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    ARHGAP29 Rho GTPase activating protein 29 [ Homo sapiens (human) ]

    Gene ID: 9411, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ARHGAP29provided by HGNC
    Official Full Name
    Rho GTPase activating protein 29provided by HGNC
    Primary source
    HGNC:HGNC:30207
    See related
    Ensembl:ENSG00000137962 MIM:610496; AllianceGenome:HGNC:30207
    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
    PARG1
    Summary
    Rap1 is a small GTPase that, through effectors, regulates Rho GTPase signaling. These effectors- Rasip1, Radil, and the protein encoded by this gene- translocate to the cell membrane, where they form a multiprotein complex. This complex is necessary for Rap1-induced inhibition of Rho signaling. Defects in this gene may be a cause of nonsyndromic cleft lip with or without cleft palate. [provided by RefSeq, Jun 2016]
    Expression
    Broad expression in lung (RPKM 15.0), thyroid (RPKM 13.9) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARHGAP29 in Genome Data Viewer
    Location:
    1p22.1-p21.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (94168905..94314592, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94017108..94123270, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (94634461..94713302, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378858 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 7015 Neighboring gene RNA, 7SL, cytoplasmic 440, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:94660072-94660283 Neighboring gene NANOG hESC enhancer GRCh37_chr1:94664929-94665459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1093 Neighboring gene ARHGAP29 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1094 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:94736061-94737260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1346 Neighboring gene Sharpr-MPRA regulatory region 2220 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 29 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:94792875-94793386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:94883134-94883925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1347 Neighboring gene ATP binding cassette subfamily D member 3 Neighboring gene ribosomal protein L21 pseudogene 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1097 Neighboring gene coagulation factor III, tissue factor

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. ARHGAP29 Is Involved in Increased Invasiveness of Tamoxifen-resistant Breast Cancer Cells and its Expression Levels Correlate With Clinical Tumor Parameters of Breast Cancer Patients. Kansy M, et al. Cancer Genomics Proteomics, 2024 Jul-Aug. PMID 38944420, Free PMC Article
    2. Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate. Liu H, et al. Birth Defects Res, 2017 Jan 20. PMID 28029220, Free PMC Article
    3. Impact of rare variants in ARHGAP29 to the etiology of oral clefts: role of loss-of-function vs missense variants. Savastano CP, et al. Clin Genet, 2017 May. PMID 27350171
    4. Further evidence suggesting a role for variation in ARHGAP29 variants in nonsyndromic cleft lip/palate. Letra A, et al. Birth Defects Res A Clin Mol Teratol, 2014 Sep. PMID 25163644, Free PMC Article
    5. ARHGAP29 expression may be a novel prognostic factor of cell proliferation and invasion in prostate cancer. Shimizu K, et al. Oncol Rep, 2020 Dec. PMID 33125156

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ARHGAP29 Is Involved in Increased Invasiveness of Tamoxifen-resistant Breast Cancer Cells and its Expression Levels Correlate With Clinical Tumor Parameters of Breast Cancer Patients.
      Title: ARHGAP29 Is Involved in Increased Invasiveness of Tamoxifen-resistant Breast Cancer Cells and its Expression Levels Correlate With Clinical Tumor Parameters of Breast Cancer Patients.
    2. TBX21 attenuates colorectal cancer progression via an ARHGAP29/RSK/GSK3beta dependent manner.
      Title: TBX21 attenuates colorectal cancer progression via an ARHGAP29/RSK/GSK3β dependent manner.
    3. ARHGAP29 expression may be a novel prognostic factor of cell proliferation and invasion in prostate cancer.
      Title: ARHGAP29 expression may be a novel prognostic factor of cell proliferation and invasion in prostate cancer.
    4. Influence of ARHGAP29 on the Invasion of Mesenchymal-Transformed Breast Cancer Cells.
      Title: Influence of ARHGAP29 on the Invasion of Mesenchymal-Transformed Breast Cancer Cells.
    5. Identification of a Novel Variant of ARHGAP29 in a Chinese Family with Nonsyndromic Cleft Lip and Palate.
      Title: Identification of a Novel Variant of ARHGAP29 in a Chinese Family with Nonsyndromic Cleft Lip and Palate.
    6. The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts.
      Title: The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts.
    7. Risk haplotypes affect ARHGAP29 expression causing non-syndromic orofacial clefting.
      Title: Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting.
    8. The variant in question segregates as an autosomal dominant trait caused by an heterozygous missense variant in ARHGAP29 (p.Ser552Pro) that had not previously been identified in a population genomic databases. The p.Ser552Pro ARHGAP29 variant was not present in genomic databases and was predicted to be pathogenic by multiple in silico programs.
      Title: Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate.
    9. YAP promotes the expression of ARHGAP29 to suppress the RhoA-LIMK-cofilin pathway, destabilizing F-actin.
      Title: YAP Regulates Actin Dynamics through ARHGAP29 and Promotes Metastasis.
    10. The of loss-of-function and ARHGAP29 missense variants in the etiology of oral clefts
      Title: Impact of rare variants in ARHGAP29 to the etiology of oral clefts: role of loss-of-function vs missense variants.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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
    Genetic predictors of fibrin D-dimer levels in healthy adults.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    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)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity TAS
    Traceable Author Statement
    more info
    		  
