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    PIGV phosphatidylinositol glycan anchor biosynthesis class V [ Homo sapiens (human) ]

    Gene ID: 55650, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PIGVprovided by HGNC
    Official Full Name
    phosphatidylinositol glycan anchor biosynthesis class Vprovided by HGNC
    Primary source
    HGNC:HGNC:26031
    See related
    Ensembl:ENSG00000060642 MIM:610274; AllianceGenome:HGNC:26031
    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
    PIG-V; HPMRS1; GPI-MT-II
    Summary
    This gene encodes a mannosyltransferase enzyme involved in the biosynthesis of glycosylphosphatidylinositol (GPI). GPI is a complex glycolipid that functions as a membrane anchor for many proteins and plays a role in multiple cellular processes including protein sorting and signal transduction. The encoded protein is localized to the endoplasmic reticulum and transfers the second mannose to the GPI backbone. Mutations in this gene are associated with hyperphosphatasia cognitive disability syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]
    Expression
    Broad expression in testis (RPKM 19.4), thyroid (RPKM 7.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PIGV in Genome Data Viewer
    Location:
    1p36.11
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (26787054..26800659)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26625009..26638614)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27113545..27127150)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928728 Neighboring gene translation initiation factor IF-2-like Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27019176-27019690 Neighboring gene hESC enhancers GRCh37_chr1:27021339-27022275 and GRCh37_chr1:27022276-27023211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 489 Neighboring gene Sharpr-MPRA regulatory region 12508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27033907-27034406 Neighboring gene AT-rich interaction domain 1A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27048400-27048980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27048981-27049560 Neighboring gene heart enhancer 10 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:27051301-27051880 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27051881-27052460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27057943-27058472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 517 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:27098665-27099864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 519 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27114367-27115193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27130608-27131323 Neighboring gene RNA, 7SL, cytoplasmic 165, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27152961-27153113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 523 Neighboring gene zinc finger DHHC-type palmitoyltransferase 18 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 525 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27179723-27180224 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27181471-27181643

    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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    Related articles in PubMed

    1. Delineation of PIGV mutation spectrum and associated phenotypes in hyperphosphatasia with mental retardation syndrome. Horn D, et al. Eur J Hum Genet, 2014 Jun. PMID 24129430, Free PMC Article
    2. Glycosylphosphatidylinositol mannosyltransferase II is the rate-limiting enzyme in glycosylphosphatidylinositol biosynthesis under limited dolichol-phosphate mannose availability. Hirata T, et al. J Biochem, 2013 Sep. PMID 23694781
    3. Hyperphosphatasia-mental retardation syndrome due to PIGV mutations: expanded clinical spectrum. Horn D, et al. Am J Med Genet A, 2011 Aug. PMID 21739589
    4. Mechanism for release of alkaline phosphatase caused by glycosylphosphatidylinositol deficiency in patients with hyperphosphatasia mental retardation syndrome. Murakami Y, et al. J Biol Chem, 2012 Feb 24. PMID 22228761, Free PMC Article
    5. Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Krawitz PM, et al. Nat Genet, 2010 Oct. PMID 20802478

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data indicate that mannosyltransferases PIGV mutations are the major cause of hyperphosphatasia-mental retardation syndrome (HPMRS) which displays a broad clinical variability regarding associated malformations and growth patterns.
      Title: Delineation of PIGV mutation spectrum and associated phenotypes in hyperphosphatasia with mental retardation syndrome.
    2. PIGV is the rate-limiting enzyme in GPI biosynthesis under limited dolicholphosphate mannose availability.
      Title: Glycosylphosphatidylinositol mannosyltransferase II is the rate-limiting enzyme in glycosylphosphatidylinositol biosynthesis under limited dolichol-phosphate mannose availability.
    3. Hyperphosphatasia resulted from secretion of ALP, a GPI-anchored protein normally expressed on the cell surface, into serum due to PIGV deficiency.
      Title: Mechanism for release of alkaline phosphatase caused by glycosylphosphatidylinositol deficiency in patients with hyperphosphatasia mental retardation syndrome.
    4. novel compound heterozygous mutations in the PIGV gene c.467G>A and c.1022C>A and a homozygous mutation c.1022C>A in hyperphosphatasia-mental retardation syndrome
      Title: Hyperphosphatasia-mental retardation syndrome due to PIGV mutations: expanded clinical spectrum.
    5. PIGV mutations are associated with hyperphosphatasia mental retardation syndrome.
      Title: Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome.
    6. PIG-V is the second mannosyltransferase in GPI anchor biosynthesis.
      Title: PIG-V involved in transferring the second mannose in glycosylphosphatidylinositol.
    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
    Hyperphosphatasia with intellectual disability syndrome 1
    MedGen: C4551502 OMIM: 239300 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    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

    • FLJ20477

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables alpha-1,6-mannosyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycolipid mannosyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables mannosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mannosyltransferase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables mannosyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in GPI anchor biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in GPI anchor biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in GPI anchor biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 mannosyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    GPI mannosyltransferase 2
    Names
    GPI mannosyltransferase II
    Ybr004c homolog
    dol-P-Man dependent GPI mannosyltransferase
    dol-P-Man dependent GPI mannosyltransferase II
    NP_001189483.1
    NP_001361407.1
    NP_001361409.1
    NP_001361410.1
    NP_001361411.1
    NP_001361412.1
    NP_001361413.1
    NP_001361414.1
    NP_001361415.1
    NP_060307.2

