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

    Gene ID: 5279, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (172441457..172444069, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (171798151..171800763, complement)
    RS_2024_09 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 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?
    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
    		not available

    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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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