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PIGT phosphatidylinositol glycan anchor biosynthesis class T [ Homo sapiens (human) ]

Gene ID: 51604, updated on 5-Mar-2024

Summary

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Official Symbol
PIGTprovided by HGNC
Official Full Name
phosphatidylinositol glycan anchor biosynthesis class Tprovided by HGNC
Primary source
HGNC:HGNC:14938
See related
Ensembl:ENSG00000124155 MIM:610272; AllianceGenome:HGNC:14938
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
NDAP; PNH2; PIG-T; CGI-06; MCAHS3
Summary
This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This protein is an essential component of the multisubunit enzyme, GPI transamidase. GPI transamidase mediates GPI anchoring in the endoplasmic reticulum, by catalyzing the transfer of fully assembled GPI units to proteins. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
Expression
Ubiquitous expression in heart (RPKM 45.9), colon (RPKM 41.3) and 25 other tissues See more
Orthologs
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Genomic context

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See PIGT in Genome Data Viewer
Location:
20q13.12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45416141..45426241)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47152004..47162091)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (44044781..44054881)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene SYS1-DBNDD2 readthrough (NMD candidate) Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 10 Neighboring gene uncharacterized LOC107985404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44035517-44036066 Neighboring gene uncharacterized LOC107985405 Neighboring gene dysbindin domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17951 Neighboring gene uncharacterized LOC105372631 Neighboring gene microRNA 6812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12959 Neighboring gene WAP four-disulfide core domain 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Bilateral anterior segment dysgenesis and peripheral avascular retina with tractional retinal detachment in an infant with multiple congenital anomalies-hypotony-seizures syndrome 3. Wu F, et al. Ophthalmic Genet, 2021 Jun. PMID 33620284
  2. Evidence of the milder phenotypic spectrum of c.1582G>A PIGT variant: Delineation based on seven novel Polish patients. Jezela-Stanek A, et al. Clin Genet, 2020 Nov. PMID 32725661
  3. Epileptic apnea in a patient with inherited glycosylphosphatidylinositol anchor deficiency and PIGT mutations. Kohashi K, et al. Brain Dev, 2018 Jan. PMID 28728837
  4. Novel compound heterozygous PIGT mutations caused multiple congenital anomalies-hypotonia-seizures syndrome 3. Nakashima M, et al. Neurogenetics, 2014 Aug. PMID 24906948
  5. A case of paroxysmal nocturnal hemoglobinuria caused by a germline mutation and a somatic mutation in PIGT. Krawitz PM, et al. Blood, 2013 Aug 15. PMID 23733340

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bilateral anterior segment dysgenesis and peripheral avascular retina with tractional retinal detachment in an infant with multiple congenital anomalies-hypotony-seizures syndrome 3.
    Title: Bilateral anterior segment dysgenesis and peripheral avascular retina with tractional retinal detachment in an infant with multiple congenital anomalies-hypotony-seizures syndrome 3.
  2. Evidence of the milder phenotypic spectrum of c.1582G>A PIGT variant: Delineation based on seven novel Polish patients.
    Title: Evidence of the milder phenotypic spectrum of c.1582G>A PIGT variant: Delineation based on seven novel Polish patients.
  3. Whole-exome sequencing revealed compound heterozygous mutations (c.250G > T, p.Glu84X and c.1096G > T, p.Gly366Trp) in PIGT (NM_015937.5), which were confirmed using Sanger sequencing. Thus inherited GPI anchor deficiency associated with these PIGT mutations was diagnosed
    Title: Epileptic apnea in a patient with inherited glycosylphosphatidylinositol anchor deficiency and PIGT mutations.
  4. PIGT-knockout HEK293 cells showed that p.(E237Q) results in a small reduction in the amount of CD59 anchored to the cell membrane.
    Title: Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.
  5. mutations in PIGT as the cause of a novel autosomal recessive intellectual disability syndrome
    Title: A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.
  6. Germline mutation and a somatic mutation in PIGT is associated with paroxysmal nocturnal hemoglobinuria.
    Title: A case of paroxysmal nocturnal hemoglobinuria caused by a germline mutation and a somatic mutation in PIGT.
  7. GPI8 and PIG-T form a functionally important intermolecular disulfide bridge
    Title: Two subunits of glycosylphosphatidylinositol transamidase, GPI8 and PIG-T, form a functionally important intermolecular disulfide bridge.
  8. ER-localized because of information in its transmembrane span
    Title: Endoplasmic reticulum localization of Gaa1 and PIG-T, subunits of the glycosylphosphatidylinositol transamidase complex.
Submit: New GeneRIF Correction

