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    PGAP4 post-GPI attachment to proteins GalNAc transferase 4 [ Homo sapiens (human) ]

    Gene ID: 84302, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PGAP4provided by HGNC
    Official Full Name
    post-GPI attachment to proteins GalNAc transferase 4provided by HGNC
    Primary source
    HGNC:HGNC:28180
    See related
    Ensembl:ENSG00000165152 MIM:620264; AllianceGenome:HGNC:28180
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TMEM246; C9orf125
    Summary
    Enables glycosyltransferase activity. Involved in GPI anchor biosynthetic process. Located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in brain (RPKM 25.2), heart (RPKM 14.2) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PGAP4 in Genome Data Viewer
    Location:
    9q31.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (101473170..101533686, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (113644475..113660514, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (104235452..104249455, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28725 Neighboring gene uncharacterized LOC105376184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20142 Neighboring gene aldolase, fructose-bisphosphate B Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:104223504-104224020 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:104224021-104224537 Neighboring gene NFE2L2 motif-containing MPRA enhancer 257 Neighboring gene TMEM246 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:104275376-104275886 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:104275887-104276395 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:104276396-104276905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:104286647-104287146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28726 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:104316489-104316706 Neighboring gene ring finger protein 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28727 Neighboring gene glutamate ionotropic receptor NMDA type subunit 3A Neighboring gene protein phosphatase 3 regulatory subunit B, beta

    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. Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain. Hirata T, et al. Nat Commun, 2018 Jan 26. PMID 29374258, Free PMC Article
    2. Electronic medical records and genomics (eMERGE) network exploration in cataract: several new potential susceptibility loci. Ritchie MD, et al. Mol Vis, 2014. PMID 25352737, Free PMC Article
    3. GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles. Welch LG, et al. J Cell Biol, 2021 Oct 4. PMID 34473204, Free PMC Article
    4. Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs. Almasy KM, et al. Mol Cell Proteomics, 2021. PMID 34186245, Free PMC Article
    5. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Electronic medical records and genomics (eMERGE) network exploration in cataract: Several new potential susceptibility loci.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ37094, MGC12992

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glycosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in GPI anchor biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in GPI anchor biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    post-GPI attachment to proteins factor 4
    Names
    transmembrane protein 246
    transmembrane protein C9orf125

    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.

    mRNA and Protein(s)

    1. NM_001303107.2 → NP_001290036.1  post-GPI attachment to proteins factor 4

      See identical proteins and their annotated locations for NP_001290036.1

      Status: VALIDATED

      Source sequence(s)
      AJ420439, AL353621, AL521069, BC033550, HY174800
      Consensus CDS
      CCDS6757.1
      UniProtKB/Swiss-Prot
      Q49AQ4, Q9BRR3
      Related
      ENSP00000363980.1, ENST00000374847.5
      Conserved Domains (1) summary
      cd22190
      Location:25 → 395
      PGAP4; Post-GPI attachment to proteins factor 4

    2. NM_001303108.2 → NP_001290037.1  post-GPI attachment to proteins factor 4

      See identical proteins and their annotated locations for NP_001290037.1

      Status: VALIDATED

      Source sequence(s)
      AL353621
      Consensus CDS
      CCDS6757.1
      UniProtKB/Swiss-Prot
      Q49AQ4, Q9BRR3
      Conserved Domains (1) summary
      cd22190
      Location:25 → 395
      PGAP4; Post-GPI attachment to proteins factor 4

    3. NM_001371233.1 → NP_001358162.1  post-GPI attachment to proteins factor 4

      Status: VALIDATED

      Source sequence(s)
      AL353621
      Consensus CDS
      CCDS6757.1
      UniProtKB/Swiss-Prot
      Q49AQ4, Q9BRR3
      Conserved Domains (1) summary
      cd22190
      Location:25 → 395
      PGAP4; Post-GPI attachment to proteins factor 4

    4. NM_032342.3 → NP_115718.1  post-GPI attachment to proteins factor 4

      See identical proteins and their annotated locations for NP_115718.1

      Status: VALIDATED

      Source sequence(s)
      AJ420439, AL353621, BC006115, BC033550
      Consensus CDS
      CCDS6757.1
      UniProtKB/Swiss-Prot
      Q49AQ4, Q9BRR3
      Related
      ENSP00000363981.3, ENST00000374848.8
      Conserved Domains (1) summary
      cd22190
      Location:25 → 395
      PGAP4; Post-GPI attachment to proteins factor 4

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      101473170..101533686 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447701.2 → XP_024303469.1  post-GPI attachment to proteins factor 4 isoform X1

      UniProtKB/Swiss-Prot
      Q49AQ4, Q9BRR3
      Related
      ENSP00000363984.1, ENST00000374851.1
      Conserved Domains (1) summary
      cd22190
      Location:25 → 395
      PGAP4; Post-GPI attachment to proteins factor 4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      113644475..113660514 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363984.1 → XP_054219959.1  post-GPI attachment to proteins factor 4 isoform X1

      UniProtKB/Swiss-Prot
      Q49AQ4, Q9BRR3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRR3.1 GenPept UniProtKB/Swiss-Prot:Q9BRR3

    Gene LinkOut

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

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