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RAP1GDS1 Rap1 GTPase-GDP dissociation stimulator 1 [ Homo sapiens (human) ]

Gene ID: 5910, updated on 7-Apr-2024

Summary

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Official Symbol
RAP1GDS1provided by HGNC
Official Full Name
Rap1 GTPase-GDP dissociation stimulator 1provided by HGNC
Primary source
HGNC:HGNC:9859
See related
Ensembl:ENSG00000138698 MIM:179502; AllianceGenome:HGNC:9859
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
GDS1; SmgGDS
Summary
The smg GDP dissociation stimulator (smgGDS) protein is a stimulatory GDP/GTP exchange protein with GTPase activity (Riess et al., 1993 [PubMed 8262526]).[supplied by OMIM, Feb 2010]
Expression
Ubiquitous expression in brain (RPKM 27.0), testis (RPKM 10.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q23
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (98261384..98443858)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (101576339..101758825)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (99182535..99365009)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene sperm tail PG-rich repeat containing 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:99031922-99032747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21732 Neighboring gene deoxyuridine triphosphatase pseudogene 8 Neighboring gene uncharacterized LOC105377340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:99125201-99125922 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:99181827-99182389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15577 Neighboring gene uncharacterized LOC124900919 Neighboring gene ribosomal protein L21 pseudogene 48 Neighboring gene Sharpr-MPRA regulatory region 12770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:99457519-99458032 Neighboring gene tetraspanin 5 Neighboring gene Sharpr-MPRA regulatory region 11258 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:99518736-99519334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21735 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:99574420-99575619 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:99579327-99579486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15578 Neighboring gene uncharacterized LOC112267901 Neighboring gene TSPAN5 divergent transcript

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Silencing of SmgGDS, a Novel mTORC1 Inducer That Binds to RHEBs, Inhibits Malignant Mesothelioma Cell Proliferation.
    Title: Silencing of SmgGDS, a Novel mTORC1 Inducer That Binds to RHEBs, Inhibits Malignant Mesothelioma Cell Proliferation.
  2. Mutated RAP1GDS1 causes a new syndrome of dysmorphic feature, intellectual disability & speech delay.
    Title: Mutated RAP1GDS1 causes a new syndrome of dysmorphic feature, intellectual disability & speech delay.
  3. Targeting SmgGDS splicing to lower the protein isoform ratio is effective to inhibit the malignant phenotype generated by small GTPases.
    Title: Splice switching an oncogenic ratio of SmgGDS isoforms as a strategy to diminish malignancy.
  4. The competitive binding affinities of the small GTPase for SmgGDS-607 and FTase dictate the extent of this inhibition. SmgGDS-607 increases the rate of farnesylation of HRas by enhancing product release from FTase.
    Title: The chaperone SmgGDS-607 has a dual role, both activating and inhibiting farnesylation of small GTPases.
  5. SmgGDS-607 completely inhibits RhoA prenylation catalyzed by protein geranylgeranyltransferase I (GGTase-I) in an in vitro radiolabel incorporation assay. SmgGDS-607 inhibits prenylation by binding to and blocking access to the C-terminal tail of the small GTPase (substrate sequestration mechanism) rather than via inhibition of the prenyltransferase activity.
    Title: SmgGDS-607 Regulation of RhoA GTPase Prenylation Is Nucleotide-Dependent.
  6. Study reveals a cryptic pocket by which SmgGDS-558 accommodates RhoA prenylation, loosening the structure of Rho when it interacts with SmgGDS, which may enable drug development strategies for targeting SmgGDS and small GTPases.
    Title: GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism.
  7. a novel nuclear role for SmgGDS in protecting malignant cells from nucleolar stress, thus promoting cell cycle progression and tumorigenesis.
    Title: SmgGDS is a transient nucleolar protein that protects cells from nucleolar stress and promotes the cell cycle by regulating DREAM complex gene expression.
  8. Data suggest that SmgGDS-558 splice variant exhibits a fold containing tandem copies of armadillo-repeat motifs not present in other guanine nucleotide exchange factors (GEFs); SmgGDS harbors distinct positively and negatively charged regions, both of which play critical roles in binding to RhoA and in GEF activity. (SmgGDS = smg p21 stimulatory GDP exchange protein; RhoA = ras homolog gene family, member A)
    Title: Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding.
  9. Unlike Rap1B, phosphorylation in the polybasic region of Rap1A does not detectably inhibit its prenylation or its binding to SmgGDS-607.
    Title: Differences in the Phosphorylation-Dependent Regulation of Prenylation of Rap1A and Rap1B.
  10. In addition, a PINK1 mutant, which induced mitochondrial enlargement and had been considered as a Drosophila model of Parkinson's disease (PD), caused fly muscle defects, and the loss of vimar could rescue these defects. Furthermore, we found that the mammalian homolog of Vimar, RAP1GDS1, played a similar role in regulating mitochondrial morphology, suggesting a functional conservation of this GEF member.
    Title: Vimar Is a Novel Regulator of Mitochondrial Fission through Miro.
Submit: New GeneRIF Correction See all GeneRIFs (27)

