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

Gene ID: 84253, updated on 3-Apr-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
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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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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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