Aliases for GARNL3 Gene

Aliases for GARNL3 Gene

  • GTPase Activating Rap/RanGAP Domain Like 3 2 3 5
  • GTPase-Activating Rap/Ran-GAP Domain-Like Protein 3 3 4
  • GTPase Activating RANGAP Domain-Like 3 2 3
  • BA356B19.1 2 3
  • GTPase Activating Rap/RanGAP Domain-Like 3 2
  • DKFZp761J1523 2
  • GARNL3 5

External Ids for GARNL3 Gene

Previous GeneCards Identifiers for GARNL3 Gene

  • GC09P125403
  • GC09P127106
  • GC09P129045
  • GC09P129987
  • GC09P099642

Summaries for GARNL3 Gene

GeneCards Summary for GARNL3 Gene

GARNL3 (GTPase Activating Rap/RanGAP Domain Like 3) is a Protein Coding gene. Diseases associated with GARNL3 include Developmental And Epileptic Encephalopathy 4 and Nail-Patella Syndrome. Gene Ontology (GO) annotations related to this gene include GTPase activator activity. An important paralog of this gene is SIPA1L1.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GARNL3 Gene

Genomics for GARNL3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for GARNL3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J127223 Promoter/Enhancer 1.6 Ensembl ENCODE CraniofacialAtlas 256.7 +0.8 836 2.6 SP1 ZBTB10 MNT MBD2 CTCF BHLHE40 NONO ZIC2 ZNF610 SIN3A GARNL3 lnc-RALGPS1-1 lnc-RALGPS1-2 DNM1 STXBP1 NAIF1 SLC2A8
GH09J127264 Promoter 0.3 EPDnew 250.3 +40.3 40295 0.1 lnc-RALGPS1-3 GARNL3 RF00017-7921 SLC2A8
GH09J127392 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.2 +171.5 171469 7.1 CHD2 SP1 MXD4 CEBPA NR2C1 FOXA1 MNT BRCA1 SMAD5 ZFP64 SLC2A8 DNM1 STXBP1 ZNF79 ENSG00000207955 ENSG00000228487 GARNL3 SNORA65 CIZ1 RPL12
GH09J127714 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 10 +491.2 491222 2.7 CHD2 SP1 MXD4 CEBPA SIX5 NR2C1 MNT DEK SMAD5 ETS1 TTC16 lnc-TOR2A-3 PTRH1 GLE1 ZNF79 ENSG00000228510 GARNL3 TOR2A piR-47980 CFAP157
GH09J128124 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10 +903.0 903047 5.4 TBP SP1 MXD4 NR2C1 MNT IKZF1 SMAD5 ETS1 ZNF217 CTCF SLC25A25-AS1 PTGES2 PTGES2-AS1 GLE1 ENSG00000234055 ZNF79 ENSG00000228510 GARNL3 URM1 piR-38005-063
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GARNL3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GARNL3

Top Transcription factor binding sites by QIAGEN in the GARNL3 gene promoter:
  • AP-1
  • c-Fos
  • Chx10
  • E47
  • Evi-1
  • GATA-1
  • MRF-2
  • POU3F2
  • STAT5A
  • Tal-1beta

Genomic Locations for GARNL3 Gene

Latest Assembly
169,396 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
129,762 bases
Plus strand

(GRCh37/hg19 by Ensembl)
169,396 bases
Plus strand

Genomic View for GARNL3 Gene

Genes around GARNL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GARNL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GARNL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GARNL3 Gene

Proteins for GARNL3 Gene

  • Protein details for GARNL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    GTPase-activating Rap/Ran-GAP domain-like protein 3
    Protein Accession:
    Secondary Accessions:
    • B4DEP7
    • B7Z3Q6
    • Q8IYU1
    • Q8N951
    • Q8ND89
    • Q9BQH6

    Protein attributes for GARNL3 Gene

    1013 amino acids
    Molecular mass:
    112852 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH34983.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAB66508.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GARNL3 Gene


neXtProt entry for GARNL3 Gene

Post-translational modifications for GARNL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GARNL3 Gene

Domains & Families for GARNL3 Gene

Gene Families for GARNL3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for GARNL3 Gene

  • Citron-like
  • Rap/ran-GAP

Suggested Antigen Peptide Sequences for GARNL3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59309, highly similar to Homo sapiens GTPase activating Rap/RanGAP domain-like 3 (GARNL3), mRNA (B7Z3Q6_HUMAN)
  • GTPase-activating Rap/Ran-GAP domain-like protein 3 (GARL3_HUMAN)
  • GTPase activating Rap/RanGAP domain-like 3 (Q5VVW4_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the GARNL3 family.
  • Belongs to the GARNL3 family.
genes like me logo Genes that share domains with GARNL3: view

Function for GARNL3 Gene

Phenotypes From GWAS Catalog for GARNL3 Gene

Gene Ontology (GO) - Molecular Function for GARNL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA,IBA 21873635
genes like me logo Genes that share ontologies with GARNL3: view
genes like me logo Genes that share phenotypes with GARNL3: view

miRNA for GARNL3 Gene

miRTarBase miRNAs that target GARNL3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GARNL3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GARNL3 Gene