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
Alfadhel syndrome
MedGen: CN375873 OMIM: 620655 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide association study of biochemical traits in Korcula Island, Croatia.
EBI GWAS Catalog

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of RAP1GDS1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat downregulates the expression of RAP1, GTP-GDP dissociation stimulator 1 (RAP1GDS1; GDS1) in human primary T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC118859, MGC118861

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in CAAX-box protein maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in angiotensin-activated signaling pathway involved in heart process IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle hypertrophy IEA
Inferred from Electronic Annotation
more info
  
involved_in myosin filament assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of endoplasmic reticulum calcium ion concentration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of mitochondrial calcium ion concentration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of ERK5 cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of matrix metallopeptidase secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vascular associated smooth muscle contraction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
rap1 GTPase-GDP dissociation stimulator 1
Names
RAP1, GTP-GDP dissociation stimulator 1
SMG GDS protein
SMG P21 stimulatory GDP/GTP exchange protein
exchange factor smgGDS

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_001100426.2 → NP_001093896.1  rap1 GTPase-GDP dissociation stimulator 1 isoform 1

    See identical proteins and their annotated locations for NP_001093896.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC058823, AF215923, AI800264, BC098269, DC367998
    Consensus CDS
    CCDS47105.1
    UniProtKB/TrEMBL
    B3KNU0
    Related
    ENSP00000340454.5, ENST00000339360.9
    Conserved Domains (2) summary
    cd00020
    Location:318 → 431
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    sd00043
    Location:92 → 117
    ARM; armadillo repeat [structural motif]

  2. NM_001100427.2 → NP_001093897.1  rap1 GTPase-GDP dissociation stimulator 1 isoform 3

    See identical proteins and their annotated locations for NP_001093897.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AC058823, AI800264, AK055032, BC098269, DC367998
    Consensus CDS
    CCDS43253.1
    UniProtKB/Swiss-Prot
    E9PH06, G5E9P9, P52306, Q499L7, Q4KMV2, Q4QQI8, Q9BUW9, Q9BUX6, Q9NYM2, Q9NZA8
    UniProtKB/TrEMBL
    B3KNU0
    Related
    ENSP00000386153.4, ENST00000408927.8
    Conserved Domains (2) summary
    cd00020
    Location:317 → 430
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    sd00043
    Location:91 → 116
    ARM; armadillo repeat [structural motif]

  3. NM_001100428.2 → NP_001093898.1  rap1 GTPase-GDP dissociation stimulator 1 isoform 4

    See identical proteins and their annotated locations for NP_001093898.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the mid-coding region, compared to variant 1, resulting in a shorter protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AC058823, AI800264, BC001851, BC099845, DC367998
    Consensus CDS
    CCDS47107.1
    UniProtKB/TrEMBL
    B7Z2V8
    Related
    ENSP00000369503.4, ENST00000380158.8
    Conserved Domains (3) summary
    cd00020
    Location:44 → 163
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    sd00043
    Location:45 → 76
    ARM; armadillo repeat [structural motif]
    cl22454
    Location:391 → 459
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

  4. NM_001100429.2 → NP_001093899.1  rap1 GTPase-GDP dissociation stimulator 1 isoform 5

    See identical proteins and their annotated locations for NP_001093899.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region and lacks an alternate in-frame exon in the mid-coding region, compared to variant 1, resulting in a shorter protein (isoform 5), compared to isoform 1.
    Source sequence(s)
    AC058823, AI800264, BC098334, DC367998
    Consensus CDS
    CCDS43254.1
    UniProtKB/TrEMBL
    B7Z2V8
    Related
    ENSP00000386223.3, ENST00000408900.7
    Conserved Domains (3) summary
    cd00020
    Location:43 → 162
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    sd00043
    Location:44 → 75
    ARM; armadillo repeat [structural motif]
    cl22454
    Location:390 → 458
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

