Free for academic non-profit institutions. Other users need a Commercial license

Aliases for EFR3A Gene

Aliases for EFR3A Gene

  • EFR3 Homolog A 2 3 5
  • EFR3 Homolog A (S. Cerevisiae) 2
  • Protein EFR3-Like 4
  • KIAA0143 4

External Ids for EFR3A Gene

Previous GeneCards Identifiers for EFR3A Gene

  • GC08P132985
  • GC08P128233

Summaries for EFR3A Gene

Entrez Gene Summary for EFR3A Gene

  • The protein encoded by this gene is part of a complex that plays a role in maintaining an active pool of phosphatidylinositol 4-kinase (PI4K) at the plasma membrane. This protein is thought to be a peripheral membrane protein that associates with the plasma membrane through palmitoylation. Studies indicate that this gene product plays a role in controlling G protein-coupled receptor (GPCR) activity by affecting receptor phosphorylation. Whole exome sequencing studies have implicated mutations in this gene with autism spectrum disorders. [provided by RefSeq, Apr 2016]

GeneCards Summary for EFR3A Gene

EFR3A (EFR3 Homolog A) is a Protein Coding gene. Diseases associated with EFR3A include Autism. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is EFR3B.

UniProtKB/Swiss-Prot for EFR3A 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, EFR3A 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).

Additional gene information for EFR3A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EFR3A Gene

Genomics for EFR3A Gene

GeneHancer (GH) Regulatory Elements for EFR3A Gene

Promoters and enhancers for EFR3A 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
GH08I131903 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 555.8 +1.1 1110 4.4 PKNOX1 SMAD1 ATF1 FOXA2 ZFP64 SIN3A ZBTB7B YY1 ZNF766 ZNF207 EFR3A GC08P131997
GH08I131814 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.9 -88.1 -88087 4 PKNOX1 SMAD1 BMI1 BATF IRF4 RFX5 ZNF766 SMARCC2 ATF7 FOS EFR3A GC08M131865 LOC100420215
GH08I131946 Enhancer 0.7 ENCODE 19 +42.9 42938 2 BACH1 EBF1 BATF ZNF316 ATF7 NFE2 IKZF2 RUNX3 MAFK NFE2L2 EFR3A GC08P131997
GH08I131855 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 8.3 -46.6 -46618 3 SIN3A RFX5 RCOR1 FOS CREM SMARCC1 USF2 CEBPB REST SMARCB1 EFR3A HHLA1 GC08M131865 LOC100420215
GH08I131915 Enhancer 1.1 Ensembl ENCODE 5.2 +13.0 12999 2.6 HDGF FOXA2 YY1 ATF7 FOS RXRA JUNB REST KAT8 MEF2D EFR3A GC08P131997
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EFR3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EFR3A gene promoter:

Genomic Locations for EFR3A Gene

Genomic Locations for EFR3A Gene
109,555 bases
Plus strand

Genomic View for EFR3A Gene

Genes around EFR3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFR3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFR3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFR3A Gene

Proteins for EFR3A Gene

  • Protein details for EFR3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein EFR3 homolog A
    Protein Accession:
    Secondary Accessions:
    • A7MD19
    • Q2VPK2
    • Q63HL7
    • Q68DX1
    • Q6IQ18

    Protein attributes for EFR3A Gene

    821 amino acids
    Molecular mass:
    92924 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) (PubMed:26571211).
    • Sequence=AAH71611.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAI08668.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAI08668.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA09764.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for EFR3A Gene


neXtProt entry for EFR3A Gene

Post-translational modifications for EFR3A Gene

  • Palmitoylated at its N-terminus, anchoring the protein to the plasma membrane.
  • Ubiquitination at posLast=3939 and Lys50

No data available for DME Specific Peptides for EFR3A Gene

Domains & Families for EFR3A Gene

Gene Families for EFR3A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for EFR3A Gene


Suggested Antigen Peptide Sequences for EFR3A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the EFR3 family.
  • Belongs to the EFR3 family.
genes like me logo Genes that share domains with EFR3A: view

Function for EFR3A Gene

Molecular function for EFR3A 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, EFR3A 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 EFR3A Gene

genes like me logo Genes that share phenotypes with EFR3A: view

miRNA for EFR3A Gene

miRTarBase miRNAs that target EFR3A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EFR3A Gene

Localization for EFR3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFR3A Gene

Cell membrane; Lipid-anchor. Cytoplasm, cytosol. Note=Palmitoylation anchors the protein to the plasma membrane (PubMed:23229899, PubMed:25380825, PubMed:26571211). A small amount is observed in the cytosol (PubMed:25380825). {ECO:0000269 PubMed:23229899, ECO:0000269 PubMed:25380825, ECO:0000269 PubMed:26571211}.

