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

Summary

Official Symbol: PIGAprovided by HGNC
Official Full Name: phosphatidylinositol glycan anchor biosynthesis class Aprovided by HGNC
Primary source: HGNC:HGNC:8957
See related: Ensembl:ENSG00000165195 MIM:311770; AllianceGenome:HGNC:8957
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; PNH1; PIG-A; MCAHS2; NEDEPH
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]
Expression: Ubiquitous expression in bone marrow (RPKM 9.8), urinary bladder (RPKM 3.0) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xp22.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (15319451..15335554, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (14902337..14918440, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (15337573..15353676, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Congenital diaphragmatic hernia in siblings with PIGA-related congenital disorder of glycosylation.
Title: Congenital diaphragmatic hernia in siblings with PIGA-related congenital disorder of glycosylation.
PIG-A gene mutation as a mutagenicity biomarker among coke oven workers.
Title: PIG-A gene mutation as a mutagenicity biomarker among coke oven workers.
Constitutional PIGA mutations cause a novel subtype of hemochromatosis in patients with neurologic dysfunction.
Title: Constitutional PIGA mutations cause a novel subtype of hemochromatosis in patients with neurologic dysfunction.
Mutations in PIGA cause a CD52-/GPI-anchor-deficient phenotype complicating alemtuzumab treatment in T-cell prolymphocytic leukemia.
Title: Mutations in PIGA cause a CD52-/GPI-anchor-deficient phenotype complicating alemtuzumab treatment in T-cell prolymphocytic leukemia.
Implication of PIGA genotype on erythrocytes phenotype in Paroxysmal Nocturnal Hemoglobinuria.
Title: Implication of PIGA genotype on erythrocytes phenotype in Paroxysmal Nocturnal Hemoglobinuria.
PIGA-related epileptic encephalopathy demonstrating intrafamilial phenotypic heterogeneity.
Title: PIGA-related epileptic encephalopathy demonstrating intrafamilial phenotypic heterogeneity.
Evaluation of PIG-A-mutated granulocytes and ex-vivo binucleated micronucleated lymphocytes frequencies after breast cancer radiotherapy in humans.
Title: Evaluation of PIG-A-mutated granulocytes and ex-vivo binucleated micronucleated lymphocytes frequencies after breast cancer radiotherapy in humans.
Early-onset epileptic encephalopathy related to germline PIGA mutations: A series of 5 cases.
Title: Early-onset epileptic encephalopathy related to germline PIGA mutations: A series of 5 cases.
Identification of acquired PIGA mutations and additional variants by next-generation sequencing in paroxysmal nocturnal hemoglobinuria.
Title: Identification of acquired PIGA mutations and additional variants by next-generation sequencing in paroxysmal nocturnal hemoglobinuria.
Lessons learned from 40 novel PIGA patients and a review of the literature.
Title: Lessons learned from 40 novel PIGA patients and a review of the literature.

Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Multiple congenital anomalies-hypotonia-seizures syndrome 2 MedGen: C3275508 OMIM: 300868 GeneReviews: Not available	Compare labs
Neurodevelopmental disorder with epilepsy and hemochromatosis MedGen: CN307964 OMIM: 301072 GeneReviews: Not available	Compare labs
Paroxysmal nocturnal hemoglobinuria 1 MedGen: C3806670 OMIM: 300818 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-11-09) ClinGen Genome Curation Page Haploinsufficency Some evidence for dosage pathogenicity (Last evaluated 2021-11-09) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in GPI anchor biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in preassembly of GPI anchor in ER membrane	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
part_of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex	IBA Inferred from Biological aspect of Ancestor more info
part_of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex	IDA Inferred from Direct Assay more info	PubMed
part_of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex	IPI Inferred from Physical Interaction more info	PubMed
located_in membrane	HDA more info	PubMed

General protein information

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Preferred Names: phosphatidylinositol N-acetylglucosaminyltransferase subunit A

Names: GLCNAC-PI synthesis protein; GPI anchor biosynthesis; 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

XP_011543841.1

EC 2.4.1.198

XP_054183185.1

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

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GenBank, FASTA, Sequence Viewer (Graphics), LRG_160

mRNA and Protein(s)

NM_002641.4 → NP_002632.1 phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform 1

See identical proteins and their annotated locations for NP_002632.1

Status: REVIEWED

Description

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

Source sequence(s)

BQ026877, D11466

Consensus CDS

CCDS14165.1

UniProtKB/Swiss-Prot

B4E0V2, P37287, Q16025, Q16250

UniProtKB/TrEMBL

A0A2K4Z9P8, A0A2K4Z9Q9, A0A2K4Z9S0, A0A2K4Z9S8, A0A2K4Z9T1, A0A2K4Z9T4, A0A2K4Z9T5, A0A2K4Z9T7, A0A2K4Z9T8, A0A2K4Z9U3, A0A2K4Z9V6, A0A2K4Z9V8, A0A2K4Z9W0, A0A2K4Z9W1, A0A2K4Z9W2, A0A2K4Z9W5, A0A2K4Z9W7, A0A2K4Z9W8, A0A2K4Z9X1, A0A2K4Z9X3, A0A2K4Z9X9, A0A2K4Z9Y1, A0A2K4Z9Z2, A0A2K4ZA02, B2RCE0

Related

ENSP00000369820.3, ENST00000333590.6

Conserved Domains (1) summary

cd03796
Location:34 → 432

GT1_PIG-A_like; This family is most closely related to the GT1 family of glycosyltransferases. Phosphatidylinositol glycan-class A (PIG-A), an X-linked gene in humans, is necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, a very early intermediate ...
NM_020473.3 → NP_065206.3 phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform 3

See identical proteins and their annotated locations for NP_065206.3

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/TrEMBL

A0A2K4Z9X5

Related

ENSP00000489540.1, ENST00000634582.1

Conserved Domains (1) summary

cl10013
Location:5 → 198

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

Related

ENST00000635598.1
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

Related

ENST00000638131.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

15319451..15335554 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011545539.3 → XP_011543841.1 phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform X1

UniProtKB/TrEMBL

A0A2K4Z9X5

Conserved Domains (2) summary

COG0438
Location:3 → 170

RfaB; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]

cl10013
Location:6 → 201

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 ...

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

14902337..14918440 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054327210.1 → XP_054183185.1 phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform X1

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.