GPN1 GPN-loop GTPase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: GPN1provided by HGNC
Official Full Name: GPN-loop GTPase 1provided by HGNC
Primary source: HGNC:HGNC:17030
See related: Ensembl:ENSG00000198522 MIM:611479; AllianceGenome:HGNC:17030
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: XAB1; MBDIN; NTPBP; RPAP4; ATPBD1A
Summary: This gene encodes a guanosine triphosphatase enzyme. The encoded protein may play a role in DNA repair and may function in activation of transcription. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
Expression: Ubiquitous expression in testis (RPKM 15.4), thyroid (RPKM 13.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p23.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (27628247..27651511)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (27671332..27694600)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (27851114..27874378)

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 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?

Results show that Gpn1-inhibitable, nuclear polyubiquitination on lysine 216 regulates the half-life of Gpn3 by tagging it for proteasomal degradation.
Title: Gpn3 is polyubiquitinated on lysine 216 and degraded by the proteasome in the cell nucleus in a Gpn1-inhibitable manner.
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.
GPN1 gene variation is associated with oral cavity and pharyngeal cancer.
Title: Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.
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.
A highly active, evolutionarily conserved nuclear export sequences in XAB1/Gpn1, was identified.
Title: A nuclear export sequence in GPN-loop GTPase 1, an essential protein for nuclear targeting of RNA polymerase II, is necessary and sufficient for nuclear export.
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.
RPAP4/GPN1 is a member of a newly discovered GTPase family that contains a highly conserved GPN loop motif that is essential, along with its GTP-binding motifs, for nuclear localization of POLR2A/RPB1 in a process that also requires microtubule assembly
Title: The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II.
relieves MBD2-mediated transcriptional repression and reactivates transcription from methylated promoters
Title: MBDin, a novel MBD2-interacting protein, relieves MBD2 repression potential and reactivates transcription from methylated promoters.

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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

EBI GWAS Catalog

Description
A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, GPN-loop GTPase 1 (GPN1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa 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

RH16648 (e-PCR)
- UniSTS:43778

G20810 (e-PCR)
- UniSTS:66848

A006H24 (e-PCR)
- UniSTS:66849

SGC32173 (e-PCR)
- UniSTS:16285

RH98653 (e-PCR)
- UniSTS:89509

D2S1424 (e-PCR)
- UniSTS:61629

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
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
located_in cytosol	IDA Inferred from Direct Assay more info
located_in mitochondrion	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: GPN-loop GTPase 1

Names: ATP(GTP)-binding protein; MBD2-interacting protein; RNA polymerase II associated protein 4; RNAPII-associated protein 4; XPA binding protein 1, GTPase

NP_001138519.1

EC 3.6.5.-

NP_001138520.1

EC 3.6.5.-

NP_001138521.1

EC 3.6.5.-

NP_009197.3

EC 3.6.5.-

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_001145047.2 → NP_001138519.1 GPN-loop GTPase 1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, contains two alternate exons in the 5' coding region and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a shorter, distinct N-terminus, compared to isoform a.

Source sequence(s)

AC074091, AJ010842, AK298827, AK310340

Consensus CDS

CCDS46248.1

UniProtKB/Swiss-Prot

Q9HCN4

Related

ENSP00000384255.3, ENST00000407583.7

Conserved Domains (2) summary

COG1100
Location:23 → 217

Gem1; GTPase SAR1 family domain [General function prediction only]

pfam03029
Location:23 → 249

ATP_bind_1; Conserved hypothetical ATP binding protein
NM_001145048.2 → NP_001138520.1 GPN-loop GTPase 1 isoform c

See identical proteins and their annotated locations for NP_001138520.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a segment of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.

Source sequence(s)

AC074091, AJ010842, AK298827

Consensus CDS

CCDS46250.1

UniProtKB/Swiss-Prot

Q9HCN4

Related

ENSP00000398115.1, ENST00000424214.5

Conserved Domains (2) summary

COG1100
Location:1 → 150

Gem1; GTPase SAR1 family domain [General function prediction only]

pfam03029
Location:1 → 182

ATP_bind_1; Conserved hypothetical ATP binding protein
NM_001145049.2 → NP_001138521.1 GPN-loop GTPase 1 isoform d

See identical proteins and their annotated locations for NP_001138521.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) has multiple coding region differences compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (d) with a shorter N-terminus compared to isoform a.

Source sequence(s)

AC074091, AJ010842, AK316404

Consensus CDS

CCDS46249.1

UniProtKB/Swiss-Prot

Q9HCN4

Related

ENSP00000412170.2, ENST00000458167.6

Conserved Domains (2) summary

COG1100
Location:22 → 160

Gem1; GTPase SAR1 family domain [General function prediction only]

pfam03029
Location:5 → 166

ATP_bind_1; Conserved hypothetical ATP binding protein
NM_007266.4 → NP_009197.3 GPN-loop GTPase 1 isoform a

Status: REVIEWED

Description

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

Source sequence(s)

AC074091, AJ010842, AK298866, BC007451

Consensus CDS

CCDS1760.3

UniProtKB/Swiss-Prot

B4DQJ5, B4DQM4, B4DXU4, B5MBZ5, O76004, Q9HCN4

UniProtKB/TrEMBL

Q53RZ9

Related

ENSP00000476446.1, ENST00000610189.2

Conserved Domains (1) summary

pfam03029
Location:24 → 261

ATP_bind_1; Conserved hypothetical ATP binding protein

RNA

NR_026735.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074091, AJ010842, AK302131