Aliases for EFR3B Gene

Aliases for EFR3B Gene

  • EFR3 Homolog B 2 3 5
  • KIAA0953 2 3 4
  • Protein EFR3 Homolog B 3 4
  • EFR3 Homolog B (S. Cerevisiae) 2
  • FLJ37871 2
  • EFR3B 5

External Ids for EFR3B Gene

Previous HGNC Symbols for EFR3B Gene

  • KIAA0953

Previous GeneCards Identifiers for EFR3B Gene

  • GC02P025118
  • GC02P025264

Summaries for EFR3B Gene

GeneCards Summary for EFR3B Gene

EFR3B (EFR3 Homolog B) is a Protein Coding gene. Diseases associated with EFR3B include Gastrointestinal Defects And Immunodeficiency Syndrome and Hypomyelinating Leukoencephalopathy. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is EFR3A.

UniProtKB/Swiss-Prot Summary for EFR3B Gene

  • Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:25608530, PubMed:26571211). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, EFR3B probably acts as the membrane-anchoring component (PubMed:23229899). Also involved in responsiveness to G-protein-coupled receptors; it is however unclear whether this role is direct or indirect (PubMed:25380825).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EFR3B Gene

Genomics for EFR3B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for EFR3B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J025041 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +0.5 461 2.8 CHD2 ZBTB10 MXD4 ZNF217 ELF1 CTCF ZIC2 REST ZNF639 VEZF1 EFR3B lnc-DNAJC27-1 ADCY3 lnc-CENPO-4-001 POMC
GH02J025119 Promoter 0.3 EPDnew 261.4 +77.5 77490 0.1 EFR3B LINC01381 POMC DNAJC27 DNAJC27-AS1 ENSG00000202479 RPS13P5 piR-43105-341 piR-46939
GH02J024970 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 24.6 -69.8 -69809 3.9 CHD2 TBP ZBTB10 SP1 MXD4 CEBPA NR2C1 MNT IKZF1 BRCA1 DNAJC27-AS1 DNAJC27 lnc-ADCY3-3 ADCY3 EFR3B FKBP1B DTNB LINC01381 POMC PTRHD1
GH02J024791 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 13.3 -248.6 -248577 4.7 TBP SP1 ZBTB10 MXD4 CEBPA SIX5 NR2C1 MNT IKZF1 SMAD5 PTRHD1 CENPO HSALNG0013620 LOC105369164 lnc-ADCY3-1 ATAD2B FKBP1B EFR3B DTNB WDCP
GH02J024045 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 13.2 -993.6 -993641 5.5 CHD2 TBP MXD4 SP1 CEBPA SIX5 MNT IKZF1 SMAD5 ETS1 WDCP FKBP1B ATAD2B FAM228B SF3B6 ITSN2 EFR3B PFN4 MFSD2B TP53I3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EFR3B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EFR3B

Top Transcription factor binding sites by QIAGEN in the EFR3B gene promoter:
  • AML1a
  • Arnt
  • FOXJ2
  • FOXJ2 (long isoform)
  • GATA-1
  • POU2F1
  • POU2F1a
  • Zic1

Genomic Locations for EFR3B Gene

Latest Assembly
chr2:25,042,076-25,159,137
(GRCh38/hg38)
Size:
117,062 bases
Orientation:
Plus strand

Previous Assembly
chr2:25,264,945-25,382,004
(GRCh37/hg19 by Entrez Gene)
Size:
117,060 bases
Orientation:
Plus strand

chr2:25,264,999-25,378,243
(GRCh37/hg19 by Ensembl)
Size:
113,245 bases
Orientation:
Plus strand

Genomic View for EFR3B Gene

Genes around EFR3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFR3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFR3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFR3B Gene

Proteins for EFR3B Gene

  • Protein details for EFR3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2G0-EFR3B_HUMAN
    Recommended name:
    Protein EFR3 homolog B
    Protein Accession:
    Q9Y2G0
    Secondary Accessions:
    • B7WPL8
    • Q86XU6

    Protein attributes for EFR3B Gene

    Size:
    817 amino acids
    Molecular mass:
    92487 Da
    Quaternary structure:
    • Component of a phosphatidylinositol 4-kinase (PI4K) complex, composed of PI4KA, EFR3 (EFR3A or EFR3B), TTC7 (TTC7A or TTC7B) and FAM126 (FAM126A or FAM126B).
    SequenceCaution:
    • Sequence=BAA76797.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for EFR3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EFR3B Gene

Post-translational modifications for EFR3B Gene

  • Palmitoylated at its N-terminus, anchoring the protein to the plasma membrane.
  • Ubiquitination at Lys38
  • Modification sites at PhosphoSitePlus

Other Protein References for EFR3B Gene

No data available for DME Specific Peptides for EFR3B Gene

Domains & Families for EFR3B Gene

Gene Families for EFR3B Gene

Protein Domains for EFR3B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EFR3B Gene

GenScript: Design optimal peptide antigens:
  • Protein EFR3 homolog B (EFR3B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y2G0

UniProtKB/Swiss-Prot:

EFR3B_HUMAN :
  • Belongs to the EFR3 family.
Family:
  • Belongs to the EFR3 family.
genes like me logo Genes that share domains with EFR3B: view

Function for EFR3B Gene

Molecular function for EFR3B Gene

UniProtKB/Swiss-Prot Function:
Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:25608530, PubMed:26571211). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, EFR3B probably acts as the membrane-anchoring component (PubMed:23229899). Also involved in responsiveness to G-protein-coupled receptors; it is however unclear whether this role is direct or indirect (PubMed:25380825).

