AGBL5 AGBL carboxypeptidase 5 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 2p23.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (27050364..27070618)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (27092051..27112291)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (27274291..27293486)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mutations in AGBL5 associated with Retinitis pigmentosa.
Title: Mutations in AGBL5 associated with Retinitis pigmentosa.
Tubulin code eraser CCP5 binds branch glutamates by substrate deformation.
Title: Tubulin code eraser CCP5 binds branch glutamates by substrate deformation.
CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
Title: CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
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.
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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

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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)

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

RH80719 (e-PCR)
- UniSTS:86018

RH69213 (e-PCR)
- UniSTS:33593

MARC_23457-23458:1027109061:1 (e-PCR)
- UniSTS:268705

MARC_12887-12888:999876636:1 (e-PCR)
- UniSTS:267469

NoName (e-PCR)
- UniSTS:489939

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metallocarboxypeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metallocarboxypeptidase activity	ISS Inferred from Sequence or Structural Similarity more info
enables tubulin binding	IBA Inferred from Biological aspect of Ancestor 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
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
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
is_active_in microtubule cytoskeleton	IBA Inferred from Biological aspect of Ancestor 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

EC 3.4.17.24

NP_068603.4

EC 3.4.17.24

XP_005264534.1

EC 3.4.17.24

XP_011531313.1

EC 3.4.17.24

XP_011531314.1

EC 3.4.17.24

XP_011531315.1

EC 3.4.17.24

XP_047301330.1

EC 3.4.17.24

XP_047301331.1

EC 3.4.17.24

XP_047301332.1

EC 3.4.17.24

XP_047301333.1

EC 3.4.17.24

XP_054199250.1

EC 3.4.17.24

XP_054199251.1

EC 3.4.17.24

XP_054199252.1

EC 3.4.17.24

XP_054199253.1

EC 3.4.17.24

XP_054199254.1

EC 3.4.17.24

XP_054199255.1

EC 3.4.17.24

XP_054199256.1

EC 3.4.17.24

XP_054199257.1

EC 3.4.17.24

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

NG_052914.1 RefSeqGene

Range

5246..24196

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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
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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

27050364..27070618

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047445376.1 → XP_047301332.1 cytosolic carboxypeptidase-like protein 5 isoform X4
XM_047445377.1 → XP_047301333.1 cytosolic carboxypeptidase-like protein 5 isoform X4
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
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
XM_047445375.1 → XP_047301331.1 cytosolic carboxypeptidase-like protein 5 isoform X3
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
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
XM_047445374.1 → XP_047301330.1 cytosolic carboxypeptidase-like protein 5 isoform X2

Related

ENSP00000433830.1, ENST00000487078.5