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AGBL4 AGBL carboxypeptidase 4 [ Homo sapiens (human) ]

Gene ID: 84871, updated on 3-Apr-2024

Summary

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Official Symbol
AGBL4provided by HGNC
Official Full Name
AGBL carboxypeptidase 4provided by HGNC
Primary source
HGNC:HGNC:25892
See related
Ensembl:ENSG00000186094 MIM:616476; AllianceGenome:HGNC:25892
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
CCP6
Summary
Predicted to enable metallocarboxypeptidase activity and tubulin binding activity. Predicted to be involved in C-terminal protein deglutamylation; defense response to virus; and protein side chain deglutamylation. Predicted to act upstream of or within several processes, including axonal transport of mitochondrion; positive regulation of ubiquitin-dependent protein catabolic process; and regulation of blastocyst development. Located in Golgi apparatus; centriole; and ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See AGBL4 in Genome Data Viewer
Location:
1p33
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (48522511..50023954, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (48393346..49902907, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (48998526..50489626, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 6 Neighboring gene uncharacterized LOC124904175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1010 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:48945175-48946016 Neighboring gene Sharpr-MPRA regulatory region 6906 Neighboring gene NANOG hESC enhancer GRCh37_chr1:48991897-48992398 Neighboring gene ribosomal protein L21 pseudogene 25 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49110904-49111546 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49111547-49112189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:49152780-49153280 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:49174571-49174927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1011 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:49357925-49358617 Neighboring gene BEN domain containing 5 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:49471420-49472013 Neighboring gene uncharacterized LOC105378706 Neighboring gene uncharacterized LOC124904851 Neighboring gene AGBL4 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:49872569-49872784 Neighboring gene AGBL4 intronic transcript 1 Neighboring gene uncharacterized LOC107984954 Neighboring gene zinc finger protein 859, pseudogene Neighboring gene uncharacterized LOC105378708 Neighboring gene uncharacterized LOC105378709 Neighboring gene MT-ND2 pseudogene 29 Neighboring gene ELAV like RNA binding protein 4

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. CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis. Wang Y, et al. BMC Biol, 2023 May 24. PMID 37226238, Free PMC Article
  2. Association of FAM65B, AGBL4, and CUX2 genetic polymorphisms with susceptibility to antituberculosis drug-induced hepatotoxicity: validation study in a Chinese Han population. Pan H, et al. Pharmacogenet Genomics, 2019 Jun. PMID 30720667
  3. Integrative mutation, haplotype and G × G interaction evidence connects ABGL4, LRP8 and PCSK9 genes to cardiometabolic risk. Guo T, et al. Sci Rep, 2016 Nov 17. PMID 27853278, Free PMC Article
  4. Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array. Lin PC, et al. Ann Surg Oncol, 2015 Dec. PMID 25472652
  5. Comparison of the enzymatic and functional properties of three cytosolic carboxypeptidase family members. Wu HY, et al. J Biol Chem, 2015 Jan 9. PMID 25416787, Free PMC Article

See all (15) 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. Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly.
    Title: Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly.
  3. this is the first study to explore and validate the relationships between seven SNPs in the FAM65B, AGBL4, and CUX2 genes and ATDH in a Chinese population. On the basis of this case-control study, SNP rs10946737 in FAM65B may be associated with susceptibility to ATDH in Chinese Han anti-TB treatment patients.
    Title: Association of FAM65B, AGBL4, and CUX2 genetic polymorphisms with susceptibility to antituberculosis drug-induced hepatotoxicity: validation study in a Chinese Han population.
  4. ABGL4, LRP8 and PCSK9 polymorphisms and gene interactions increase cardiometabolic risk.
    Title: Integrative mutation, haplotype and G × G interaction evidence connects ABGL4, LRP8 and PCSK9 genes to cardiometabolic risk.
  5. AGBL4 promoter hypermethylation is associated with Colorectal Cancer.
    Title: Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array.
  6. Nna1 and CCP4 remove the C-terminal glutamate from substrates with two or more glutamates, whereas CCP6 requires four or more glutamates. CCP4 behaves as a promiscuous glutamase with little preference for chain length or neighboring amino acid composition
    Title: Comparison of the enzymatic and functional properties of three cytosolic carboxypeptidase family members.
  7. 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.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
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

