AGBL2 (AGBL carboxypeptidase 2)

Gene

• Entrez ID: 79841
• Gene name: AGBL carboxypeptidase 2
• Gene symbol: AGBL2
• Synonyms (NCBI Gene): CCP2
• Chromosome: 11
• Chromosome location: 11p11.2

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs764666741	G>A	Likely-pathogenic	Coding sequence variant, stop gained, intron variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017461	hsa-miR-335-5p	Microarray	18185580
MIRT021583	hsa-miR-142-3p	Microarray	17612493
MIRT047542	hsa-miR-10a-5p	CLASH	23622248
MIRT1927738	hsa-miR-140-3p	CLIP-seq
MIRT1927739	hsa-miR-144	CLIP-seq
MIRT2168532	hsa-let-7a	CLIP-seq
MIRT2168533	hsa-let-7b	CLIP-seq
MIRT2168534	hsa-let-7c	CLIP-seq
MIRT2168535	hsa-let-7d	CLIP-seq
MIRT2168536	hsa-let-7e	CLIP-seq
MIRT2168537	hsa-let-7f	CLIP-seq
MIRT2168538	hsa-let-7g	CLIP-seq
MIRT2168539	hsa-let-7i	CLIP-seq
MIRT2168540	hsa-miR-202	CLIP-seq
MIRT2168541	hsa-miR-3155	CLIP-seq
MIRT2168542	hsa-miR-3155b	CLIP-seq
MIRT2168543	hsa-miR-3163	CLIP-seq
MIRT2168544	hsa-miR-3688-5p	CLIP-seq
MIRT2168545	hsa-miR-3941	CLIP-seq
MIRT2168546	hsa-miR-4282	CLIP-seq
MIRT2168547	hsa-miR-4284	CLIP-seq
MIRT2168548	hsa-miR-4458	CLIP-seq
MIRT2168549	hsa-miR-4500	CLIP-seq
MIRT2168550	hsa-miR-4643	CLIP-seq
MIRT2168551	hsa-miR-4659a-5p	CLIP-seq
MIRT2168552	hsa-miR-4659b-5p	CLIP-seq
MIRT2168553	hsa-miR-466	CLIP-seq
MIRT2168554	hsa-miR-4672	CLIP-seq
MIRT2168555	hsa-miR-4690-3p	CLIP-seq
MIRT2168556	hsa-miR-4769-3p	CLIP-seq
MIRT2168557	hsa-miR-4789-3p	CLIP-seq
MIRT2168558	hsa-miR-4803	CLIP-seq
MIRT2168559	hsa-miR-484	CLIP-seq
MIRT2168560	hsa-miR-548ag	CLIP-seq
MIRT2168561	hsa-miR-548ai	CLIP-seq
MIRT2168562	hsa-miR-644	CLIP-seq
MIRT2168563	hsa-miR-98	CLIP-seq
MIRT2426092	hsa-miR-485-3p	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:0005515	Function	Protein binding	IPI	21303978, 32296183
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IDA	23085998
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0005856	Component	Cytoskeleton	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:0016787	Function	Hydrolase activity	IEA
GO:0035610	Process	Protein side chain deglutamylation	ISS
GO:0036064	Component	Ciliary basal body	IDA	23085998
GO:0042995	Component	Cell projection	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 617345
• HGNC: 26296
• e!Ensembl: ENSG00000165923

Protein

• UniProt ID: Q5U5Z8
• Protein name: Cytosolic carboxypeptidase 2 (EC 3.4.17.-) (ATP/GTP-binding protein-like 2) (Protein deglutamylase CCP2)
• 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	268 → 395	Cytosolic carboxypeptidase N-terminal domain	Domain
  PF00246	Peptidase_M14	413 → 596	Zinc carboxypeptidase	Domain

• Sequence:

