AGBL1 (AGBL carboxypeptidase 1)

Gene

• Entrez ID: 123624
• Gene name: AGBL carboxypeptidase 1
• Gene symbol: AGBL1
• Synonyms (NCBI Gene): CCP4, FECD8
• Chromosome: 15
• Chromosome location: 15q25.3
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs181958589	G>C	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant
rs185919705	C>T	Conflicting-interpretations-of-pathogenicity	Stop gained, missense variant, genic downstream transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2168531	hsa-miR-665	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004180	Function	Carboxypeptidase activity	IEA
GO:0004181	Function	Metallocarboxypeptidase activity	IBA
GO:0004181	Function	Metallocarboxypeptidase activity	IEA
GO:0004181	Function	Metallocarboxypeptidase activity	ISS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0006508	Process	Proteolysis	IEA
GO:0008233	Function	Peptidase activity	IEA
GO:0008237	Function	Metallopeptidase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0015630	Component	Microtubule cytoskeleton	IBA
GO:0015631	Function	Tubulin binding	IBA
GO:0015631	Function	Tubulin binding	ISS
GO:0016787	Function	Hydrolase activity	IEA
GO:0035609	Process	C-terminal protein deglutamylation	ISS
GO:0035610	Process	Protein side chain deglutamylation	ISS
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 615496
• HGNC: 26504
• e!Ensembl: ENSG00000273540

Protein

• UniProt ID: Q96MI9
• Protein name: Cytosolic carboxypeptidase 4 (EC 3.4.17.-) (EC 3.4.17.24) (ATP/GTP-binding protein-like 1) (Protein deglutamylase CCP4)
• Protein function: Metallocarboxypeptidase that mediates deglutamylation of tubulin and non-tubulin target proteins. Catalyzes the removal of polyglutamate side chains present on the gamma-carboxyl group of glutamate residues within the C-terminal tail of tubulin
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF18027	Pepdidase_M14_N	596 → 731	Cytosolic carboxypeptidase N-terminal domain	Domain
  PF00246	Peptidase_M14	756 → 1010	Zinc carboxypeptidase	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in corneal endothelium. {ECO:0000269|PubMed:24094747}.
• Sequence:

  MAEQEASGLQVLLHTLQSSSDKESILTILKVLGDLLSVGTDRRIHYMISKGGSEALLQTL
  VDTARTAPPDYDILLPLFRLLAKVGLRDKKIGRKALELEALDVTLILARKNLSHGQNLLH
  CLWALRVFASSVSMGAMLGINGAMELLFKVITPYTRKRTQAIRAATEVLAALLKSKSNGR
  RAVNRGYVTSLLGLHQDWHSHDTANAYVQIRRGLLLCLRHIAALRSGREAFLAAQGMEIL
  FSTTQNCLDDKSMEPVISVVLQILRQCYPTSPLPLVTASSAYAFPVPGCITTEPPHDLPE
  EDFEDDGDDEVDKDSDTEDGKVEDDDLETDVNKLSSKPGLDRPEEELMQYEVMCLELSYS
  FEELQSKLGDDLNSEKTQYANHHHIPAAASSKQHCYSKDQSSCGQEREYAVQTSLLCRVK
  TGRSTVHLGSKKNPGVNLYQNVQSNSLRRDSSESEIPDIQASPKADAWDVDAIFCPRMSA
  SFSNSTRTREVVKVIDKLLQTHLKRVPFHDPYLYMAKARRTSSVVDFKMMAFPDVWGHCP
  PPTTQPMLERKCGVQRIRIFEDIRRLIQPSDVINKVVFSLDEPWPLQDNASNCLRFFSKF
  ESGNLRKAIQVREFEYDLLVNADVNSTQHQQWFYFKVSGMQAAIPYHFNIINCEKPNSQF
  NYGMQPTLYSVKEALLGKPTWIRTGHEICYYKNHYRQSTAVAGGASGKCYYTLTFAVTFP
  HSEDVCYLAYHYPYTYTALMTHLDILEKSVNLKEVYFRQDVLCQTLGGNPCPLVTITAMP
  ESNSDEHLEQFRHRPYQVITARVHPGESNASWVMKGTLEFLVSSDPVARLLRENFIFKII
  PMLNPDGVINGNHRCSLSGEDLNRQWLSPSAHLQPTIYHAKGLLYHLSSIGRSPVVFCDF
  HGHSQKKNVFLYGCSIKETLWQAACTVGTSTILEEVNYRTLPKILDKLAPAFTMSSCSFL
  VEKSRASTARVVVWREMGVSRSYTMESSYCGCNQGPYQCTQRLLERTKNERAHPVDGLQG
  LQFGTRELEEMGAMFCLGLLILELKSASCSHQLLAQAATLLSAEEDALDQHLQRLKSSNF
  LPKHIWFAYHFFAITNFFKMNLLLHVSPVCDT

• Sequence length: 1112

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AGBL1-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARRETT'S ESOPHAGUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BULIMIA NERVOSA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHAGAS CARDIOMYOPATHY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corneal dystrophy, Fuchs endothelial, 8	Uncertain significance; Benign; Conflicting classifications of pathogenicity	ClinVar CTD, ClinVar, Disgenet, GWAS catalog, HPO CTD, ClinVar, Disgenet, GWAS catalog, HPO CTD, ClinVar, Disgenet, GWAS catalog, HPO CTD, ClinVar, Disgenet, GWAS catalog, HPO	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
FUCHS ENDOTHELIAL CORNEAL DYSTROPHY	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FUCHS ENDOTHELIAL DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fuchs' endothelial dystrophy	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Gastric cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GESTATIONAL DIABETES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC PULMONARY FIBROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MIGRAINE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STROKE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VENOUS THROMBOEMBOLISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer`s Disease	Alzheimer disease	GWASCAT_DG	26830138		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	31647196		★☆☆☆☆ Found in Text Mining only
Bronchopulmonary Dysplasia	Bronchopulmonary Dysplasia	GWASDB_DG	21836138		★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	31885738	Associate	★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular disease	Pubtator	22503546	Associate	★☆☆☆☆ Found in Text Mining only
Carotid Stenosis	Carotid artery stenosis	Pubtator	22503546	Associate	★☆☆☆☆ Found in Text Mining only
Corneal dystrophy	Corneal Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 8	Corneal Endothelial Dystrophy	UNIPROT_DG	24094747		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 8	Corneal Endothelial Dystrophy	GENOMICS_ENGLAND_DG	24094747		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 8	Corneal Endothelial Dystrophy	CTD_human_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 8	Corneal Endothelial Dystrophy	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Fleck corneal dystrophy	Fleck Corneal Dystrophy	BEFREE	24094747		★☆☆☆☆ Found in Text Mining only
Fuchs endothelial corneal dystrophy	Fuchs Endothelial Dystrophy	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fuchs Endothelial Dystrophy	Fuchs Endothelial Dystrophy	BEFREE	24094747, 30267097		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fuchs Endothelial Dystrophy	Fuchs Endothelial Dystrophy	ORPHANET_DG	24094747		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fuchs' Endothelial Dystrophy	Fuchs endothelial dystrophy	Pubtator	24094747, 40244234	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ischemic stroke	Ischemic Stroke	GWASCAT_DG	26089329		★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	GWASDB_DG	19629137		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	22503546	Associate	★☆☆☆☆ Found in Text Mining only