AGTPBP1 ATP/GTP binding carboxypeptidase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AGTPBP1provided by HGNC
Official Full Name: ATP/GTP binding carboxypeptidase 1provided by HGNC
Primary source: HGNC:HGNC:17258
See related: Ensembl:ENSG00000135049 MIM:606830; AllianceGenome:HGNC:17258
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: CCP1; NNA1; CONDCA
Summary: NNA1 is a zinc carboxypeptidase that contains nuclear localization signals and an ATP/GTP-binding motif that was initially cloned from regenerating spinal cord neurons of the mouse.[supplied by OMIM, Jul 2002]
Expression: Broad expression in bone marrow (RPKM 7.2), brain (RPKM 4.8) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q21.33

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (85546539..85805483, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (97697026..97955976, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (88161454..88356944, complement)

Chromosome 9 - NC_000009.12 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?

Deleterious genetic changes in AGTPBP1 result in teratozoospermia with sperm head and flagella defects.
Title: Deleterious genetic changes in AGTPBP1 result in teratozoospermia with sperm head and flagella defects.
A novel pathogenic variant in the 3' end of the AGTPBP1 gene gives rise to neurodegeneration without cerebellar atrophy: an expansion of the disease phenotype?
Title: A novel pathogenic variant in the 3' end of the AGTPBP1 gene gives rise to neurodegeneration without cerebellar atrophy: an expansion of the disease phenotype?
The AGTPBP1 gene in neurobiology.
Title: The AGTPBP1 gene in neurobiology.
We conclude that complete loss-of-function of AGTPBP1 in humans, just like in mice and sheep, is associated with cerebellar and motor neuron disease, reminiscent of Pontocerebellar Hypoplasia Type 1 (PCH1).
Title: Biallelic variants in AGTPBP1, involved in tubulin deglutamylation, are associated with cerebellar degeneration and motor neuropathy.
biallelic rare and damaging variants in the gene encoding CCP1 in 13 individuals with infantile-onset neurodegeneration and confirmed the absence of functional CCP1 along with dysregulated tubulin polyglutamylation.
Title: Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration.
we identified seven new putative CCP1 substrates, all of them harboring acidic amino acids in their gene-encoded C terminus
Title: C-terminomics screen for natural substrates of cytosolic carboxypeptidase 1 reveals processing of acidic protein C termini.
Data indicate that a functional nuclear export signals (NESs) in CCP1 that mediates direct binding to the export receptor CRM1.
Title: Identification of CRM1-dependent Nuclear Export Cargos Using Quantitative Mass Spectrometry.

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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
Neurodegeneration, childhood-onset, with cerebellar atrophy MedGen: C4748934 OMIM: 618276 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A006N11 (e-PCR)
- UniSTS:60426

D9S1865 (e-PCR)
- UniSTS:71462

RH65354 (e-PCR)
- UniSTS:108

D9S1981 (e-PCR)
- UniSTS:46966

RH11900 (e-PCR)
- UniSTS:77240

G20277 (e-PCR)
- UniSTS:11718

A005K03 (e-PCR)
- UniSTS:11719

D9S954 (e-PCR)
- UniSTS:55776

D9S1067E (e-PCR)
- UniSTS:151284

RH99172 (e-PCR)
- UniSTS:86269

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metallocarboxypeptidase activity	IDA Inferred from Direct Assay more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor more info
involved_in C-terminal protein deglutamylation	IDA Inferred from Direct Assay more info	PubMed
involved_in C-terminal protein deglutamylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in adult walking behavior	IEA Inferred from Electronic Annotation 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 cerebellar Purkinje cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in eye photoreceptor cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitochondrion organization	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 neuromuscular process	ISS Inferred from Sequence or Structural Similarity more info
involved_in olfactory bulb development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in protein deglutamylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein side chain deglutamylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein side chain deglutamylation	IDA Inferred from Direct Assay more info	PubMed
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 retina development in camera-type eye	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 axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cytosolic carboxypeptidase 1

Names: ATP/GTP binding protein 1; carboxypeptidase-tubulin; nervous system nuclear protein induced by axotomy protein 1 homolog; protein deglutamylase CCP1; soluble carboxypeptidase; tubulinyl-Tyr carboxypeptidase; tyrosine carboxypeptidase

