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

Gene ID: 9901, updated on 3-Apr-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. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 6.5), urinary bladder (RPKM 1.5) and 16 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (8980591..9363027, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (8971761..9354865, complement)
105.20220307 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

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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Related articles in PubMed

  1. A link between the nuclear-localized srGAP3 and the SWI/SNF chromatin remodeler Brg1. Dai YK, et al. Mol Cell Neurosci, 2014 May. PMID 24561795
  2. Interstitial 3p25 deletion in a patient with features of 3p deletion syndrome: further evidence for the role of SRGAP3 in mental retardation. Ellery PM, et al. Clin Dysmorphol, 2014 Jan. PMID 24300292
  3. A tumor suppressor role for srGAP3 in mammary epithelial cells. Lahoz A, et al. Oncogene, 2013 Oct. PMID 23108406
  4. Microarray based analysis of 3p25-p26 deletions (3p- syndrome). Shuib S, et al. Am J Med Genet A, 2009 Oct. PMID 19760623
  5. No association between SRGAP3/MEGAP haploinsufficiency and mental retardation. Hamdan FF, et al. Arch Neurol, 2009 May. PMID 19433673

See all (41) 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)

Genotypes

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
  

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_2023_10

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

  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

  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

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

  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

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

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

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

  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

  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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