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    SRGAP3 SLIT-ROBO Rho GTPase activating protein 3 [ Homo sapiens (human) ]

    Gene ID: 9901, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SRGAP3provided by HGNC
    Official Full Name
    SLIT-ROBO Rho GTPase activating protein 3provided by HGNC
    Primary source
    HGNC:HGNC:19744
    See related
    Ensembl:ENSG00000196220 MIM:606525; AllianceGenome:HGNC:19744
    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
    WRP; MEGAP; SRGAP2; ARHGAP14
    Summary
    Predicted to enable GTPase activator activity. Predicted to be involved in negative regulation of cell migration and regulation of postsynapse assembly. Is active in postsynapse. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in brain (RPKM 6.5), urinary bladder (RPKM 1.5) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SRGAP3 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (8980591..9363027, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (8971761..9354865, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9022275..9291330, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984112 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:8911034-8912233 Neighboring gene small nucleolar RNA SNORA43 Neighboring gene RAD18 E3 ubiquitin protein ligase Neighboring gene Sharpr-MPRA regulatory region 4351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19395 Neighboring gene Sharpr-MPRA regulatory region 3594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9028728-9029228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9029229-9029729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9038453-9038952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9119367-9119867 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:9146925-9147681 Neighboring gene uncharacterized LOC124909343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19396 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:9221274-9221774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9244405-9244905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9243904-9244404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9245577-9246081 Neighboring gene SRGAP3 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19397 Neighboring gene SRGAP3 antisense RNA 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19398 Neighboring gene SRGAP3 antisense RNA 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19400 Neighboring gene phosphoglycerate mutase 1 pseudogene 4 Neighboring gene THUMPD3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19403 Neighboring gene Sharpr-MPRA regulatory region 11896 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:9444537-9445037 Neighboring gene THUMP domain containing 3 Neighboring gene SET domain containing 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The novel Rho-GTPase activating gene MEGAP/ srGAP3 has a putative role in severe mental retardation. Endris V, et al. Proc Natl Acad Sci U S A, 2002 Sep 3. PMID 12195014, Free PMC Article
    2. MEGAP impedes cell migration via regulating actin and microtubule dynamics and focal complex formation. Yang Y, et al. Exp Cell Res, 2006 Jul 15. PMID 16730001
    3. No association between SRGAP3/MEGAP haploinsufficiency and mental retardation. Hamdan FF, et al. Arch Neurol, 2009 May. PMID 19433673
    4. Microarray based analysis of 3p25-p26 deletions (3p- syndrome). Shuib S, et al. Am J Med Genet A, 2009 Oct. PMID 19760623
    5. A tumor suppressor role for srGAP3 in mammary epithelial cells. Lahoz A, et al. Oncogene, 2013 Oct. PMID 23108406

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population.
      Title: C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population.
    2. A single PXXP motif in the C-terminal region of srGAP3 mediates binding to multiple SH3 domains.
      Title: A single PXXP motif in the C-terminal region of srGAP3 mediates binding to multiple SH3 domains.
    3. Nuclear-localized srGAP3 interacts with Brg1. This interaction is mediated by the C-terminal of srGAP3 and the ATPase motif of Brg1.
      Title: A link between the nuclear-localized srGAP3 and the SWI/SNF chromatin remodeler Brg1.
    4. deletion of SRGAP3 provides the most convincing explanation for our patient's phenotype, and our observations lend further weight to a causative role of SRGAP3 haploinsufficiency in mental retardation.
      Title: Interstitial 3p25 deletion in a patient with features of 3p deletion syndrome: further evidence for the role of SRGAP3 in mental retardation.
    5. conclude that srGAP3 has tumor suppressor-like activity in HMECs, likely through its activity as a negative regulator of Rac1
      Title: A tumor suppressor role for srGAP3 in mammary epithelial cells.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    8. Current evidence suggests that SRGAP3 is the major determinant of mental retardation in distal 3p deletions.
      Title: Microarray based analysis of 3p25-p26 deletions (3p- syndrome).
    9. We found no association between SRGAP3/MEGAP haploinsufficiency and mental retardation.
      Title: No association between SRGAP3/MEGAP haploinsufficiency and mental retardation.
    10. putative role in severe mental retardation
      Title: The novel Rho-GTPase activating gene MEGAP/ srGAP3 has a putative role in severe mental retardation.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0411

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of small GTPase mediated signal transduction TAS
    Traceable Author Statement
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in postsynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in postsynapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SLIT-ROBO Rho GTPase-activating protein 3
    Names
    SLIT-ROBO Rho GTPase activating protein 2
    WAVE-associated Rac GTPase activating protein
    mental disorder-associated GAP
    rho GTPase-activating protein 14

    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_001033117.3 → NP_001028289.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform b

      See identical proteins and their annotated locations for NP_001028289.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AF464189, AK054831, BM976179, DA532895
      Consensus CDS
      CCDS33689.1
      UniProtKB/TrEMBL
      A0A2X0U4U8
      Related
      ENSP00000353587.3, ENST00000360413.7
      Conserved Domains (3) summary
      cd07684
      Location:26 → 278
      F-BAR_srGAP3; The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3
      cd11955
      Location:724 → 776
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:481 → 665
      RhoGAP_srGAP; RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an ...

