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

Gene ID: 9411, updated on 2-Nov-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
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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: 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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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

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

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

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

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