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AGBL1 AGBL carboxypeptidase 1 [ Homo sapiens (human) ]

Gene ID: 123624, updated on 5-Mar-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
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Genomic context

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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
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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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