    2. NM_014850.4 → NP_055665.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform a

      See identical proteins and their annotated locations for NP_055665.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AF427144, AK054831, BM976179, DA532895
      Consensus CDS
      CCDS2572.1
      UniProtKB/Swiss-Prot
      O43295, Q8IX13, Q8IZV8
      UniProtKB/TrEMBL
      A0A2X0U4U8
      Related
      ENSP00000373347.3, ENST00000383836.8
      Conserved Domains (3) summary
      cd07684
      Location:26 → 278
      F-BAR_srGAP3; The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3
      cd11955
      Location:748 → 800
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:502 → 689
      RhoGAP_srGAP; RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an ...

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      8980591..9363027 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453843.2 → XP_024309611.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X7

      UniProtKB/TrEMBL
      A0A2X0U4U8
      Conserved Domains (3) summary
      cd11955
      Location:633 → 685
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:390 → 574
      RhoGAP_srGAP; RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an ...
      cl12013
      Location:1 → 158
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. XM_047449335.1 → XP_047305291.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X11

    3. XM_047449333.1 → XP_047305289.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X6

      UniProtKB/TrEMBL
      A0A2X0U4U8

    4. XM_024453842.2 → XP_024309610.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X5

      UniProtKB/TrEMBL
      A0A2X0U4U8
      Conserved Domains (3) summary
      cd11955
      Location:732 → 784
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:489 → 673
      RhoGAP_srGAP; RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs ...
      cl12013
      Location:26 → 257
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    5. XM_047449336.1 → XP_047305292.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X12

    6. XM_047449334.1 → XP_047305290.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X10

    7. XM_011534295.3 → XP_011532597.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011532597.1

      UniProtKB/TrEMBL
      A0A2X0U4U8
      Conserved Domains (3) summary
      cd07684
      Location:26 → 278
      F-BAR_srGAP3; The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3
      cd11955
      Location:753 → 805
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:510 → 694
      RhoGAP_srGAP; RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs ...

    8. XM_011534296.3 → XP_011532598.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X4

      UniProtKB/TrEMBL
      A0A2X0U4U8
      Conserved Domains (3) summary
      cd07684
      Location:7 → 259
      F-BAR_srGAP3; The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3
      cd11955
      Location:734 → 786
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:491 → 675
      RhoGAP_srGAP; RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs ...

    9. XM_017007575.2 → XP_016863064.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A2X0U4U8

    10. XM_017007574.2 → XP_016863063.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A2X0U4U8

    11. XM_017007579.2 → XP_016863068.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X9

    12. XM_011534301.4 → XP_011532603.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X8

      UniProtKB/TrEMBL
      A0A2X0U4U8
      Conserved Domains (3) summary
      cd11955
      Location:590 → 642
      SH3_srGAP1-3; Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3
      cd04383
      Location:347 → 531
      RhoGAP_srGAP; RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs ...
      cl12013
      Location:1 → 115
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    13. XM_047449337.1 → XP_047305293.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X13

    14. XM_047449338.1 → XP_047305294.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X14

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      8971761..9354865 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348602.1 → XP_054204577.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X7

      UniProtKB/TrEMBL
      A0A2X0U4U8

    2. XM_054348606.1 → XP_054204581.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X11

    3. XM_054348601.1 → XP_054204576.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X6

      UniProtKB/TrEMBL
      A0A2X0U4U8

    4. XM_054348600.1 → XP_054204575.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X5

      UniProtKB/TrEMBL
      A0A2X0U4U8

    5. XM_054348607.1 → XP_054204582.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X12

    6. XM_054348605.1 → XP_054204580.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X10

    7. XM_054348597.1 → XP_054204572.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A2X0U4U8

    8. XM_054348599.1 → XP_054204574.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X4

      UniProtKB/TrEMBL
      A0A2X0U4U8

    9. XM_054348598.1 → XP_054204573.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A2X0U4U8

    10. XM_054348596.1 → XP_054204571.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A2X0U4U8

    11. XM_054348604.1 → XP_054204579.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X9

    12. XM_054348603.1 → XP_054204578.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X8

      UniProtKB/TrEMBL
      A0A2X0U4U8

    13. XM_054348608.1 → XP_054204583.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X13

    14. XM_054348609.1 → XP_054204584.1  SLIT-ROBO Rho GTPase-activating protein 3 isoform X14

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001033116.1: Suppressed sequence

      Description
      NM_001033116.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43295.3 GenPept UniProtKB/Swiss-Prot:O43295

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