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    RASGEF1B RasGEF domain family member 1B [ Homo sapiens (human) ]

    Gene ID: 153020, updated on 11-Apr-2024

    Summary

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    Official Symbol
    RASGEF1Bprovided by HGNC
    Official Full Name
    RasGEF domain family member 1Bprovided by HGNC
    Primary source
    HGNC:HGNC:24881
    See related
    Ensembl:ENSG00000138670 MIM:614532; AllianceGenome:HGNC:24881
    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
    GPIG4
    Summary
    Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity and small GTPase mediated signal transduction. Predicted to be located in early endosome; late endosome; and midbody. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in skin (RPKM 10.2), bone marrow (RPKM 8.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4q21.21
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (81426393..81471907, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (84756088..84801612, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (82347547..82393061, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene protein kinase cGMP-dependent 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:82135909-82136409 Neighboring gene uncharacterized LOC124900726 Neighboring gene RNA, U5A small nuclear 2, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:82296443-82296942 Neighboring gene Sharpr-MPRA regulatory region 8336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15524 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:82407561-82408106 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:82414778-82415977 Neighboring gene uncharacterized LOC105377306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21657 Neighboring gene Sharpr-MPRA regulatory region 9952 Neighboring gene MT-CYB pseudogene 44

    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. Genome-wide association study of white-coat effect in hypertensive patients. Rimpelä JM, et al. Blood Press, 2019 Aug. PMID 31044621
    2. Inducible RasGEF1B circular RNA is a positive regulator of ICAM-1 in the TLR4/LPS pathway. Ng WL, et al. RNA Biol, 2016 Sep. PMID 27362560, Free PMC Article
    3. Identification and characterization of a novel mouse gene encoding a Ras-associated guanine nucleotide exchange factor: expression in macrophages and myocarditis elicited by Trypanosoma cruzi parasites. Ferreira LR, et al. J Leukoc Biol, 2002 Dec. PMID 12488504
    4. 8.6Mb interstitial deletion of chromosome 4q13.3q21.23 in a boy with cognitive impairment, short stature, hearing loss, skeletal abnormalities and facial dysmorphism. Lipska BS, et al. Genet Couns, 2011. PMID 22303795
    5. RasGEF1A and RasGEF1B are guanine nucleotide exchange factors that discriminate between Rap GTP-binding proteins and mediate Rap2-specific nucleotide exchange. Yaman E, et al. FEBS J, 2009 Aug. PMID 19645719

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. study provides evidence for two novel candidate genes, SPG7 and RASGEF1B, associating with white coat effect
      Title: Genome-wide association study of white-coat effect in hypertensive patients.
    2. We show that knockdown of the expression of mcircRasGEF1B reduces LPS-induced ICAM-1 expression. Additionally, we demonstrate that mcircRasGEF1B regulates the stability of mature ICAM-1 mRNAs.
      Title: Inducible RasGEF1B circular RNA is a positive regulator of ICAM-1 in the TLR4/LPS pathway.
    3. As an addition to PRKG2 and RASGEFIB genes, we propose to include BMP3 gene as the principal determinant of the observed common phenotype.
      Title: 8.6Mb interstitial deletion of chromosome 4q13.3q21.23 in a boy with cognitive impairment, short stature, hearing loss, skeletal abnormalities and facial dysmorphism.
    4. Mutation of the Ser39 in Rap1 changed the specificity and allowed the nucleotide exchange of Rap1(S39F) to be stimulated by RasGEF1B
      Title: RasGEF1A and RasGEF1B are guanine nucleotide exchange factors that discriminate between Rap GTP-binding proteins and mediate Rap2-specific nucleotide exchange.
    Submit: New GeneRIF Correction

    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
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ31695, MGC46251

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Ras protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in late endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in midbody IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ras-GEF domain-containing family member 1B
    Names
    GPI gamma-4

    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_001300735.2 → NP_001287664.1  ras-GEF domain-containing family member 1B isoform 2

      See identical proteins and their annotated locations for NP_001287664.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC006287, BC121003, DR002387
      Consensus CDS
      CCDS75152.1
      UniProtKB/TrEMBL
      A8K5Z4
      Related
      ENSP00000425393.1, ENST00000509081.5
      Conserved Domains (2) summary
      cd06224
      Location:42 → 166
      REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
      smart00147
      Location:202 → 453
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases

    2. NM_001300736.2 → NP_001287665.1  ras-GEF domain-containing family member 1B isoform 3

      See identical proteins and their annotated locations for NP_001287665.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AC006287, BC121004, DR002387
      Consensus CDS
      CCDS75151.1
      UniProtKB/TrEMBL
      A8K5Z4
      Related
      ENSP00000338437.7, ENST00000335927.11
      Conserved Domains (2) summary
      pfam00617
      Location:167 → 360
      RasGEF; RasGEF domain
      cl02520
      Location:43 → 125
      REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...

    3. NM_152545.3 → NP_689758.1  ras-GEF domain-containing family member 1B isoform 1

      See identical proteins and their annotated locations for NP_689758.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC006287, AK056257
      Consensus CDS
      CCDS34022.1
      UniProtKB/Swiss-Prot
      Q0VAM1, Q0VAM2, Q4W5L7, Q4W5M3, Q96MY8
      UniProtKB/TrEMBL
      A8K5Z4
      Related
      ENSP00000264400.2, ENST00000264400.7
      Conserved Domains (2) summary
      cd06224
      Location:42 → 167
      REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
      pfam00617
      Location:209 → 403
      RasGEF; RasGEF domain

    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
      81426393..81471907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      84756088..84801612 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0VAM2.2 GenPept UniProtKB/Swiss-Prot:Q0VAM2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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