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    AGBL1 AGBL carboxypeptidase 1 [ Homo sapiens (human) ]

    Gene ID: 123624, updated on 17-Jun-2024

    Summary

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    Official Symbol
    AGBL1provided by HGNC
    Official Full Name
    AGBL carboxypeptidase 1provided by HGNC
    Primary source
    HGNC:HGNC:26504
    See related
    Ensembl:ENSG00000273540 MIM:615496; AllianceGenome:HGNC:26504
    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
    CCP4; FECD8
    Summary
    Polyglutamylation is a reversible posttranslational modification catalyzed by polyglutamylases that results in the addition of glutamate side chains on the modified protein. This gene encodes a glutamate decarboxylase that catalyzes the deglutamylation of polyglutamylated proteins. Mutations in this gene result in dominant late-onset Fuchs corneal dystrophy. [provided by RefSeq, Nov 2013]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See AGBL1 in Genome Data Viewer
    Location:
    15q25.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (86079620..87031476)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (83834387..84785395)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (86622851..87572283)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10025 Neighboring gene uncharacterized LOC105370953 Neighboring gene Sharpr-MPRA regulatory region 8767 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:86665465-86666002 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:86666003-86666540 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:86666541-86667078 Neighboring gene long intergenic non-protein coding RNA 1584 Neighboring gene uncharacterized LOC124900360 Neighboring gene RNA, 5S ribosomal pseudogene 400 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:86780158-86781036 Neighboring gene AGBL1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:87071578-87072162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:87115127-87115756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:87115757-87116385 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:87133415-87134144 Neighboring gene NANOG hESC enhancer GRCh37_chr15:87155001-87155502 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:87449462-87450661 Neighboring gene uncharacterized LOC105370954 Neighboring gene uncharacterized LOC102724452 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:87529804-87530750 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:87531164-87531805 Neighboring gene uncharacterized LOC105370955 Neighboring gene uncharacterized LOC107984735

    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. A Case/Control Study: AGBL1 Polymorphism Related to Lung Cancer Risk in Chinese Nonsmoking Females. Zhang L, et al. DNA Cell Biol, 2019 Dec. PMID 31603707
    2. Mutations in AGBL1 cause dominant late-onset Fuchs corneal dystrophy and alter protein-protein interaction with TCF4. Riazuddin SA, et al. Am J Hum Genet, 2013 Oct 3. PMID 24094747, Free PMC Article
    3. Meta-analysis of genome-wide association for migraine in six population-based European cohorts. Ligthart L, et al. Eur J Hum Genet, 2011 Aug. PMID 21448238, Free PMC Article
    4. A third approach to gene prediction suggests thousands of additional human transcribed regions. Glusman G, et al. PLoS Comput Biol, 2006 Mar. PMID 16543943, Free PMC Article
    5. Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus. Su Z, et al. Nat Genet, 2012 Oct. PMID 22961001, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. rs4513061 in AGBL1 Gene is associated with decrease in the risk of lung cancer.
      Title: A Case/Control Study: AGBL1 Polymorphism Related to Lung Cancer Risk in Chinese Nonsmoking Females.
    2. That AGBL1 interacts biochemically with the FCD-associated protein TCF4.
      Title: Mutations in AGBL1 cause dominant late-onset Fuchs corneal dystrophy and alter protein-protein interaction with TCF4.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    Corneal dystrophy, Fuchs endothelial, 8
    MedGen: C3809798 OMIM: 615523 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
    EBI GWAS Catalog
    Evidence for shared genetic risk between methamphetamine-induced psychosis and schizophrenia.
    EBI GWAS Catalog
    Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease.
    EBI GWAS Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    EBI GWAS Catalog
    Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response.
    EBI GWAS Catalog
    Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
    EBI GWAS Catalog
    Genomewide association for schizophrenia in the CATIE study: results of stage 1.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association for migraine in six population-based European cohorts.
    EBI GWAS Catalog
    Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D.
    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