NP_001273644.1

EC 3.4.17.24

NP_001273646.1

EC 3.4.17.24

NP_001317630.1

EC 3.4.17.24

NP_056054.2

EC 3.4.17.24

XP_005251905.1

EC 3.4.17.24

XP_011516720.1

EC 3.4.17.24

XP_011516722.1

EC 3.4.17.24

XP_011516723.1

EC 3.4.17.24

XP_016870034.1

EC 3.4.17.24

XP_047279042.1

EC 3.4.17.24

XP_047279043.1

EC 3.4.17.24

XP_047279044.1

EC 3.4.17.24

XP_047279045.1

EC 3.4.17.24

XP_047279046.1

EC 3.4.17.24

XP_047279047.1

EC 3.4.17.24

XP_047279048.1

EC 3.4.17.24

XP_047279049.1

EC 3.4.17.24

XP_047279050.1

EC 3.4.17.24

XP_047279051.1

EC 3.4.17.24

XP_047279052.1

EC 3.4.17.24

XP_047279053.1

EC 3.4.17.24

XP_047279054.1

EC 3.4.17.24

XP_047279055.1

EC 3.4.17.24

XP_047279056.1

EC 3.4.17.24

XP_047279057.1

EC 3.4.17.24

XP_054218489.1

EC 3.4.17.24

XP_054218490.1

EC 3.4.17.24

XP_054218491.1

EC 3.4.17.24

XP_054218492.1

EC 3.4.17.24

XP_054218493.1

EC 3.4.17.24

XP_054218494.1

EC 3.4.17.24

XP_054218495.1

EC 3.4.17.24

XP_054218496.1

EC 3.4.17.24

XP_054218497.1

EC 3.4.17.24

XP_054218498.1

EC 3.4.17.24

XP_054218499.1

EC 3.4.17.24

XP_054218500.1

EC 3.4.17.24

XP_054218501.1

EC 3.4.17.24

XP_054218502.1

EC 3.4.17.24

XP_054218503.1

EC 3.4.17.24

XP_054218504.1

EC 3.4.17.24

XP_054218505.1

EC 3.4.17.24

XP_054218506.1

EC 3.4.17.24

XP_054218507.1

EC 3.4.17.24

XP_054218508.1

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.

mRNA and Protein(s)

NM_001286715.1 → NP_001273644.1 cytosolic carboxypeptidase 1 isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AB028958, AK295774, CA449535

Consensus CDS

CCDS75854.1

UniProtKB/TrEMBL

J3KNS1

Related

ENSP00000338512.5, ENST00000337006.8

Conserved Domains (1) summary

cd06906
Location:911 → 1188

M14_Nna1; Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases
NM_001286717.1 → NP_001273646.1 cytosolic carboxypeptidase 1 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.

Source sequence(s)

AK295774, AL157882, AL451131, CA449535

Consensus CDS

CCDS69615.1

UniProtKB/Swiss-Prot

Q9UPW5

Related

ENSP00000487074.1, ENST00000628899.1

Conserved Domains (1) summary

cd06906
Location:871 → 1148

M14_Nna1; Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases
NM_001330701.2 → NP_001317630.1 cytosolic carboxypeptidase 1 isoform d

Status: VALIDATED

Source sequence(s)

AK295774, AL157882, AL833359, CA449535, CN354118, CN354120, DA326833, DB078109

Consensus CDS

CCDS83382.1

UniProtKB/Swiss-Prot

B4DIT6, B4DRZ8, Q5VV80, Q63HM7, Q658P5, Q6P9D6, Q9H8U6, Q9H9W8, Q9NVK1, Q9UPW5

Related

ENSP00000349592.3, ENST00000357081.8
NM_015239.3 → NP_056054.2 cytosolic carboxypeptidase 1 isoform b

See identical proteins and their annotated locations for NP_056054.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) includes an additional exon in the 5' region and thus differs in its 5' UTR and initiates translation from an alternate start codon, and it also uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

BC060815, CA449535

Consensus CDS

CCDS6672.1

Related

ENSP00000365251.3, ENST00000376083.7

Conserved Domains (1) summary

cd06906
Location:819 → 1096

M14_Nna1; Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases