHUMG00000021174
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GPI3; PIG-A; MCAHS2
Summary: This gene encodes a protein required for synthesis of N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI), the first intermediate in the biosynthetic pathway of GPI anchor. The GPI anchor is a glycolipid found on many blood cells and which serves to anchor proteins to the cell surface. Paroxysmal nocturnal hemoglobinuria, an acquired hematologic disorder, has been shown to result from mutations in this gene. Alternate splice variants have been characterized. A related pseudogene is located on chromosome 12. [provided by RefSeq, Jun 2010]

Genomic context

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Location :: Xp22.1

Sequence :: Chromosome: X; NC_000023.10 (15337573..15353676, complement)

See PIGA in Epigenomics, MapViewer

Chromosome X - NC_000023.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

The small population of PIG-A mutant cells in myelodysplastic syndromes do not arise from multipotent hematopoietic stem cells.
Title: The small population of PIG-A mutant cells in myelodysplastic syndromes do not arise from multipotent hematopoietic stem cells.
An X chromosome exome next-generation sequencing screen identified a single nonsense PIGA mutation.
Title: The phenotype of a germline mutation in PIGA: the gene somatically mutated in paroxysmal nocturnal hemoglobinuria.
loss of PIG-A or a combination of genes within the 0.5 Mb commonly deleted region leads to a phenotype capable of avoiding immune surveillance, but is not inherently malignant.
Title: Deletions of Xp22.2 including PIG-A locus lead to paroxysmal nocturnal hemoglobinuria.
the PIG-A mutations in paroxysmal nocturnal hemoglobinuria patients
Title: [Somatic mutations of PIG-A gene in Chinese patients with paroxysmal nocturnal hemoglobinuria].
Paroxysmal nocturnal hemoglobinuria is an acquired hemolytic anemia caused by the expansion of a hematopoietic progenitor cell that has acquired a mutation in the X-linked PIGA gene.
Title: The pathophysiology of disease in patients with paroxysmal nocturnal hemoglobinuria.
PIG-A mutations contribute to clonal expansion in PNH by conferring a survival advantage to hematopoietic progenitors under proapoptotic stresses.
Title: Glycosylphosphatidylinositol-anchored protein deficiency confers resistance to apoptosis in PNH.
In patients with paroxysmal nocturnal hemoglobinuria, it is very unlikely that more than one PIG-A mutated clone arises at the level of the hematopoietic stem cells.
Title: On the origin of multiple mutant clones in paroxysmal nocturnal hemoglobinuria.
Decreased susceptibility of leukemic cells with PIG-A mutation to natural killer cells in vitro allows paroxysmal nocturnal hemoglobinuria clones to escape immune attack.
Title: Decreased susceptibility of leukemic cells with PIG-A mutation to natural killer cells in vitro.
Molecular testing for mutations in the PIG-A gene can serve as a confirmation test of paroxysmal nocturnal hemoglobinuria.
Title: Mutation analysis of the PIG-A gene in Korean patients with paroxysmal nocturnal haemoglobinuria.
PIG-A gene abnormality in precursor cells and changes of expression of GPI-anchored protein and contribution of paroxysmal nocturnal hemoglobinuria clones with PIG-A gene abnormalities among various cell lineages during differentiation and maturation
Title: Phenotypes and phosphatidylinositol glycan-class A gene abnormalities during cell differentiation and maturation from precursor cells to mature granulocytes in patients with paroxysmal nocturnal hemoglobinuria.

Submit: New GeneRIF Correction See all (13)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Multiple congenital anomalies-hypotonia-seizures syndrome 2

MIM: 300868

Genetic Testing Registry

Paroxysmal nocturnal hemoglobinuria

MIM: 300818

Genetic Testing Registry

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
P37287	O94777	DPM2	HPRD	PubMed
P37287	Q14442	PIGH	HPRD	PubMed
P37287	Q9BRB3	PIGQ	HPRD	PubMed
P37287	Q96I23	PIGY	HPRD	PubMed
BioGRID:111295	BioGRID:108309	ELAVL1	BioGRID	PubMed	Affinity Capture-RNA
BioGRID:111295	BioGRID:111301	PIGH	BioGRID	PubMed	Reconstituted Complex
BioGRID:111295	BioGRID:119391	PIGP	BioGRID	PubMed	Affinity Capture-Western
BioGRID:111295	BioGRID:114545	PIGQ	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex
BioGRID:111295	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS

Pathways from BioSystems

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GPI-anchor biosynthesis, core oligosaccharide, organism-specific biosystem (from KEGG)
GPI-anchor biosynthesis, core oligosaccharide, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Glycan metabolism
GPI-anchor biosynthesis, core oligosaccharide, conserved biosystem (from KEGG)
GPI-anchor biosynthesis, core oligosaccharide, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Glycan metabolism
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis, organism-specific biosystem (from KEGG)
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis, organism-specific biosystemCell surface proteins can be attached to the cell membrane via the glycolipid structure called glycosylphosphatidylinositol (GPI) anchor. Hundreds of GPI-anchored proteins have been identified in man...
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis, conserved biosystem (from KEGG)
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis, conserved biosystemCell surface proteins can be attached to the cell membrane via the glycolipid structure called glycosylphosphatidylinositol (GPI) anchor. Hundreds of GPI-anchored proteins have been identified in man...
Metabolism of proteins, organism-specific biosystem (from REACTOME)
Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
Post-translational modification: synthesis of GPI-anchored proteins, organism-specific biosystem (from REACTOME)
Post-translational modification: synthesis of GPI-anchored proteins, organism-specific biosystemGlycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of eleven reactio...
Post-translational protein modification, organism-specific biosystem (from REACTOME)
Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
Synthesis of glycosylphosphatidylinositol (GPI), organism-specific biosystem (from REACTOME)
Synthesis of glycosylphosphatidylinositol (GPI), organism-specific biosystemGlycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of nine reactions...