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

  • FLJ14442

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 anterograde axonal transport of mitochondrion IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system neuron development IEA
Inferred from Electronic Annotation
more info
  
involved_in defense response to virus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
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
  
involved_in regulation of blastocyst development IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde axonal transport of mitochondrion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in axon cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in centriole IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
cytosolic carboxypeptidase 6
Names
ATP/GTP binding protein like 4
protein deglutamylase CCP6
NP_001310502.1
NP_001310503.1
NP_001310504.1
NP_116174.3
XP_011540610.1
XP_011540612.1
XP_016858084.1
XP_016858085.1
XP_016858087.1
XP_054195235.1
XP_054195236.1
XP_054195237.1
XP_054195238.1

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.

mRNA and Protein(s)

  1. NM_001323573.2 → NP_001310502.1  cytosolic carboxypeptidase 6 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730
    UniProtKB/Swiss-Prot
    Q5VU57
    Conserved Domains (1) summary
    cd06908
    Location:190 → 450
    M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins

  2. NM_001323574.2 → NP_001310503.1  cytosolic carboxypeptidase 6 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730

  3. NM_001323575.2 → NP_001310504.1  cytosolic carboxypeptidase 6 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730
    Conserved Domains (2) summary
    cd06908
    Location:178 → 438
    M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
    COG2866
    Location:48 → 450
    MpaA; Murein tripeptide amidase MpaA [Cell wall/membrane/envelope biogenesis]

  4. NM_032785.4 → NP_116174.3  cytosolic carboxypeptidase 6 isoform 1

    See identical proteins and their annotated locations for NP_116174.3

    Status: VALIDATED

    Source sequence(s)
    AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730
    Consensus CDS
    CCDS44137.1
    UniProtKB/Swiss-Prot
    B3KT26, B4DG37, Q5VU57
    Related
    ENSP00000360905.1, ENST00000371839.6
    Conserved Domains (2) summary
    cd06908
    Location:178 → 438
    M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
    COG2866
    Location:48 → 450
    MpaA; Murein tripeptide amidase MpaA [Cell wall/membrane/envelope biogenesis]

RNA

  1. NR_136623.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC097062, AC099788, AL355809, AL391844, AL590432, AL591602, AL645507, AL645730

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    48522511..50023954 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002595.3 → XP_016858084.1  cytosolic carboxypeptidase 6 isoform X2

  2. XM_011542308.3 → XP_011540610.1  cytosolic carboxypeptidase 6 isoform X1

    Conserved Domains (1) summary
    cd06908
    Location:190 → 475
    M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins

  3. XM_017002596.3 → XP_016858085.1  cytosolic carboxypeptidase 6 isoform X3

  4. XM_017002598.3 → XP_016858087.1  cytosolic carboxypeptidase 6 isoform X5

    UniProtKB/TrEMBL
    B1ANV5

  5. XM_011542310.3 → XP_011540612.1  cytosolic carboxypeptidase 6 isoform X4

    Conserved Domains (1) summary
    cl11393
    Location:190 → 225
    Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    48393346..49902907 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339260.1 → XP_054195235.1  cytosolic carboxypeptidase 6 isoform X1

  2. XM_054339261.1 → XP_054195236.1  cytosolic carboxypeptidase 6 isoform X3

  3. XM_054339263.1 → XP_054195238.1  cytosolic carboxypeptidase 6 isoform X5

  4. XM_054339262.1 → XP_054195237.1  cytosolic carboxypeptidase 6 isoform X4

RNA

  1. XR_008486185.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VU57.3 GenPept UniProtKB/Swiss-Prot:Q5VU57

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