  5. NM_001100430.2 → NP_001093900.1  rap1 GTPase-GDP dissociation stimulator 1 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks two alternate in-frame exons in the mid-coding region, compared to variant 1, resulting in a shorter protein (isoform 6), compared to isoform 1.
    Source sequence(s)
    AC058823, AI800264, AY376900, BC098334, BC099845, DC367998
    Consensus CDS
    CCDS47108.1
    UniProtKB/TrEMBL
    Q6U7G8
    Related
    ENSP00000264572.7, ENST00000264572.11
    Conserved Domains (2) summary
    cd00020
    Location:226 → 339
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    sd00043
    Location:45 → 76
    ARM; armadillo repeat [structural motif]

  6. NM_021159.5 → NP_066982.3  rap1 GTPase-GDP dissociation stimulator 1 isoform 2

    See identical proteins and their annotated locations for NP_066982.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC058823, AI800264, BC001851, BC098269, DC367998
    Consensus CDS
    CCDS47106.1
    UniProtKB/TrEMBL
    B3KNU0
    Related
    ENSP00000407157.2, ENST00000453712.6
    Conserved Domains (2) summary
    cd00020
    Location:318 → 431
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    sd00043
    Location:92 → 117
    ARM; armadillo repeat [structural motif]

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    98261384..98443858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454165.2 → XP_024309933.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X2

    UniProtKB/TrEMBL
    B7Z2V8
    Conserved Domains (5) summary
    smart00185
    Location:298 → 341
    ARM; Armadillo/beta-catenin-like repeats
    pfam00514
    Location:87 → 118
    Arm; Armadillo/beta-catenin-like repeat
    sd00043
    Location:45 → 76
    ARM; armadillo repeat [structural motif]
    cl26969
    Location:178 → 343
    Vitellogenin_N; Lipoprotein amino terminal region
    cl27106
    Location:31 → 216
    PLN03200; cellulose synthase-interactive protein; Provisional

  2. XM_024454164.2 → XP_024309932.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X1

    UniProtKB/TrEMBL
    B3KNU0
    Conserved Domains (3) summary
    sd00043
    Location:91 → 116
    ARM; armadillo repeat [structural motif]
    cl26969
    Location:226 → 391
    Vitellogenin_N; Lipoprotein amino terminal region
    cl27106
    Location:18 → 264
    PLN03200; cellulose synthase-interactive protein; Provisional

  3. XM_024454166.2 → XP_024309934.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X3

    UniProtKB/TrEMBL
    B7Z2V8
    Conserved Domains (5) summary
    smart00185
    Location:297 → 340
    ARM; Armadillo/beta-catenin-like repeats
    pfam00514
    Location:86 → 117
    Arm; Armadillo/beta-catenin-like repeat
    sd00043
    Location:44 → 75
    ARM; armadillo repeat [structural motif]
    cl26969
    Location:177 → 342
    Vitellogenin_N; Lipoprotein amino terminal region
    cl27106
    Location:30 → 215
    PLN03200; cellulose synthase-interactive protein; Provisional

  4. XM_047416051.1 → XP_047272007.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X4

  5. XM_024454168.2 → XP_024309936.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X4

    UniProtKB/TrEMBL
    B7Z4M5
    Conserved Domains (4) summary
    smart00185
    Location:266 → 309
    ARM; Armadillo/beta-catenin-like repeats
    pfam00514
    Location:6 → 37
    Arm; Armadillo/beta-catenin-like repeat
    sd00043
    Location:11 → 36
    ARM; armadillo repeat [structural motif]
    cl27106
    Location:6 → 184
    PLN03200; cellulose synthase-interactive protein; Provisional

  6. XM_047416052.1 → XP_047272008.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    101576339..101758825
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350661.1 → XP_054206636.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X2

  2. XM_054350660.1 → XP_054206635.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X1

  3. XM_054350662.1 → XP_054206637.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X3

  4. XM_054350663.1 → XP_054206638.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X4

  5. XM_054350664.1 → XP_054206639.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X4

  6. XM_054350665.1 → XP_054206640.1  rap1 GTPase-GDP dissociation stimulator 1 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P52306.3 GenPept UniProtKB/Swiss-Prot:P52306

Gene LinkOut

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