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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
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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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