    enables PDZ domain binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Rho protein signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of small GTPase mediated signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of small GTPase mediated signal transduction TAS
    Traceable Author Statement
    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
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    rho GTPase-activating protein 29
    Names
    PTPL1-associated RhoGAP 1 (PARG1)
    PTPL1-associated RhoGAP protein 1
    rho-type GTPase-activating protein 29

    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

    1. NG_050965.2 RefSeqGene

      Range
      82008..150687
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001328664.2 → NP_001315593.1  rho GTPase-activating protein 29 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC097059, AL162735
      Consensus CDS
      CCDS748.1
      UniProtKB/Swiss-Prot
      O15463, Q52LW3, Q59H86, Q5VYZ0, Q6NVX2, Q8TBI6
      UniProtKB/TrEMBL
      F8VWZ8
      Conserved Domains (3) summary
      smart00109
      Location:612 → 657
      C1; Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains)
      cd04409
      Location:669 → 881
      RhoGAP_PARG1; RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts ...
      cl12013
      Location:220 → 436
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. NM_001328665.2 → NP_001315594.1  rho GTPase-activating protein 29 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a. Variants 3 and 5 both encode the same isoform (b).
      Source sequence(s)
      AC097059, AL162735
      Conserved Domains (3) summary
      cd04409
      Location:605 → 817
      RhoGAP_PARG1; RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts ...
      pfam00130
      Location:549 → 594
      C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
      cl12013
      Location:156 → 372
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    3. NM_001328666.2 → NP_001315595.1  rho GTPase-activating protein 29 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AL162735
      UniProtKB/TrEMBL
      F8VWZ8

    4. NM_001328667.2 → NP_001315596.1  rho GTPase-activating protein 29 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate 5' exon compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a. Variants 3 and 5 both encode the same isoform (b).
      Source sequence(s)
      AL162735
      Conserved Domains (3) summary
      cd04409
      Location:605 → 817
      RhoGAP_PARG1; RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts ...
      pfam00130
      Location:549 → 594
      C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
      cl12013
      Location:156 → 372
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    5. NM_004815.4 → NP_004806.3  rho GTPase-activating protein 29 isoform a

      See identical proteins and their annotated locations for NP_004806.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AL162735, BC093767, BF115799
      Consensus CDS
      CCDS748.1
      UniProtKB/Swiss-Prot
      O15463, Q52LW3, Q59H86, Q5VYZ0, Q6NVX2, Q8TBI6
      UniProtKB/TrEMBL
      F8VWZ8
      Related
      ENSP00000260526.6, ENST00000260526.11
      Conserved Domains (3) summary
      smart00109
      Location:612 → 657
      C1; Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains)
      cd04409
      Location:669 → 881
      RhoGAP_PARG1; RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts ...
      cl12013
      Location:220 → 436
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    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

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      94168905..94314592 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434759.1 → XP_047290715.1  rho GTPase-activating protein 29 isoform X1

      UniProtKB/Swiss-Prot
      O15463, Q52LW3, Q59H86, Q5VYZ0, Q6NVX2, Q8TBI6
      UniProtKB/TrEMBL
      F8VWZ8

    2. XM_047434754.1 → XP_047290710.1  rho GTPase-activating protein 29 isoform X1

      UniProtKB/Swiss-Prot
      O15463, Q52LW3, Q59H86, Q5VYZ0, Q6NVX2, Q8TBI6
      UniProtKB/TrEMBL
      F8VWZ8

    3. XM_011542439.3 → XP_011540741.1  rho GTPase-activating protein 29 isoform X1

      See identical proteins and their annotated locations for XP_011540741.1

      UniProtKB/Swiss-Prot
      O15463, Q52LW3, Q59H86, Q5VYZ0, Q6NVX2, Q8TBI6
      UniProtKB/TrEMBL
      F8VWZ8
      Conserved Domains (3) summary
      smart00109
      Location:612 → 657
      C1; Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains)
      cd04409
      Location:669 → 881
      RhoGAP_PARG1; RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts ...
      cl12013
      Location:220 → 436
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      94017108..94123270 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339679.1 → XP_054195654.1  rho GTPase-activating protein 29 isoform X1

      UniProtKB/TrEMBL
      A0A2X0U4J5, F8VWZ8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q52LW3.2 GenPept UniProtKB/Swiss-Prot:Q52LW3

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