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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
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Genomic context

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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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