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    GGCX gamma-glutamyl carboxylase [ Homo sapiens (human) ]

    Gene ID: 2677, updated on 17-Jun-2019

    Summary

    Official Symbol
    GGCXprovided by HGNC
    Official Full Name
    gamma-glutamyl carboxylaseprovided by HGNC
    Primary source
    HGNC:HGNC:4247
    See related
    Ensembl:ENSG00000115486 MIM:137167
    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
    VKCFD1
    Summary
    This gene encodes an integral membrane protein of the rough endoplasmic reticulum that carboxylates glutamate residues of vitamin K-dependent proteins to gamma carboxyl glutamate, a modification that is required for their activity. The vitamin K-dependent protein substrates have a propeptide that binds the enzyme, with carbon dioxide, dioxide, and reduced vitamin K acting as co-substrates. Vitamin K-dependent proteins affect a number of physiologic processes including blood coagulation, prevention of vascular calcification, and inflammation. Allelic variants of this gene have been associated with pseudoxanthoma elasticum-like disorder with associated multiple coagulation factor deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in liver (RPKM 18.5), thyroid (RPKM 16.4) and 25 other tissues See more
    Orthologs

    Genomic context

    See GGCX in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (85544720..85561527, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (85771978..85788657, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA pseudogene 22 Neighboring gene promoter of MAT2A antisense radiation-induced circulating long non-coding RNA Neighboring gene methionine adenosyltransferase 2A Neighboring gene RNA, 7SL, cytoplasmic 126, pseudogene Neighboring gene vesicle associated membrane protein 8

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Pseudoxanthoma elasticum-like disorder with multiple coagulation factor deficiency
    MedGen: C1835813 OMIM: 610842 GeneReviews: Not available
    not available
    Vitamin k-dependent clotting factors, combined deficiency of, 1
    MedGen: C1848534 OMIM: 277450 GeneReviews: Not available
    not available

    NHGRI GWAS Catalog

    Description
    Seven prostate cancer susceptibility loci identified by a multi-stage genome-wide association study.
    NHGRI GWA Catalog

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ26629

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    gamma-glutamyl carboxylase activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    blood coagulation TAS
    Traceable Author Statement
    more info
    PubMed 
    cellular protein modification process TAS
    Traceable Author Statement
    more info
    PubMed 
    peptidyl-glutamic acid carboxylation TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    membrane TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    vitamin K-dependent gamma-carboxylase
    Names
    peptidyl-glutamate 4-carboxylase
    NP_000812.2
    NP_001135741.1
    NP_001298241.1
    XP_005264316.1
    XP_011531066.1
    XP_011531067.1
    XP_016859292.1

    NCBI Reference Sequences (RefSeq)

    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_011811.2 RefSeqGene

      Range
      5001..21815
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000821.7NP_000812.2  vitamin K-dependent gamma-carboxylase isoform 1

      See identical proteins and their annotated locations for NP_000812.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC016753, BC013979, BM974022, BQ000150, DC296316
      Consensus CDS
      CCDS1978.1
      UniProtKB/Swiss-Prot
      P38435
      Related
      ENSP00000233838.3, ENST00000233838.9
      Conserved Domains (1) summary
      pfam05090
      Location:66502
      VKG_Carbox; Vitamin K-dependent gamma-carboxylase
    2. NM_001142269.4NP_001135741.1  vitamin K-dependent gamma-carboxylase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC016753, AK297397, BC013979, BM974022, BQ000150, DC296316
      Consensus CDS
      CCDS46353.1
      UniProtKB/Swiss-Prot
      P38435
      Related
      ENSP00000408045.3, ENST00000430215.7
      Conserved Domains (2) summary
      smart00752
      Location:15258
      HTTM; Horizontally Transferred TransMembrane Domain
      pfam05090
      Location:15445
      VKG_Carbox; Vitamin K-dependent gamma-carboxylase
    3. NM_001311312.2NP_001298241.1  vitamin K-dependent gamma-carboxylase isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC016753, BM704752
      Related
      ENSP00000389426.1, ENST00000423570.5
      Conserved Domains (1) summary
      cl02773
      Location:56125
      HTTM; Horizontally Transferred TransMembrane Domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      85544720..85561527 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003803.2XP_016859292.1  vitamin K-dependent gamma-carboxylase isoform X2

    2. XM_011532765.3XP_011531067.1  vitamin K-dependent gamma-carboxylase isoform X3

      See identical proteins and their annotated locations for XP_011531067.1

      Conserved Domains (1) summary
      pfam05090
      Location:24228
      VKG_Carbox; Vitamin K-dependent gamma-carboxylase
    3. XM_011532764.3XP_011531066.1  vitamin K-dependent gamma-carboxylase isoform X3

      See identical proteins and their annotated locations for XP_011531066.1

      Conserved Domains (1) summary
      pfam05090
      Location:24228
      VKG_Carbox; Vitamin K-dependent gamma-carboxylase
    4. XM_005264259.5XP_005264316.1  vitamin K-dependent gamma-carboxylase isoform X1

      Conserved Domains (2) summary
      smart00752
      Location:56315
      HTTM; Horizontally Transferred TransMembrane Domain
      pfam05090
      Location:66502
      VKG_Carbox; Vitamin K-dependent gamma-carboxylase

    RNA

    1. XR_001738703.2 RNA Sequence

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