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    GARNL3 GTPase activating Rap/RanGAP domain like 3 [ Homo sapiens (human) ]

    Gene ID: 84253, updated on 5-May-2024

    Summary

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    Official Symbol
    GARNL3provided by HGNC
    Official Full Name
    GTPase activating Rap/RanGAP domain like 3provided by HGNC
    Primary source
    HGNC:HGNC:25425
    See related
    Ensembl:ENSG00000136895 AllianceGenome:HGNC:25425
    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
    bA356B19.1
    Summary
    Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 5.0), heart (RPKM 3.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q33.3
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127224613..127393660)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139431005..139600139)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130026178..130155939)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Ral GEF with PH domain and SH3 binding motif 1 Neighboring gene uncharacterized LOC105376278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129943177-129943676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129946409-129946979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129948384-129948884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129957118-129957618 Neighboring gene Sharpr-MPRA regulatory region 1494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129961533-129962521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129969788-129970288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129970289-129970789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129972323-129972840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129974395-129974912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129978722-129979222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129979223-129979723 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129981929-129982488 Neighboring gene uncharacterized LOC124902273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129985710-129986210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129986211-129986711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20300 Neighboring gene uncharacterized LOC124902274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29037 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130047596-130047803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20301 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:130094714-130095913 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:130098321-130099520 Neighboring gene DENR pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 1510 Neighboring gene uncharacterized LOC124902275 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130146967-130147700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130168662-130169228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130180180-130180827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130180828-130181474 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:130185748-130186690 Neighboring gene solute carrier family 2 member 8 Neighboring gene zinc finger protein 79

    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. Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. Ferreira MA, et al. Nat Genet, 2008 Sep. PMID 18711365, Free PMC Article
    2. F-box only protein 9 is an E3 ubiquitin ligase of PPARγ. Lee KW, et al. Exp Mol Med, 2016 May 20. PMID 27197753, Free PMC Article
    3. The global gene-expression profiles of U-937 human macrophages treated with Tat peptide and Tat-FITC conjugate. Lin CW, et al. J Drug Target, 2012 Jul. PMID 22632162
    4. Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. Luykx JJ, et al. Mol Psychiatry, 2014 Feb. PMID 23319000
    5. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? Nathan JA, et al. EMBO J, 2013 Feb 20. PMID 23314748, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    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
    Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat FITC-labeled Tat 47-59 peptide downregulates gene expression of GTPase activating Rap/RanGAP domain-like 3 (GARNL3) in U-937 macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38360, DKFZp434O131, DKFZp761J1523

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of small GTPase mediated 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
    		  

    General protein information

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    Preferred Names
    GTPase-activating Rap/Ran-GAP domain-like protein 3
    Names
    GTPase activating RANGAP domain-like 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001286779.2 → NP_001273708.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform b

      See identical proteins and their annotated locations for NP_001273708.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AK296246, AL445222, BC034983
      Consensus CDS
      CCDS69663.1
      UniProtKB/Swiss-Prot
      Q5VVW2
      Related
      ENSP00000396205.2, ENST00000435213.6
      Conserved Domains (2) summary
      pfam00780
      Location:471 → 775
      CNH; CNH domain
      pfam02145
      Location:199 → 377
      Rap_GAP; Rap/ran-GAP

    2. NM_032293.5 → NP_115669.3  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform a

      See identical proteins and their annotated locations for NP_115669.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AK293732, AL445222, BC034983, DA183830
      Consensus CDS
      CCDS6869.2
      UniProtKB/Swiss-Prot
      B4DEP7, B7Z3Q6, Q5VVW2, Q8IYU1, Q8N951, Q8ND89, Q9BQH6
      Related
      ENSP00000362485.4, ENST00000373387.9
      Conserved Domains (2) summary
      pfam00780
      Location:493 → 797
      CNH; CNH domain
      pfam02145
      Location:221 → 399
      Rap_GAP; Rap/ran-GAP

    RNA

    1. NR_104591.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL136573, AL445222, BC034983, DA406716
      Related
      ENST00000373386.6

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      127224613..127393660
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423963.1 → XP_047279919.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X3

    2. XM_011519086.4 → XP_011517388.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011517388.1

      Conserved Domains (2) summary
      pfam00780
      Location:542 → 846
      CNH; CNH domain
      pfam02145
      Location:270 → 448
      Rap_GAP; Rap/ran-GAP

    3. XM_005252268.3 → XP_005252325.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X3

      See identical proteins and their annotated locations for XP_005252325.1

      Conserved Domains (2) summary
      pfam00780
      Location:516 → 820
      CNH; CNH domain
      pfam02145
      Location:244 → 422
      Rap_GAP; Rap/ran-GAP

    4. XM_047423967.1 → XP_047279923.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X7

    5. XM_047423966.1 → XP_047279922.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X6

    6. XM_005252267.4 → XP_005252324.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X1

      Conserved Domains (2) summary
      pfam00780
      Location:556 → 860
      CNH; CNH domain
      pfam02145
      Location:284 → 462
      Rap_GAP; Rap/ran-GAP

    7. XM_011519087.3 → XP_011517389.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011517389.1

      Conserved Domains (2) summary
      pfam00780
      Location:542 → 846
      CNH; CNH domain
      pfam02145
      Location:270 → 448
      Rap_GAP; Rap/ran-GAP

    8. XM_047423964.1 → XP_047279920.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    9. XM_011519090.3 → XP_011517392.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      See identical proteins and their annotated locations for XP_011517392.1

      UniProtKB/TrEMBL
      B4DH81
      Conserved Domains (2) summary
      pfam00780
      Location:324 → 628
      CNH; CNH domain
      pfam02145
      Location:52 → 230
      Rap_GAP; Rap/ran-GAP

    10. XM_024447694.2 → XP_024303462.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81
      Conserved Domains (2) summary
      pfam00780
      Location:324 → 628
      CNH; CNH domain
      pfam02145
      Location:52 → 230
      Rap_GAP; Rap/ran-GAP

    11. XM_024447696.2 → XP_024303464.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81
      Conserved Domains (2) summary
      pfam00780
      Location:324 → 628
      CNH; CNH domain
      pfam02145
      Location:52 → 230
      Rap_GAP; Rap/ran-GAP

    12. XM_047423965.1 → XP_047279921.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    13. XM_047423968.1 → XP_047279924.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X8

    14. XM_017015202.2 → XP_016870691.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      139431005..139600139
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363969.1 → XP_054219944.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X2

    2. XM_054363967.1 → XP_054219942.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X1

    3. XM_054363968.1 → XP_054219943.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X2

    4. XM_054363977.1 → XP_054219952.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X7

    5. XM_054363976.1 → XP_054219951.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X6

    6. XM_054363974.1 → XP_054219949.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    7. XM_054363973.1 → XP_054219948.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    8. XM_054363972.1 → XP_054219947.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    9. XM_054363971.1 → XP_054219946.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    10. XM_054363975.1 → XP_054219950.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X5

      UniProtKB/TrEMBL
      B4DH81

    11. XM_054363978.1 → XP_054219953.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X8

    12. XM_054363970.1 → XP_054219945.1  GTPase-activating Rap/Ran-GAP domain-like protein 3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VVW2.2 GenPept UniProtKB/Swiss-Prot:Q5VVW2

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