Phenotypes From GWAS Catalog for EFR3B Gene

Gene Ontology (GO) - Molecular Function for EFR3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 23229899
genes like me logo Genes that share ontologies with EFR3B: view
genes like me logo Genes that share phenotypes with EFR3B: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EFR3B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EFR3B Gene

Localization for EFR3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFR3B Gene

Cell membrane. Lipid-anchor. Cytoplasm, cytosol. Note=Palmitoylation anchors the protein to the plasma membrane (PubMed:23229899, PubMed:25380825). A small amount is observed in the cytosol (PubMed:25380825). {ECO:0000269 PubMed:23229899, ECO:0000269 PubMed:25380825}.

Subcellular locations from

COMPARTMENTS
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 EFR3B gene
Compartment Confidence
plasma membrane 5
cytoskeleton 4
cytosol 4
nucleus 2
endoplasmic reticulum 1
endosome 1
golgi apparatus 1
extracellular 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
  • Actin filaments (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EFR3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA 23229899
GO:0015629 actin cytoskeleton IDA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with EFR3B: view

Pathways & Interactions for EFR3B Gene

PathCards logo

SuperPathways for EFR3B Gene

No Data Available

Gene Ontology (GO) - Biological Process for EFR3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046854 phosphatidylinositol phosphorylation IDA 23229899
GO:0072659 protein localization to plasma membrane IDA 23229899
genes like me logo Genes that share ontologies with EFR3B: view

No data available for Pathways by source and SIGNOR curated interactions for EFR3B Gene

Drugs & Compounds for EFR3B Gene

No Compound Related Data Available

Transcripts for EFR3B Gene

mRNA/cDNA for EFR3B Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
5 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 EFR3B

Alternative Splicing Database (ASD) splice patterns (SP) for EFR3B Gene

No ASD Table

Relevant External Links for EFR3B Gene

GeneLoc Exon Structure for
EFR3B

Expression for EFR3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EFR3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for EFR3B Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.5) and Brain - Nucleus accumbens (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for EFR3B Gene

This gene is overexpressed in Frontal cortex (33.8) and Brain (30.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EFR3B Gene



Protein tissue co-expression partners for EFR3B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EFR3B

SOURCE GeneReport for Unigene cluster for EFR3B Gene:

Hs.4892

Evidence on tissue expression from TISSUES for EFR3B Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with EFR3B: 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 EFR3B Gene

Orthologs for EFR3B Gene

This gene was present in the common ancestor of animals.

Orthologs for EFR3B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia EFR3B 30 31
  • 97.76 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia EFR3B 31
  • 95 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 68 (a)
OneToMany
-- 31
  • 51 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia EFR3B 30 31
  • 91.8 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia EFR3B 30 31
  • 91.55 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Efr3b 30
  • 90.06 (n)
Mouse
(Mus musculus)
Mammalia Efr3b 30 17 31
  • 90.04 (n)
OneToOne
Chicken
(Gallus gallus)
Aves EFR3B 30 31
  • 82.21 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 96 (a)
OneToMany
-- 31
  • 83 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia efr3b 30
  • 78.12 (n)
Zebrafish
(Danio rerio)
Actinopterygii efr3ba 31
  • 75 (a)
OneToMany
efr3bb 30 31
  • 74.55 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012183 30
  • 53.13 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta stmA 30 31
  • 51.48 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea C32D5.3 30 31
  • 50.03 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 38 (a)
OneToMany
Species where no ortholog for EFR3B 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 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 EFR3B Gene

ENSEMBL:
Gene Tree for EFR3B (if available)
TreeFam:
Gene Tree for EFR3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EFR3B: view image

Paralogs for EFR3B Gene

Paralogs for EFR3B Gene

(1) SIMAP similar genes for EFR3B Gene using alignment to 3 proteins:

  • EFR3B_HUMAN
  • E7ESK9_HUMAN
  • H7BXG9_HUMAN
genes like me logo Genes that share paralogs with EFR3B: view

Variants for EFR3B Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for EFR3B 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 EFR3B Gene

Variant ID Type Subtype PubMed ID
dgv57n68 CNV loss 17160897
esv1006182 OTHER inversion 20482838
esv24844 CNV gain 19812545
esv2666849 CNV deletion 23128226
esv2762426 CNV loss 21179565
esv33372 CNV loss 17666407
esv3590085 CNV gain 21293372
esv3590086 CNV loss 21293372
esv3590087 CNV loss 21293372
esv3590089 CNV loss 21293372
nsv1008732 CNV loss 25217958
nsv1133465 CNV deletion 24896259
nsv2647 CNV insertion 18451855
nsv997725 CNV gain 25217958

Variation tolerance for EFR3B Gene

Gene Damage Index Score: 1.72; 32.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFR3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFR3B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EFR3B Gene

Disorders for EFR3B Gene

MalaCards: The human disease database

(2) MalaCards diseases for EFR3B Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search EFR3B in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EFR3B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with EFR3B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EFR3B Gene

Publications for EFR3B Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  2. The leukodystrophy protein FAM126A (hyccin) regulates PtdIns(4)P synthesis at the plasma membrane. (PMID: 26571211) Baskin JM … De Camilli P (Nature cell biology 2016) 3 4
  3. EFR3s are palmitoylated plasma membrane proteins that control responsiveness to G-protein-coupled receptors. (PMID: 25380825) Bojjireddy N … Balla T (Journal of cell science 2015) 3 4
  4. PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. (PMID: 23229899) Nakatsu F … De Camilli P (The Journal of cell biology 2012) 3 4
  5. A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. (PMID: 21980299) Bradfield JP … Hakonarson H (PLoS genetics 2011) 3 41

Products for EFR3B Gene

Sources for EFR3B Gene