AGBL1 Gene (Protein Coding)

ATP/GTP Binding Protein Like 1

GC15P086141
GIFtS:
37
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... See more...

Aliases for AGBL1 Gene

Aliases for AGBL1 Gene

  • ATP/GTP Binding Protein Like 1 2 3 5
  • Cytosolic Carboxypeptidase 4 2 3 4
  • CCP4 3 4
  • ATP/GTP-Binding Protein-Like 1 4
  • EC 3.4.17.- 4
  • EC 3.4.17 54
  • FECD8 3

External Ids for AGBL1 Gene

Previous GeneCards Identifiers for AGBL1 Gene

  • GC00U921509
  • GC15P084601
  • GC15P084486
  • GC15P086685
  • GC15P062798

Summaries for AGBL1 Gene

Entrez Gene Summary for AGBL1 Gene

  • 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]

GeneCards Summary for AGBL1 Gene

AGBL1 (ATP/GTP Binding Protein Like 1) is a Protein Coding gene. Diseases associated with AGBL1 include Corneal Dystrophy, Fuchs Endothelial, 8 and Fuchs' Endothelial Dystrophy. Gene Ontology (GO) annotations related to this gene include binding and metallocarboxypeptidase activity. An important paralog of this gene is AGTPBP1.

UniProtKB/Swiss-Prot Summary for AGBL1 Gene

  • Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes gene-encoded polyglutamates from the carboxy-terminus of target proteins such as MYLK. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5.

Additional gene information for AGBL1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for AGBL1 Gene

Genomics for AGBL1 Gene

GeneHancer (GH) Regulatory Elements for AGBL1 Gene

Promoters and enhancers for AGBL1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH15J086079 Enhancer 0.7 Ensembl ENCODE dbSUPER 750.6 +0.0 13 1.6 ZIC2 ZNF143 AGBL1 NONHSAG017772.2 LINC01584
GH15J086160 Enhancer 0.8 Ensembl ENCODE 11.6 +83.7 83714 6.2 FOSL2 POLR2A TCF7L2 ZEB2 ZNF629 KLF8 HIC1 FOS JUND GLIS1 RNA5SP400 AGBL1 ENSG00000200206 ENSG00000261077 lnc-KLHL25-15
GH15J086062 Enhancer 0.4 FANTOM5 dbSUPER 17.9 -17.2 -17240 0.3 AGBL1 KLHL25 NONHSAG017772.2 HSALNG0107896
GH15J086201 Enhancer 0.3 Ensembl 10.9 +122.1 122114 0.6 MAFK JUND RNA5SP400 AGBL1 piR-55948-036 ENSG00000200206
GH15J086159 Enhancer 0.3 ENCODE 11.1 +79.8 79818 0.2 JUND RNA5SP400 AGBL1 ENSG00000200206 ENSG00000261077 lnc-KLHL25-15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around AGBL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AGBL1 gene promoter:
  • Chx10
  • Nkx2-5
  • Oct-B1
  • oct-B2
  • oct-B3
  • p53
  • Pax-3
  • POU2F1
  • POU2F1a
  • POU2F2

Genomic Locations for AGBL1 Gene

Genomic Locations for AGBL1 Gene
chr15:86,079,787-87,031,178
(GRCh38/hg38)
Size:
951,392 bases
Orientation:
Plus strand
chr15:86,685,227-87,572,283
(GRCh37/hg19)
Size:
887,057 bases
Orientation:
Plus strand

Genomic View for AGBL1 Gene

Genes around AGBL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AGBL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AGBL1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for AGBL1 Gene

Proteins for AGBL1 Gene

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  • Protein details for AGBL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96MI9-CBPC4_HUMAN
    Recommended name:
    Cytosolic carboxypeptidase 4
    Protein Accession:
    Q96MI9
    Secondary Accessions:
    • A0A1C7CYX3
    • A1A4X5
    • A6NJH6
    • C9JHL5

    Protein attributes for AGBL1 Gene

    Size:
    1112 amino acids
    Molecular mass:
    125330 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Interacts with MYLK (By similarity). Interacts with TCF4.
    SequenceCaution:
    • Sequence=AAI28153.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=BAB71299.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Probable cloning artifact.; Evidence={ECO:0000305};

neXtProt entry for AGBL1 Gene

Protein Expression for AGBL1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for AGBL1 Gene

Q96MI9:
  • ICYYKNH
  • ARVHPGE
  • PMLNPDGV
  • FNIINCEK
  • CDFHGHS
  • YGCSIKET

Post-translational modifications for AGBL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for AGBL1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for AGBL1 Gene

Gene Families for AGBL1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for AGBL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for AGBL1 Gene

GenScript: Design optimal peptide antigens:
  • ATP/GTP-binding protein-like 1 (CBPC4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96MI9

UniProtKB/Swiss-Prot:

CBPC4_HUMAN :
  • Belongs to the peptidase M14 family.
Family:
  • Belongs to the peptidase M14 family.
genes like me logo Genes that share domains with AGBL1: view

Function for AGBL1 Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for AGBL1 Gene

UniProtKB/Swiss-Prot Function:
Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes gene-encoded polyglutamates from the carboxy-terminus of target proteins such as MYLK. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5.