    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_028133.2 RefSeqGene

      Range
      5898..18607
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001202554.2 → NP_001189483.1  GPI mannosyltransferase 2 isoform a

      See identical proteins and their annotated locations for NP_001189483.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1-6 all encode the same isoform (a).
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS287.1
      UniProtKB/Swiss-Prot
      D3DPL2, Q5JYG7, Q5JYG8, Q5JYG9, Q9NUD9, Q9NX26
      UniProtKB/TrEMBL
      A0A8I5KPJ1
      Related
      ENSP00000501527.1, ENST00000674273.1
      Conserved Domains (1) summary
      pfam04188
      Location:8 → 493
      Mannosyl_trans2; Mannosyltransferase (PIG-V)

    2. NM_001374478.1 → NP_001361407.1  GPI mannosyltransferase 2 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-6 all encode the same isoform (a).
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS287.1
      UniProtKB/Swiss-Prot
      D3DPL2, Q5JYG7, Q5JYG8, Q5JYG9, Q9NUD9, Q9NX26
      UniProtKB/TrEMBL
      A0A8I5KPJ1
      Related
      ENSP00000406080.2, ENST00000455364.2
      Conserved Domains (1) summary
      pfam04188
      Location:8 → 493
      Mannosyl_trans2; Mannosyltransferase (PIG-V)

    3. NM_001374480.1 → NP_001361409.1  GPI mannosyltransferase 2 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-6 all encode the same isoform (a).
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS287.1
      UniProtKB/Swiss-Prot
      D3DPL2, Q5JYG7, Q5JYG8, Q5JYG9, Q9NUD9, Q9NX26
      UniProtKB/TrEMBL
      A0A8I5KPJ1
      Related
      ENSP00000501335.1, ENST00000674222.1
      Conserved Domains (1) summary
      pfam04188
      Location:8 → 493
      Mannosyl_trans2; Mannosyltransferase (PIG-V)

    4. NM_001374481.1 → NP_001361410.1  GPI mannosyltransferase 2 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1-6 all encode the same isoform (a).
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS287.1
      UniProtKB/Swiss-Prot
      D3DPL2, Q5JYG7, Q5JYG8, Q5JYG9, Q9NUD9, Q9NX26
      UniProtKB/TrEMBL
      A0A8I5KPJ1
      Conserved Domains (1) summary
      pfam04188
      Location:8 → 493
      Mannosyl_trans2; Mannosyltransferase (PIG-V)

    5. NM_001374482.1 → NP_001361411.1  GPI mannosyltransferase 2 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1-6 all encode the same isoform (a).
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS287.1
      UniProtKB/Swiss-Prot
      D3DPL2, Q5JYG7, Q5JYG8, Q5JYG9, Q9NUD9, Q9NX26
      UniProtKB/TrEMBL
      A0A8I5KPJ1
      Related
      ENSP00000363260.1, ENST00000374145.6
      Conserved Domains (1) summary
      pfam04188
      Location:8 → 493
      Mannosyl_trans2; Mannosyltransferase (PIG-V)

    6. NM_001374483.1 → NP_001361412.1  GPI mannosyltransferase 2 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS90894.1
      UniProtKB/TrEMBL
      A0A6I8PU65
      Related
      ENSP00000501446.1, ENST00000674335.1
      Conserved Domains (1) summary
      cl21590
      Location:1 → 366
      PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

    7. NM_001374484.1 → NP_001361413.1  GPI mannosyltransferase 2 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8), as well as variant 9, encodes isoform c.
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS90892.1
      UniProtKB/TrEMBL
      A0A8I5KQ29, B4DWP9
      Related
      ENSP00000509240.1, ENST00000686194.1
      Conserved Domains (1) summary
      cl21590
      Location:81 → 284
      PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

    8. NM_001374485.1 → NP_001361414.1  GPI mannosyltransferase 2 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9), as well as variant 8, encodes isoform c.
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS90892.1
      UniProtKB/TrEMBL
      A0A8I5KQ29, B4DWP9
      Conserved Domains (1) summary
      cl21590
      Location:81 → 284
      PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

    9. NM_001374486.1 → NP_001361415.1  GPI mannosyltransferase 2 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS90893.1
      UniProtKB/TrEMBL
      A0A8I5KRV8
      Related
      ENSP00000509280.1, ENST00000693629.1
      Conserved Domains (1) summary
      cl21590
      Location:12 → 119
      PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

    10. NM_017837.4 → NP_060307.2  GPI mannosyltransferase 2 isoform a

      See identical proteins and their annotated locations for NP_060307.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-6 all encode the same isoform (a).
      Source sequence(s)
      AL034380
      Consensus CDS
      CCDS287.1
      UniProtKB/Swiss-Prot
      D3DPL2, Q5JYG7, Q5JYG8, Q5JYG9, Q9NUD9, Q9NX26
      UniProtKB/TrEMBL
      A0A8I5KPJ1
      Related
      ENSP00000501479.1, ENST00000674202.1
      Conserved Domains (1) summary
      pfam04188
      Location:8 → 493
      Mannosyl_trans2; Mannosyltransferase (PIG-V)

    RNA

    1. NR_164651.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL034380

    2. NR_164652.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL034380

    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
      26787054..26800659
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      26625009..26638614
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NUD9.1 GenPept UniProtKB/Swiss-Prot:Q9NUD9

    Gene LinkOut

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

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