    • FLJ32310, FLJ39578, MGC149239

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metallocarboxypeptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables tubulin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in C-terminal protein deglutamylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in C-terminal protein deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein side chain deglutamylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein side chain deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cytosolic carboxypeptidase 4
    Names
    ATP/GTP binding protein like 1
    protein deglutamylase CCP4
    NP_001373023.1
    NP_689549.3
    XP_011519529.1
    XP_011519530.1
    XP_011519532.1
    XP_016877407.1
    XP_016877408.1
    XP_016877409.1
    XP_016877410.1
    XP_054233261.1
    XP_054233262.1
    XP_054233263.1
    XP_054233264.1
    XP_054233265.1
    XP_054233266.1
    XP_054233267.1

    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_033836.3 RefSeqGene

      Range
      5253..841538
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001386094.1 → NP_001373023.1  cytosolic carboxypeptidase 4 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC012229, AC016180, AC016987, AC022817, AC025842, AC069197, AC107978
      Consensus CDS
      CCDS92052.1
      UniProtKB/TrEMBL
      A0A1B0GVQ2
      Related
      ENSP00000490608.2, ENST00000614907.3
      Conserved Domains (2) summary
      cd06906
      Location:754 → 1019
      M14_Nna1; Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases
      pfam18027
      Location:596 → 730
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    2. NM_152336.4 → NP_689549.3  cytosolic carboxypeptidase 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC012229, AC016180, AC016987, AC022817, AC025842, AC069197, AC078905, AC107978
      Consensus CDS
      CCDS58398.2
      UniProtKB/Swiss-Prot
      A0A1C7CYX3, A1A4X5, A6NJH6, C9JHL5, Q96MI9
      Related
      ENSP00000413001.3, ENST00000441037.7
      Conserved Domains (2) summary
      cd06906
      Location:754 → 1040
      M14_Nna1; Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases
      pfam18027
      Location:596 → 730
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      86079620..87031476
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521227.4 → XP_011519529.1  cytosolic carboxypeptidase 4 isoform X3

      Conserved Domains (1) summary
      cl11393
      Location:743 → 1019
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    2. XM_017021919.3 → XP_016877408.1  cytosolic carboxypeptidase 4 isoform X2

    3. XM_017021918.3 → XP_016877407.1  cytosolic carboxypeptidase 4 isoform X1

    4. XM_017021920.3 → XP_016877409.1  cytosolic carboxypeptidase 4 isoform X4

    5. XM_011521228.4 → XP_011519530.1  cytosolic carboxypeptidase 4 isoform X5

      Conserved Domains (1) summary
      cl11393
      Location:743 → 795
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    6. XM_017021921.3 → XP_016877410.1  cytosolic carboxypeptidase 4 isoform X6

    7. XM_011521230.4 → XP_011519532.1  cytosolic carboxypeptidase 4 isoform X7

    RNA

    1. XR_007064423.1 RNA Sequence

    2. XR_931751.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      83834387..84785395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377288.1 → XP_054233263.1  cytosolic carboxypeptidase 4 isoform X3

    2. XM_054377287.1 → XP_054233262.1  cytosolic carboxypeptidase 4 isoform X2

    3. XM_054377286.1 → XP_054233261.1  cytosolic carboxypeptidase 4 isoform X1

    4. XM_054377289.1 → XP_054233264.1  cytosolic carboxypeptidase 4 isoform X4

    5. XM_054377290.1 → XP_054233265.1  cytosolic carboxypeptidase 4 isoform X5

    6. XM_054377291.1 → XP_054233266.1  cytosolic carboxypeptidase 4 isoform X6

    7. XM_054377292.1 → XP_054233267.1  cytosolic carboxypeptidase 4 isoform X7

    RNA

    1. XR_008488918.1 RNA Sequence

    2. XR_008488919.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MI9.3 GenPept UniProtKB/Swiss-Prot:Q96MI9

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