Localization for GARNL3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GARNL3 gene
Compartment Confidence
cytosol 3
cytoskeleton 1
mitochondrion 1
nucleus 1
extracellular 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GARNL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with GARNL3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for GARNL3 Gene

Pathways & Interactions for GARNL3 Gene

PathCards logo

SuperPathways for GARNL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for GARNL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043547 positive regulation of GTPase activity IEA --
GO:0051056 regulation of small GTPase mediated signal transduction IEA --
GO:0090630 activation of GTPase activity IBA 21873635
genes like me logo Genes that share ontologies with GARNL3: view

No data available for Pathways by source and SIGNOR curated interactions for GARNL3 Gene

Drugs & Compounds for GARNL3 Gene

No Compound Related Data Available

Transcripts for GARNL3 Gene

mRNA/cDNA for GARNL3 Gene

11 NCBI additional mRNA sequence :
22 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GARNL3

Alternative Splicing Database (ASD) splice patterns (SP) for GARNL3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b ^
SP1: - - -
SP2: - - - -

ExUns: 20 ^ 21a · 21b · 21c ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29a · 29b ^ 30a · 30b · 30c ^ 31 ^ 32a · 32b
SP1: - - - - - -
SP3: - - -
SP4: - -
SP8: -

Relevant External Links for GARNL3 Gene

GeneLoc Exon Structure for

Expression for GARNL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GARNL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GARNL3 Gene

This gene is overexpressed in Brain - Cerebellum (x4.6) and Brain - Cerebellar Hemisphere (x4.3).

Protein differential expression in normal tissues from HIPED for GARNL3 Gene

This gene is overexpressed in Pancreatic juice (47.3), Peripheral blood mononuclear cells (13.4), and Fetal Brain (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for GARNL3 Gene

Protein tissue co-expression partners for GARNL3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GARNL3

SOURCE GeneReport for Unigene cluster for GARNL3 Gene:


Evidence on tissue expression from TISSUES for GARNL3 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with GARNL3: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GARNL3 Gene

Orthologs for GARNL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for GARNL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia GARNL3 30 31
  • 99.61 (n)
(Bos Taurus)
Mammalia GARNL3 30 31
  • 92.05 (n)
(Canis familiaris)
Mammalia GARNL3 30 31
  • 91.51 (n)
(Mus musculus)
Mammalia Garnl3 30 17 31
  • 88.97 (n)
(Monodelphis domestica)
Mammalia GARNL3 31
  • 86 (a)
(Rattus norvegicus)
Mammalia Garnl3 30
  • 85.18 (n)
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 84 (a)
-- 31
  • 81 (a)
(Gallus gallus)
Aves GARNL3 30 31
  • 76.8 (n)
(Anolis carolinensis)
Reptilia GARNL3 31
  • 80 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia garnl3 30
  • 73.09 (n)
(Danio rerio)
Actinopterygii GARNL3 31
  • 79 (a)
garnl3 30
  • 68.9 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002573 30
  • 56.52 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG42629 31
  • 18 (a)
(Caenorhabditis elegans)
Secernentea sipa-1 31
  • 17 (a)
Species where no ortholog for GARNL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for GARNL3 Gene

Gene Tree for GARNL3 (if available)
Gene Tree for GARNL3 (if available)
Evolutionary constrained regions (ECRs) for GARNL3: view image

Paralogs for GARNL3 Gene

Paralogs for GARNL3 Gene

genes like me logo Genes that share paralogs with GARNL3: view

Variants for GARNL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GARNL3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs11550746 - p.His108Arg
rs34608132 - p.Ala752Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for GARNL3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for GARNL3 Gene

Variant ID Type Subtype PubMed ID
esv24866 CNV loss 19812545
esv2492436 CNV deletion 19546169
esv2676607 CNV deletion 23128226
esv2739049 CNV deletion 23290073
esv3303990 CNV mobile element insertion 20981092
esv3446884 CNV insertion 20981092
esv3621777 CNV loss 21293372
esv3621778 CNV loss 21293372
esv3621780 CNV loss 21293372
nsv1042177 CNV loss 25217958
nsv516966 CNV gain+loss 19592680
nsv521594 CNV loss 19592680
nsv523364 CNV loss 19592680
nsv525053 CNV loss 19592680
nsv527127 CNV gain 19592680

Variation tolerance for GARNL3 Gene

Residual Variation Intolerance Score: 9.03% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.77; 33.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GARNL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GARNL3 Gene

Disorders for GARNL3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for GARNL3 Gene - From: CVR and COP

Disorder Aliases PubMed IDs
developmental and epileptic encephalopathy 4
  • dee4
nail-patella syndrome
  • nps
stxbp1 encephalopathy
  • dee4
dravet syndrome
  • drvt
early infantile epileptic encephalopathy
  • early infantile epileptic encephalopathy with burst-suppression
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for GARNL3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with GARNL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GARNL3 Gene

Publications for GARNL3 Gene

  1. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. (PMID: 18711365) Ferreira MA … Wellcome Trust Case Control Consortium (Nature genetics 2008) 3 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3

Products for GARNL3 Gene

Sources for GARNL3 Gene