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GPN3 GPN-loop GTPase 3 [ Homo sapiens (human) ]

Gene ID: 51184, updated on 5-Mar-2024

Summary

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Official Symbol
GPN3provided by HGNC
Official Full Name
GPN-loop GTPase 3provided by HGNC
Primary source
HGNC:HGNC:30186
See related
Ensembl:ENSG00000111231 AllianceGenome:HGNC:30186
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
ATPBD1C
Summary
Predicted to enable GTPase activity. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 19.7), fat (RPKM 10.4) and 25 other tissues See more
Orthologs
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Genomic context

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See GPN3 in Genome Data Viewer
Location:
12q24.11
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110452486..110468721, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110430179..110446415, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110890291..110906526, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110866603-110867104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7002 Neighboring gene high mobility group AT-hook 1 pseudogene 3 Neighboring gene actin related protein 2/3 complex subunit 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110886698-110887550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7003 Neighboring gene ribosomal protein L31 pseudogene 49 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7005 Neighboring gene uncharacterized LOC124903016 Neighboring gene family with sequence similarity 216 member A Neighboring gene uncharacterized LOC124903015 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene VPS29 retromer complex component

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Gpn3 Is Essential for Cell Proliferation of Breast Cancer Cells Independent of Their Malignancy Degree. Lara-Chacón B, et al. Technol Cancer Res Treat, 2019 Jan 1. PMID 31431135, Free PMC Article
  2. Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner. Méndez-Hernández LE, et al. FEBS Lett, 2017 Nov. PMID 29029378
  3. The Gpn3 Q279* cancer-associated mutant inhibits Gpn1 nuclear export and is deficient in RNA polymerase II nuclear targeting. Barbosa-Camacho AA, et al. FEBS Lett, 2017 Nov. PMID 28940195
  4. Gpn1 and Gpn3 associate tightly and their protein levels are mutually dependent in mammalian cells. Méndez-Hernández LE, et al. FEBS Lett, 2014 Nov 3. PMID 25241168
  5. Parcs/Gpn3 is required for the nuclear accumulation of RNA polymerase II. Calera MR, et al. Biochim Biophys Acta, 2011 Oct. PMID 21782856

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. our analysis of public data revealed that Gpn3 overexpression was associated with a significant decrease in overall survival in patients with estrogen receptor-positive and Human epidermal growth factor receptor 2 (HER2+) breast cancer, supporting our proposal that targeting Gpn3 could potentially benefit patients with breast cancer.
    Title: Gpn3 Is Essential for Cell Proliferation of Breast Cancer Cells Independent of Their Malignancy Degree.
  2. Results indicate that polyubiquitination on lysine 216 is a regulatory process for proteasomal degradation of Gpn3 that is not in a complex with Gpn1, a critical partner of Gpn3 in human cells.
    Title: Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner.
  3. an acquired PDZ-binding motif in Gpn3 Q279* caused Gpn3 nuclear entry, and inhibited Gpn1 nuclear export and Gpn3-mediated RNAPII nuclear targeting.
    Title: The Gpn3 Q279* cancer-associated mutant inhibits Gpn1 nuclear export and is deficient in RNA polymerase II nuclear targeting.
  4. Gpn1-Gpn3 interaction was essential to maintain steady-state protein levels of both GTPases
    Title: Gpn1 and Gpn3 associate tightly and their protein levels are mutually dependent in mammalian cells.
  5. Data show that GPN1/GPN3 define a new family of small GTPases that are specialized for the transport of RNA polymerase II into the nucleus.
    Title: Human GTPases associate with RNA polymerase II to mediate its nuclear import.
  6. Parcs/Gpn3 plays a critical role in the nuclear accumulation of RNAP II, and this function explains the relative importance of Parcs/Gpn3 in cell proliferation.
    Title: Parcs/Gpn3 is required for the nuclear accumulation of RNA polymerase II.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC14560, MGC32810

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
GPN-loop GTPase 3
Names
ATP-binding domain 1 family member C
protein x 0004

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)

  1. NM_001164372.2 → NP_001157844.1  GPN-loop GTPase 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' exon, resulting in a distinct 5' UTR and translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a longer and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK223209, BC008416, BI546381
    Consensus CDS
    CCDS53831.1
    UniProtKB/Swiss-Prot
    Q9UHW5
    Related
    ENSP00000442770.1, ENST00000543199.5
    Conserved Domains (2) summary
    COG1100
    Location:56 → 249
    Gem1; GTPase SAR1 family domain [General function prediction only]
    pfam03029
    Location:56 → 293
    ATP_bind_1; Conserved hypothetical ATP binding protein

  2. NM_001164373.2 → NP_001157845.1  GPN-loop GTPase 3 isoform 3

    See identical proteins and their annotated locations for NP_001157845.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a longer protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AK223209, BC008416, BX537973
    Consensus CDS
    CCDS53830.1
    UniProtKB/Swiss-Prot
    Q9UHW5
    Related
    ENSP00000443068.2, ENST00000537466.6
    Conserved Domains (1) summary
    pfam03029
    Location:8 → 264
    ATP_bind_1; Conserved hypothetical ATP binding protein

  3. NM_016301.4 → NP_057385.3  GPN-loop GTPase 3 isoform 1

    See identical proteins and their annotated locations for NP_057385.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (1).
    Source sequence(s)
    AK223209, BC008416
    Consensus CDS
    CCDS9147.1
    UniProtKB/Swiss-Prot
    B2RC54, D4YWV1, F5H759, Q53FS3, Q6UVZ6, Q7Z3D3, Q8NEI2, Q96HK9, Q9UHW5
    Related
    ENSP00000228827.3, ENST00000228827.8
    Conserved Domains (1) summary
    cd17872
    Location:4 → 249
    GPN3; GPN-loop GTPase 3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    110452486..110468721 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428936.1 → XP_047284892.1  GPN-loop GTPase 3 isoform X4

  2. XM_047428934.1 → XP_047284890.1  GPN-loop GTPase 3 isoform X2

  3. XM_047428935.1 → XP_047284891.1  GPN-loop GTPase 3 isoform X3

  4. XM_047428933.1 → XP_047284889.1  GPN-loop GTPase 3 isoform X1

  5. XM_017019394.2 → XP_016874883.1  GPN-loop GTPase 3 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110430179..110446415 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372187.1 → XP_054228162.1  GPN-loop GTPase 3 isoform X4

  2. XM_054372185.1 → XP_054228160.1  GPN-loop GTPase 3 isoform X2

  3. XM_054372186.1 → XP_054228161.1  GPN-loop GTPase 3 isoform X3

  4. XM_054372184.1 → XP_054228159.1  GPN-loop GTPase 3 isoform X1

  5. XM_054372188.1 → XP_054228163.1  GPN-loop GTPase 3 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UHW5.2 GenPept UniProtKB/Swiss-Prot:Q9UHW5

Gene LinkOut

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