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    AGBL5 AGBL carboxypeptidase 5 [ Homo sapiens (human) ]

    Gene ID: 60509, updated on 5-Mar-2024

    Summary

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    Official Symbol
    AGBL5provided by HGNC
    Official Full Name
    AGBL carboxypeptidase 5provided by HGNC
    Primary source
    HGNC:HGNC:26147
    See related
    Ensembl:ENSG00000084693 MIM:615900; AllianceGenome:HGNC:26147
    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
    CCP5; RP75
    Summary
    This gene encodes a metallocarboxypeptidase involved in protein deglutamylation and a member of the peptidase M14 family of proteins. The encoded protein has been described as a "dual-functional" deglutamylase that can remove glutamate residues from both carboxyl termini and side chains of protein substrates. This deglutamylase activity may be important in antiviral immunity. Mutations in this gene are associated with retinitis pigmentosa. [provided by RefSeq, Jul 2016]
    Expression
    Biased expression in testis (RPKM 145.3), thyroid (RPKM 14.3) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p23.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (27050364..27070618)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (27092051..27112291)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (27274291..27293486)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:27261678-27262877 Neighboring gene transmembrane protein 214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15484 Neighboring gene Sharpr-MPRA regulatory region 11838 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:27274291-27274790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11281 Neighboring gene tRNA-Tyr (anticodon GTA) 2-1 Neighboring gene AGBL5 antisense RNA 1 Neighboring gene tRNA-Ala (anticodon AGC) 8-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27300904-27301682 Neighboring gene oligosaccharyltransferase complex subunit 4, non-catalytic Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15488 Neighboring gene elastin microfibril interfacer 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27315477-27316062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27316063-27316648 Neighboring gene ketohexokinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27321908-27322751 Neighboring gene cell growth regulator with EF-hand domain 1

    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. The combination of whole-exome sequencing and clinical analysis allows better diagnosis of rare syndromic retinal dystrophies. Abu Diab A, et al. Acta Ophthalmol, 2019 Sep. PMID 30925032
    2. Mutations in AGBL5, Encoding α-Tubulin Deglutamylase, Are Associated With Autosomal Recessive Retinitis Pigmentosa. Astuti GD, et al. Invest Ophthalmol Vis Sci, 2016 Nov 1. PMID 27842159
    3. Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing. Branham K, et al. Physiol Genomics, 2016 Dec 1. PMID 27764769, Free PMC Article
    4. Evidence for new C-terminally truncated variants of α- and β-tubulins. Aillaud C, et al. Mol Biol Cell, 2016 Feb 15. PMID 26739754, Free PMC Article
    5. Exome Sequencing Reveals AGBL5 as Novel Candidate Gene and Additional Variants for Retinitis Pigmentosa in Five Turkish Families. Kastner S, et al. Invest Ophthalmol Vis Sci, 2015 Dec. PMID 26720455

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
      Title: CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
    2. WES identified a homozygous frameshift mutation (c.1787_1788del, p.His596Argfs*47) in AGBL5, associated with nonsyndromic RP.
      Title: The combination of whole-exome sequencing and clinical analysis allows better diagnosis of rare syndromic retinal dystrophies.
    3. Homology models indicated destabilization of AGBL5 due to the p.Arg281Cys change.
      Title: Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing.
    4. Our study expands the clinical and allelic spectrum of known Retinal dystrophies genes, and reveals AGBL5, CDH16, and DNAJC17 as novel disease candidates.
      Title: Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies.
    5. The identification of AGBL5 and TTLL5, a previously described RP-associated gene encoding the tubulin tyrosine ligase-like family, member 5 protein, highlights the importance of poly- and deglutamylation in retinal homeostasis.
      Title: Mutations in AGBL5, Encoding α-Tubulin Deglutamylase, Are Associated With Autosomal Recessive Retinitis Pigmentosa.
    6. Due to the characteristic Retinitis Pigmentosa phenotype in patients carrying the AGBL5 missense mutation we suggest this gene as a candidate for a new form of autosomal recessively inherited RP
      Title: Exome Sequencing Reveals AGBL5 as Novel Candidate Gene and Additional Variants for Retinitis Pigmentosa in Five Turkish Families.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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
    Retinitis pigmentosa 75
    MedGen: C4310759 OMIM: 617023 GeneReviews: Not available
    		Compare labs

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of ATP/GTP binding protein-like 5 (AGBL5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21839

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in defense response to virus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein branching point deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in midbody IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitotic spindle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    cytosolic carboxypeptidase-like protein 5
    Names
    ATP/GTP binding protein like 5
    cytosolic carboxypeptidase 5
    protein deglutamylase CCP5
    NP_001030584.1
    NP_068603.4
    XP_005264534.1
    XP_011531313.1
    XP_011531314.1
    XP_011531315.1
    XP_047301330.1
    XP_047301331.1
    XP_047301332.1
    XP_047301333.1
    XP_054199250.1
    XP_054199251.1
    XP_054199252.1
    XP_054199253.1
    XP_054199254.1
    XP_054199255.1
    XP_054199256.1
    XP_054199257.1

    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_052914.1 RefSeqGene

      Range
      5246..24196
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001035507.3 → NP_001030584.1  cytosolic carboxypeptidase-like protein 5 isoform 3

      See identical proteins and their annotated locations for NP_001030584.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC018584, DA901318
      Consensus CDS
      CCDS42665.1
      UniProtKB/Swiss-Prot
      Q8NDL9
      Related
      ENSP00000323681.8, ENST00000323064.12
      Conserved Domains (1) summary
      cd06236
      Location:176 → 568
      M14_AGBL5_like; Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins

    2. NM_021831.6 → NP_068603.4  cytosolic carboxypeptidase-like protein 5 isoform 1

      See identical proteins and their annotated locations for NP_068603.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL833844, DA901318
      Consensus CDS
      CCDS1732.3
      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8
      Related
      ENSP00000353249.4, ENST00000360131.5
      Conserved Domains (1) summary
      cd06236
      Location:176 → 568
      M14_AGBL5_like; Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins

    RNA

    1. NR_104246.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an additional exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL833844, BC007415, DA901318

    2. NR_138023.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains alternate exons in the 5' and 3' regions compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC013403, AC013472, BC007415

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      27050364..27070618
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445376.1 → XP_047301332.1  cytosolic carboxypeptidase-like protein 5 isoform X4

    2. XM_047445377.1 → XP_047301333.1  cytosolic carboxypeptidase-like protein 5 isoform X4

    3. XM_011533011.4 → XP_011531313.1  cytosolic carboxypeptidase-like protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011531313.1

      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8
      Conserved Domains (1) summary
      cd06236
      Location:176 → 568
      M14_AGBL5_like; Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins

    4. XM_011533012.3 → XP_011531314.1  cytosolic carboxypeptidase-like protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011531314.1

      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8
      Conserved Domains (1) summary
      cd06236
      Location:176 → 568
      M14_AGBL5_like; Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins

    5. XM_047445375.1 → XP_047301331.1  cytosolic carboxypeptidase-like protein 5 isoform X3

    6. XM_011533013.3 → XP_011531315.1  cytosolic carboxypeptidase-like protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011531315.1

      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8
      Conserved Domains (1) summary
      cd06236
      Location:176 → 568
      M14_AGBL5_like; Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins

    7. XM_005264477.4 → XP_005264534.1  cytosolic carboxypeptidase-like protein 5 isoform X3

      Conserved Domains (1) summary
      cd06236
      Location:176 → 568
      M14_AGBL5_like; Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins

    8. XM_047445374.1 → XP_047301330.1  cytosolic carboxypeptidase-like protein 5 isoform X2

      Related
      ENSP00000433830.1, ENST00000487078.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      27092051..27112291
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343281.1 → XP_054199256.1  cytosolic carboxypeptidase-like protein 5 isoform X4

    2. XM_054343282.1 → XP_054199257.1  cytosolic carboxypeptidase-like protein 5 isoform X4

    3. XM_054343275.1 → XP_054199250.1  cytosolic carboxypeptidase-like protein 5 isoform X1

      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8

    4. XM_054343276.1 → XP_054199251.1  cytosolic carboxypeptidase-like protein 5 isoform X1

      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8

    5. XM_054343280.1 → XP_054199255.1  cytosolic carboxypeptidase-like protein 5 isoform X3

    6. XM_054343277.1 → XP_054199252.1  cytosolic carboxypeptidase-like protein 5 isoform X1

      UniProtKB/Swiss-Prot
      A2VDI7, B7WPG9, B7Z7I7, D6W548, Q53SW0, Q53SZ0, Q8NDL9, Q96IK8, Q9H6V0, Q9H8P8

    7. XM_054343279.1 → XP_054199254.1  cytosolic carboxypeptidase-like protein 5 isoform X3

    8. XM_054343278.1 → XP_054199253.1  cytosolic carboxypeptidase-like protein 5 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NDL9.1 GenPept UniProtKB/Swiss-Prot:Q8NDL9

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