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 3
MedGen: C3809356 OMIM: 615398 GeneReviews: Not available
Compare labs
Paroxysmal nocturnal hemoglobinuria 2
MedGen: C3809369 OMIM: 615399 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC8909, FLJ41596

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in attachment of GPI anchor to protein IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in attachment of GPI anchor to protein NAS
Non-traceable Author Statement
more info
  
involved_in attachment of GPI anchor to protein TAS
Traceable Author Statement
more info
 PubMed 
involved_in neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of GPI-anchor transamidase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of GPI-anchor transamidase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of GPI-anchor transamidase complex IPI
Inferred from Physical Interaction
more info
  
part_of GPI-anchor transamidase complex TAS
Traceable Author Statement
more info
 PubMed 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 

General protein information

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Preferred Names
GPI transamidase component PIG-T
Names
GPI transamidase subunit
neurotrophin-regulated neuronal development-associated protein
phosphatidylinositol-glycan biosynthesis class T protein

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

  1. NG_047154.1 RefSeqGene

    Range
    5075..15175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001184728.3 → NP_001171657.1  GPI transamidase component PIG-T isoform 2 precursor

    See identical proteins and their annotated locations for NP_001171657.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK296139, AL121742, DC399420
    Consensus CDS
    CCDS54464.1
    UniProtKB/TrEMBL
    A0A1W2PNP0
    Related
    ENSP00000441577.1, ENST00000543458.7
    Conserved Domains (1) summary
    pfam04113
    Location:32 → 509
    Gpi16; Gpi16 subunit, GPI transamidase component

  2. NM_001184729.3 → NP_001171658.1  GPI transamidase component PIG-T isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AK225517, AL121742
    Consensus CDS
    CCDS54465.1
    UniProtKB/TrEMBL
    A0A1W2PPR6
    Related
    ENSP00000361774.4, ENST00000372689.9
    Conserved Domains (1) summary
    pfam04113
    Location:32 → 498
    Gpi16; Gpi16 subunit, GPI transamidase component

  3. NM_001184730.3 → NP_001171659.1  GPI transamidase component PIG-T isoform 4 precursor

    See identical proteins and their annotated locations for NP_001171659.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two consecutive exons in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AK302093, AL121742
    Consensus CDS
    CCDS54466.1
    UniProtKB/TrEMBL
    A0A1W2PP53
    Related
    ENSP00000279035.8, ENST00000279035.14
    Conserved Domains (1) summary
    pfam04113
    Location:68 → 463
    Gpi16; Gpi16 subunit, GPI transamidase component

  4. NM_015937.6 → NP_057021.2  GPI transamidase component PIG-T isoform 1 precursor

    See identical proteins and their annotated locations for NP_057021.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL121742, BC136827
    Consensus CDS
    CCDS13353.1
    UniProtKB/Swiss-Prot
    B2RND5, B7Z3N1, B7Z7I8, E1P622, G8JLF5, Q2NL69, Q7Z3N7, Q969N2, Q9BQY7, Q9BQY8, Q9UJG6, Q9Y2Z5
    UniProtKB/TrEMBL
    A0A1W2PPR6
    Related
    ENSP00000279036.6, ENST00000279036.12
    Conserved Domains (1) summary
    pfam04113
    Location:32 → 565
    Gpi16; Gpi16 subunit, GPI transamidase component

RNA

  1. NR_047691.2 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 the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK316358, AL121742, DC399420
    Related
    ENST00000638445.1

  2. NR_047692.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK296063, AL121742
    Related
    ENST00000455050.2

  3. NR_047693.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK293294, AL121742, DC384944
    Related
    ENST00000639783.1

  4. NR_047694.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK293686, AL121742, DC399420
    Related
    ENST00000638671.1

  5. NR_047695.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks three consecutive internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK299013, AL121742
    Related
    ENST00000640175.1

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

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    45416141..45426241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    47152004..47162091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969N2.1 GenPept UniProtKB/Swiss-Prot:Q969N2

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