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 EFR3A gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 5
mitochondrion 2
peroxisome 1
nucleus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for EFR3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA,IDA --
GO:0005886 plasma membrane IDA,IEA 23229899
GO:0016020 membrane IEA --
GO:0070062 extracellular exosome IDA,HDA 23376485
genes like me logo Genes that share ontologies with EFR3A: view

Pathways & Interactions for EFR3A Gene

SuperPathways for EFR3A Gene

No Data Available

Gene Ontology (GO) - Biological Process for EFR3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046854 phosphatidylinositol phosphorylation TAS 23229899
GO:0072659 protein localization to plasma membrane IMP 23229899
genes like me logo Genes that share ontologies with EFR3A: view

No data available for Pathways by source and SIGNOR curated interactions for EFR3A Gene

Drugs & Compounds for EFR3A Gene

No Compound Related Data Available

Transcripts for EFR3A Gene

Unigene Clusters for EFR3A Gene

EFR3 homolog A (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EFR3A Gene

No ASD Table

Relevant External Links for EFR3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for EFR3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EFR3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for EFR3A Gene

This gene is overexpressed in Placenta (12.2), Peripheral blood mononuclear cells (8.7), and Bone (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EFR3A Gene

Protein tissue co-expression partners for EFR3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EFR3A Gene:


SOURCE GeneReport for Unigene cluster for EFR3A Gene:


Evidence on tissue expression from TISSUES for EFR3A Gene

  • Eye(4.3)
  • Bone marrow(4.2)
  • Skin(4.2)
  • Nervous system(3.6)
genes like me logo Genes that share expression patterns with EFR3A: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EFR3A Gene

Orthologs for EFR3A Gene

This gene was present in the common ancestor of animals.

Orthologs for EFR3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia EFR3A 33 34
  • 99.72 (n)
(Bos Taurus)
Mammalia -- 34
  • 98 (a)
EFR3A 34
  • 96 (a)
(Canis familiaris)
Mammalia EFR3A 33 34
  • 94.68 (n)
(Rattus norvegicus)
Mammalia Efr3a 33
  • 90.19 (n)
(Mus musculus)
Mammalia Efr3a 33 16 34
  • 90.15 (n)
(Monodelphis domestica)
Mammalia EFR3A 34
  • 90 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 90 (a)
-- 34
  • 83 (a)
(Gallus gallus)
Aves EFR3A 33 34
  • 81.06 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 84 (a)
-- 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia efr3a 33
  • 72.17 (n)
(Danio rerio)
Actinopterygii efr3a 33 34 34
  • 69.89 (n)
zgc73123 33
fruit fly
(Drosophila melanogaster)
Insecta stmA 34
  • 37 (a)
(Caenorhabditis elegans)
Secernentea C32D5.3 34
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
Species where no ortholog for EFR3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 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 EFR3A Gene

Gene Tree for EFR3A (if available)
Gene Tree for EFR3A (if available)

Paralogs for EFR3A Gene

Paralogs for EFR3A Gene

(1) SIMAP similar genes for EFR3A Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with EFR3A: view

Variants for EFR3A Gene

Sequence variations from dbSNP and Humsavar for EFR3A Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000010424 -- 131,935,004(+) T/A intron_variant
rs1000035937 -- 131,982,218(+) A/G intron_variant
rs1000106299 -- 131,937,637(+) T/C intron_variant
rs1000109436 -- 131,963,167(+) A/G intron_variant
rs1000148439 -- 131,992,700(+) C/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EFR3A Gene

Variant ID Type Subtype PubMed ID
dgv7315n100 CNV loss 25217958
dgv7316n100 CNV loss 25217958
esv2421701 CNV deletion 20811451
esv2657891 CNV deletion 23128226
esv3306172 CNV mobile element insertion 20981092
esv3307044 CNV mobile element insertion 20981092
esv3339818 CNV insertion 20981092
esv33463 CNV loss 17666407
esv3378397 CNV insertion 20981092
esv3392034 CNV insertion 20981092
esv3618853 CNV gain 21293372
esv3618864 CNV loss 21293372
nsv1017148 CNV loss 25217958
nsv1018172 CNV gain 25217958
nsv1023761 CNV loss 25217958
nsv396604 CNV insertion 16902084
nsv397361 CNV deletion 16902084
nsv442123 CNV loss 18776908
nsv473091 CNV novel sequence insertion 20440878
nsv612325 CNV gain 21841781

Variation tolerance for EFR3A Gene

Residual Variation Intolerance Score: 27.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.52; 64.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFR3A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFR3A Gene

Disorders for EFR3A Gene

MalaCards: The human disease database

(1) MalaCards diseases for EFR3A Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
  • autistic disorder
- elite association - COSMIC cancer census association via MalaCards
Search EFR3A in MalaCards View complete list of genes associated with diseases


  • Note=Genetic variations in EFR3A may be associated with susceptibility to autism. {ECO:0000305 PubMed:24860643}.

Additional Disease Information for EFR3A

genes like me logo Genes that share disorders with EFR3A: view

No data available for Genatlas for EFR3A Gene

Publications for EFR3A Gene

  1. 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 58
  2. 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 58
  3. Rare deleterious mutations of the gene EFR3A in autism spectrum disorders. (PMID: 24860643) Gupta AR … State MW (Molecular autism 2014) 3 4 58
  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 58
  5. Mouse homolog of KIAA0143 protein: hearing deficit induces specific changes of expression in auditory brainstem neurons. (PMID: 15363888) Munemoto Y … Sugimoto T (Brain research. Molecular brain research 2004) 2 3 58

Products for EFR3A Gene

Sources for EFR3A Gene

Loading form....