  MFPALETHLKQTIPDPYEDFMYRHLQYYGYFKAQRGSLPNSATHQHVRKNNPQCLLNGSL
  GEKDDLIPDTLQKEKLLWPISLSSAVHRQIEAINRDFHSCLGWMQWRGLSSLQPPPPRFK
  DSPASAFRVAGITDSHMLSLPHLRSRQLLYDELDEVNPRLREPQELFSILSTKRPLQAPR
  WPIECEVIKENIHHIEWAPPQPEYFYQPKGNEKVPEIVGEKKGTVVYQLDSVPIEGSYFT
  SSRVGGKRGIVKELAVTLQGPEDNTLLFESRFESGNLQKAVRVDTYEYELTLRTDLYTNK
  HTQWFYFRVQNTRKDATYRFTIVNLLKPKSLYTVGMKPLLYSQLDANTRNIGWRREGNEI
  KYYKNNTDDGQQPFYCLTWTIQFPYDQDTCFFAHFYPYTYTDLQCYLLSVANNPIQSQFC
  KLQTLCRSLAGNTVYLLTITNPSQTPQEAAAKKAVVLSARVHPGESNGSWVMKGFLDFIL
  SNSPDAQLLRDIFVFKVLPMLNPDGVIVGNYRCSLAGRDLNRHYKTILKESFPCIWYTRN
  MIKRLLEEREVLLYCDFHGHSRKNNIFLYGCNNNNRKYWLHERVFPLMLCKNAPDKFSFH
  SCNFKVQKCKEGTGRVVMWRMGILNSYTMESTFGGSTLGNKRDTHFTIEDLKSLGYHVCD
  TLLDFCDPDQMKFTQCLAELKELLRQEIHKKFHELGQDVDLEGSWSDISLSDIESSTSGS
  DSSLSDGLPVHLANIADELTQKKKMFKKKKKKSLQTRKQRNEQYQKKNLMQKLKLTEDTS
  EKAGFASTLQKQPTFFKNSENSSFLPMKNENPRLNETNLNRRDKDTPLDPSMATLILPKN
  KGRMQNKKPGFTVSCSPKRTINSSQEPAPGMKPNWPRSRYPATKRGCAAMAAYPSLHIYT
  YP

• Sequence length: 902

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
Abnormal brain morphology	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETIC EYE DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETIC RETINOPATHY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epilepsy	Conflicting classifications of pathogenicity	ClinVar Disgenet, GenCC Disgenet, GenCC	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
HEART FAILURE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTENSION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOOD DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL ARTERIAL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anxiety	Anxiety Disorder	GWASCAT_DG	29942085		★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	BEFREE	15248208, 22339947, 23754702		★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	Pubtator	34093522	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	20196860, 21291540, 31474319, 34093522, 37001434	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	24884516		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	21303978	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	32307444	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	31612000		★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	BEFREE	27159164		★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	27159164		★☆☆☆☆ Found in Text Mining only
Coronary heart disease	Coronary Heart Disease	BEFREE	27159164		★☆☆☆☆ Found in Text Mining only
Glaucoma, Primary Open Angle	Glaucoma	BEFREE	28832686		★☆☆☆☆ Found in Text Mining only
IGA Glomerulonephritis	Glomerulonephritis	BEFREE	29746558		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	29126912		★☆☆☆☆ Found in Text Mining only
Low Tension Glaucoma	Low Tension Glaucoma	BEFREE	28832686		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	24884516		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	31612000		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30899431, 31612000		★☆☆☆☆ Found in Text Mining only
Medullary carcinoma of thyroid	Megalencephaly, Polymicrogyria, Polydactyly, Hydrocephalus Syndrome	BEFREE	1761559, 7691931		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	GWASCAT_DG	24076602		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Myocardial Infarction	Myocardial Infarction	BEFREE	27159164		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29126912, 31612000		★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	BEFREE	30700425		★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	BEFREE	29368271		★☆☆☆☆ Found in Text Mining only
Ovarian Carcinoma	Ovarian Carcinoma	BEFREE	31612000		★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	31612000		★☆☆☆☆ Found in Text Mining only
Primary biliary cirrhosis	Biliary Cirrhosis	BEFREE	30807792		★☆☆☆☆ Found in Text Mining only
Primary sclerosing cholangitis	Sclerosing Cholangitis	BEFREE	30807792		★☆☆☆☆ Found in Text Mining only
Refractory anemias	Anemia	BEFREE	20457731		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	17611988, 17704064, 18565246, 19447936, 20196860, 20457731, 22339947, 25406539, 27125521, 28109618, 28578492, 28619044, 29070529, 29259607, 29368271, 29895567, 30073867, 30277007, 30555464, 30611755, 30656490, 30807792, 31130713, 31413004, 31449733, 31474319		★☆☆☆☆ Found in Text Mining only
Severe periodontitis	Periodontitis	BEFREE	31130713		★☆☆☆☆ Found in Text Mining only