Enzyme Numbers (IUBMB) for AGBL1 Gene

Phenotypes From GWAS Catalog for AGBL1 Gene

Gene Ontology (GO) - Molecular Function for AGBL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004181 metallocarboxypeptidase activity ISS --
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0015631 tubulin binding ISS --
genes like me logo Genes that share ontologies with AGBL1: view
genes like me logo Genes that share phenotypes with AGBL1: view

Human Phenotype Ontology for AGBL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AGBL1

No data available for Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for AGBL1 Gene

Localization for AGBL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AGBL1 Gene

Cytoplasm, cytosol.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for AGBL1 gene
Compartment Confidence
cytosol 4
nucleus 2
peroxisome 0

Gene Ontology (GO) - Cellular Components for AGBL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with AGBL1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for AGBL1 Gene

Pathways & Interactions for AGBL1 Gene

PathCards logo

SuperPathways for AGBL1 Gene

No Data Available

Interacting Proteins for AGBL1 Gene

STRING Interaction Network Preview (showing top 5 STRING interactants - click image to see top 21)
STRING Interaction Network
Selected Interacting proteins: ENSP00000413001 Q96MI9-CBPC4_HUMAN for AGBL1 Gene via STRING IID

GPS-Prot Interaction Network for AGBL1

Gene Ontology (GO) - Biological Process for AGBL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0035609 C-terminal protein deglutamylation ISS --
GO:0035610 protein side chain deglutamylation ISS --
genes like me logo Genes that share ontologies with AGBL1: view

No data available for Pathways by source and SIGNOR curated interactions for AGBL1 Gene

Drugs & Compounds for AGBL1 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for AGBL1 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for AGBL1 Gene

(1) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AGBL1

Alternative Splicing Database (ASD) splice patterns (SP) for AGBL1 Gene

No ASD Table

Relevant External Links for AGBL1 Gene

GeneLoc Exon Structure for
AGBL1
ECgene alternative splicing isoforms for
AGBL1

Expression for AGBL1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AGBL1 Gene

mRNA expression in normal human tissues for AGBL1 Gene
mRNA expression by GTEx for AGBL1 Gene

mRNA differential expression in normal tissues according to GTEx for AGBL1 Gene

This gene is overexpressed in Muscle - Skeletal (x33.9).

Protein differential expression in normal tissues from HIPED for AGBL1 Gene

This gene is overexpressed in Islet of Langerhans (22.3), Ovary (14.8), Heart (12.9), and Adipocyte (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for AGBL1 Gene



NURSA nuclear receptor signaling pathways regulating expression of AGBL1 Gene:

AGBL1

SOURCE GeneReport for Unigene cluster for AGBL1 Gene:

Hs.679833

mRNA Expression by UniProt/SwissProt for AGBL1 Gene:

Q96MI9-CBPC4_HUMAN
Tissue specificity: Expressed in corneal endothelium.

Phenotype-based relationships between genes and organs from Gene ORGANizer for AGBL1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
Regions:
Head and neck:
  • eye
  • head
General:
  • blood vessel
genes like me logo Genes that share expression patterns with AGBL1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES for AGBL1 Gene

Orthologs for AGBL1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for AGBL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia AGBL1 32
  • 98.81 (n)
dog
(Canis familiaris)
 Mammalia AGBL1 32
  • 85.96 (n)
rat
(Rattus norvegicus)
 Mammalia Agbl1 32
  • 82.2 (n)
cow
(Bos Taurus)
 Mammalia LOC100300175 32
  • 81.68 (n)
mouse
(Mus musculus)
 Mammalia Agbl1 17 32
  • 81.2 (n)
chicken
(Gallus gallus)
 Aves AGBL1 32
  • 65.15 (n)
tropical clawed frog
(Silurana tropicalis)
 Amphibia agbl1 32
  • 61.34 (n)
zebrafish
(Danio rerio)
 Actinopterygii LOC100536841 32
  • 58.3 (n)
Species where no ortholog for AGBL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for AGBL1 Gene

ENSEMBL:
Gene Tree for AGBL1 (if available)
TreeFam:
Gene Tree for AGBL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for AGBL1: view image

Paralogs for AGBL1 Gene

Paralogs for AGBL1 Gene

(3) SIMAP similar genes for AGBL1 Gene using alignment to 3 proteins:

  • CBPC4_HUMAN
  • J3KQF5_HUMAN
  • J3QSZ9_HUMAN
genes like me logo Genes that share paralogs with AGBL1: view

Variants for AGBL1 Gene

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Sequence variations from dbSNP and Humsavar for AGBL1 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs181958589 pathogenic, Corneal dystrophy, Fuchs endothelial, 8, Corneal dystrophy, Fuchs endothelial, 8 (FECD8) [MIM:615523] 86,674,322(+) G/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs185919705 pathogenic, Corneal dystrophy, Fuchs endothelial, 8 86,674,435(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, stop_gained
rs1000003145 -- 86,182,702(+) G/A intron_variant
rs1000004947 -- 86,814,110(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000005076 -- 86,104,298(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for AGBL1 Gene

Variant ID Type Subtype PubMed ID
dgv466e199 CNV deletion 23128226
dgv755e212 CNV loss 25503493
esv1001469 CNV insertion 20482838
esv1007298 CNV deletion 20482838
esv1137649 CNV insertion 17803354
esv2537097 CNV deletion 19546169
esv2664946 CNV deletion 23128226
esv2664960 CNV deletion 23128226
esv2674599 CNV deletion 23128226
esv2675845 CNV deletion 23128226
esv2749980 CNV deletion 23290073
esv2749981 CNV deletion 23290073
esv2749982 CNV deletion 23290073
esv2749983 CNV deletion 23290073
esv2760052 CNV loss 17122850
esv2761881 CNV loss 21179565
esv3552802 CNV deletion 23714750
esv3552803 CNV deletion 23714750
esv3552804 CNV deletion 23714750
esv3581802 CNV loss 25503493
esv3637135 CNV loss 21293372
esv3637136 CNV loss 21293372
esv3637137 CNV loss 21293372
esv3637140 CNV loss 21293372
esv3637141 CNV loss 21293372
esv3637142 CNV loss 21293372
esv3637143 CNV loss 21293372
esv3637144 CNV loss 21293372
esv3637146 CNV loss 21293372
esv3637147 CNV loss 21293372
nsv1039254 CNV loss 25217958
nsv1041107 CNV loss 25217958
nsv1048118 CNV gain 25217958
nsv1048250 CNV gain 25217958
nsv1048366 CNV loss 25217958
nsv1070293 CNV deletion 25765185
nsv1071231 CNV deletion 25765185
nsv1071232 CNV deletion 25765185
nsv1116095 CNV deletion 24896259
nsv1127450 CNV deletion 24896259
nsv1138394 CNV deletion 24896259
nsv1144743 CNV deletion 24896259
nsv457231 CNV loss 19166990
nsv479459 CNV novel sequence insertion 20440878
nsv507794 OTHER sequence alteration 20534489
nsv516208 CNV loss 19592680
nsv519797 CNV gain 19592680
nsv520512 CNV loss 19592680
nsv524278 CNV gain 19592680
nsv526937 CNV loss 19592680
nsv528422 CNV loss 19592680
nsv570357 CNV loss 21841781
nsv570358 CNV gain 21841781
nsv833080 CNV gain 17160897
nsv833082 CNV loss 17160897
nsv833083 CNV gain 17160897
nsv958011 CNV deletion 24416366
nsv958025 CNV deletion 24416366

Variation tolerance for AGBL1 Gene

Residual Variation Intolerance Score: 98.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.75; 73.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AGBL1 Gene

Human Gene Mutation Database (HGMD)
AGBL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AGBL1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AGBL1 Gene

Disorders for AGBL1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for AGBL1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search AGBL1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CBPC4_HUMAN
  • Corneal dystrophy, Fuchs endothelial, 8 (FECD8) [MIM:615523]: A corneal disease caused by loss of endothelium of the central cornea. It is characterized by focal wart-like guttata that arise from Descemet membrane and develop in the central cornea, epithelial blisters, reduced vision and pain. Descemet membrane is thickened by abnormal collagenous deposition. {ECO:0000269 PubMed:24094747}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for AGBL1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with AGBL1: view

No data available for Genatlas for AGBL1 Gene

Publications for AGBL1 Gene

  1. Mutations in AGBL1 cause dominant late-onset Fuchs corneal dystrophy and alter protein-protein interaction with TCF4. (PMID: 24094747) Riazuddin SA … Gottsch JD (American journal of human genetics 2013) 2 3 4 56
  2. Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response. (PMID: 21993531) Kuparinen T … Hurme M (Genes and immunity 2012) 3 43 56
  3. Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. (PMID: 22041458) Clark SL … van den Oord EJ (Psychological medicine 2012) 3 43 56
  4. Meta-analysis of genome-wide association for migraine in six population-based European cohorts. (PMID: 21448238) Ligthart L … Boomsma DI (European journal of human genetics : EJHG 2011) 3 43 56
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 43 56

ExternalLinks

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