General gene information

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Markers

PIGA (e-PCR)
- UniSTS:498176

GDB:604019 (e-PCR)
- UniSTS:99133

GDB:604488 (e-PCR)
- UniSTS:99199

STS-D11466 (e-PCR)
- UniSTS:45711

SHGC-30072 (e-PCR)
- UniSTS:20126

DXS1296 (e-PCR)
- UniSTS:99246

WI-13794 (e-PCR)
- UniSTS:62686

GDB:604486 (e-PCR)
- UniSTS:158206

Genotypes

See PIGA SNP Geneview Report
See PIGA SNP Genotype Report
See PIGA SNP Variation Viewer Report

Homology

Homologs of the PIGA gene: The PIGA gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, and A.thaliana.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
UDP-glycosyltransferase activity	TAS Traceable Author Statement more info
phosphatidylinositol N-acetylglucosaminyltransferase activity	TAS Traceable Author Statement more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
C-terminal protein lipidation	TAS Traceable Author Statement more info
GPI anchor biosynthetic process	TAS Traceable Author Statement more info	PubMed
cellular protein metabolic process	TAS Traceable Author Statement more info
positive regulation of metabolic process	TAS Traceable Author Statement more info	PubMed
post-translational protein modification	TAS Traceable Author Statement more info
preassembly of GPI anchor in ER membrane	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
endoplasmic reticulum membrane	TAS Traceable Author Statement more info
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex	IDA Inferred from Direct Assay more info	PubMed
integral to membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: phosphatidylinositol N-acetylglucosaminyltransferase subunit A

Names: phosphatidylinositol N-acetylglucosaminyltransferase subunit A; GPI anchor biosynthesis; GLCNAC-PI synthesis protein; class A GlcNAc-inositol phospholipid assembly protein; phosphatidylinositol-glycan biosynthesis, class A protein

NP_002632.1

EC 2.4.1.198

NP_065206.3

EC 2.4.1.198

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_009786.1 RefSeqGene

Range

4985..21088

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_160

mRNA and Protein(s)

NM_002641.3 → NP_002632.1 phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

BQ026877, D11466, DA951065

Consensus CDS

CCDS14165.1

UniProtKB/Swiss-Prot

P37287

Related

ENSP00000369820, OTTHUMP00000022959, ENST00000333590, OTTHUMT00000055854

Conserved Domains (3) summary

TIGR02149
Location:37 – 401
Blast Score: 197

glgA_Coryne; glycogen synthase, Corynebacterium family

pfam08288
Location:72 – 161
Blast Score: 431

PIGA; PIGA (GPI anchor biosynthesis)

pfam00534
Location:224 – 363
Blast Score: 269

Glycos_transf_1; Glycosyl transferases group 1
NM_020473.3 → NP_065206.3 phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. The resulting isoform (3) has a distinct and shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK303538, BC038236, BQ026877, DA951065

Consensus CDS

CCDS48086.2

UniProtKB/Swiss-Prot

P37287

Related

ENSP00000442653, ENST00000542278

Conserved Domains (2) summary

COG0438
Location:5 – 167
Blast Score: 227

RfaG; Glycosyltransferase [Cell envelope biogenesis, outer membrane]

cl10013
Location:5 – 192
Blast Score: 851

Glycosyltransferase_GTB_type; Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate ...

RNA

NR_033835.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK098047, BC038236, BQ026877, DC347872
NR_033836.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the 5' coding region, as found in variant 1, and multiple upstream ORFs are present, which are predicted to interfere with the translation of the longest ORF.

Source sequence(s)

BC038236, BQ026877, CX870731, DA951065

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000023.10 Reference GRCh37.p10 Primary Assembly

Range

15337573..15353676, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000155.1 Alternate HuRef

Range

13096081..13112522, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018934.1 Alternate CHM1_1.0

Range

15252530..15268633, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_020472.1: Suppressed sequence

Description

NM_020472.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01071290.1 (1900..12580)	None
genomic	ABBA01071291.1	None
genomic	ABBA01071292.1 (1923..1949)	None
genomic	AC095351.5 (80016..96081)	None
genomic	AMYH01022105.1 (137614..153717)	None
genomic	CH471074.1	EAW98879.1
		EAW98880.1
		EAW98881.1
		EAW98882.1
		EAW98883.1
		EAW98884.1
genomic	D28791.2	BAA05966.1
genomic	X77729.1	None
mRNA	AK098047.1	BAG53569.1
mRNA	AK290497.1	BAF83186.1
mRNA	AK303538.1	BAG64564.1
mRNA	AK304144.1	BAG65037.1
mRNA	AK315063.1	BAG37537.1
mRNA	BC038236.1	AAH38236.1
mRNA	BM998465.1	None
mRNA	BQ026877.1	None
mRNA	CX870731.1	None
mRNA	D11466.1	BAA02019.1
mRNA	DA951065.1	None
mRNA	DC347872.1	None
mRNA	S61523.1	AAD13929.1
mRNA	S74936.1	AAD14160.1
other-genetic	JF432189.1	ADZ15406.1