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PIGC phosphatidylinositol glycan anchor biosynthesis class C [ Homo sapiens (human) ]

Gene ID: 5279, updated on 5-Mar-2024

Summary

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Official Symbol
PIGCprovided by HGNC
Official Full Name
phosphatidylinositol glycan anchor biosynthesis class Cprovided by HGNC
Primary source
HGNC:HGNC:8960
See related
Ensembl:ENSG00000135845 MIM:601730; AllianceGenome:HGNC:8960
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
GPI2; MRT62; GPIBD16
Summary
This gene encodes an endoplasmic reticulum associated protein that is involved in glycosylphosphatidylinositol (GPI) lipid anchor biosynthesis. The GPI lipid anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. The encoded protein is one subunit of the GPI N-acetylglucosaminyl (GlcNAc) transferase that transfers GlcNAc to phosphatidylinositol (PI) on the cytoplasmic side of the endoplasmic reticulum. Two alternatively spliced transcripts that encode the same protein have been found for this gene. A pseudogene on chromosome 11 has also been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in gall bladder (RPKM 12.5), skin (RPKM 12.3) and 25 other tissues See more
Orthologs
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Genomic context

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See PIGC in Genome Data Viewer
Location:
1q24.3
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (172441457..172444069, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (171798151..171800763, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (172410597..172413209, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene dynamin 3 Neighboring gene uncharacterized LOC102724528 Neighboring gene RNA, U6 small nuclear 157, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr1:172397968-172398490 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:172413041-172413564 Neighboring gene chromosome 1 open reading frame 105 Neighboring gene Sharpr-MPRA regulatory region 10840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:172466607-172467107 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:172466106-172466606 Neighboring gene Sharpr-MPRA regulatory region 5023 Neighboring gene Sharpr-MPRA regulatory region 3225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2094 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:172539927-172540926 Neighboring gene SUN domain containing ossification factor Neighboring gene RNA, U6 small nuclear 693, pseudogene

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. Mutations in the phosphatidylinositol glycan C (PIGC) gene are associated with epilepsy and intellectual disability. Edvardson S, et al. J Med Genet, 2017 Mar. PMID 27694521
  2. Structures and chromosomal localizations of the glycosylphosphatidylinositol synthesis gene PIGC and its pseudogene PIGCP1. Hong Y, et al. Genomics, 1997 Sep 15. PMID 9325057
  3. PIG-A and PIG-H, which participate in glycosylphosphatidylinositol anchor biosynthesis, form a protein complex in the endoplasmic reticulum. Watanabe R, et al. J Biol Chem, 1996 Oct 25. PMID 8900170
  4. PIG-C, one of the three human genes involved in the first step of glycosylphosphatidylinositol biosynthesis is a homologue of Saccharomyces cerevisiae GPI2. Inoue N, et al. Biochem Biophys Res Commun, 1996 Sep 4. PMID 8806613
  5. The first step of glycosylphosphatidylinositol biosynthesis is mediated by a complex of PIG-A, PIG-H, PIG-C and GPI1. Watanabe R, et al. EMBO J, 1998 Feb 16. PMID 9463366, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PIGC joins the list of genes in which mutations result in defective biosynthesis of GPI anchoring, manifesting by global developmental delay and seizure disorder.
    Title: Mutations in the phosphatidylinositol glycan C (PIGC) gene are associated with epilepsy and intellectual disability.
  2. Genes within recently identified loci associated with waist-hip ratio (WHR) exhibit fat depot-specific mRNA expression, which correlates with obesity-related traits. Adipose tissue (AT) mRNA expression of 6 genes (TBX15/WARS2, STAB1, PIGC, ZNRF3, GRB14
    Title: Fat depot-specific mRNA expression of novel loci associated with waist-hip ratio.
  3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
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
Glycosylphosphatidylinositol biosynthesis defect 16
MedGen: C4540521 OMIM: 617816 GeneReviews: Not available
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EBI GWAS Catalog

Description
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
EBI GWAS Catalog

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

  • MGC2049

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables catalytic 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 IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in GPI anchor biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in GPI anchor biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 

General protein information

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Preferred Names
phosphatidylinositol N-acetylglucosaminyltransferase subunit C
Names
PIG-C
phosphatidylinositol-glycan biosynthesis, class C protein
NP_002633.1
NP_714969.1

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_050631.1 RefSeqGene

    Range
    5022..7634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002642.4 → NP_002633.1  phosphatidylinositol N-acetylglucosaminyltransferase subunit C

    See identical proteins and their annotated locations for NP_002633.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 5' UTR when compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AA372370, BC006539, BG106700
    Consensus CDS
    CCDS1302.1
    UniProtKB/Swiss-Prot
    O14491, Q92535
    Related
    ENSP00000356702.1, ENST00000367728.1
    Conserved Domains (1) summary
    pfam06432
    Location:14 → 284
    GPI2; Phosphatidylinositol N-acetylglucosaminyltransferase

  2. NM_153747.2 → NP_714969.1  phosphatidylinositol N-acetylglucosaminyltransferase subunit C

    See identical proteins and their annotated locations for NP_714969.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the predominant transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AA372370, BC006539
    Consensus CDS
    CCDS1302.1
    UniProtKB/Swiss-Prot
    O14491, Q92535
    Related
    ENSP00000356701.3, ENST00000344529.5
    Conserved Domains (1) summary
    pfam06432
    Location:14 → 284
    GPI2; Phosphatidylinositol N-acetylglucosaminyltransferase

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    172441457..172444069 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    171798151..171800763 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92535.1 GenPept UniProtKB/Swiss-Prot:Q92535

Gene LinkOut

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