Aliases for EFCAB3 Gene

Aliases for EFCAB3 Gene

  • EF-Hand Calcium Binding Domain 3 2 3 5
  • EF-Hand Calcium-Binding Domain-Containing Protein 3 3 4
  • FLJ25818 2
  • EFCAB3 5

External Ids for EFCAB3 Gene

Previous GeneCards Identifiers for EFCAB3 Gene

  • GC17P057816
  • GC17P060447
  • GC17P055814
  • GC17P062370

Summaries for EFCAB3 Gene

GeneCards Summary for EFCAB3 Gene

EFCAB3 (EF-Hand Calcium Binding Domain 3) is a Protein Coding gene. Diseases associated with EFCAB3 include Koolen-De Vries Syndrome. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is EFCAB12.

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 EFCAB3 Gene

Genomics for EFCAB3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for EFCAB3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EFCAB3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EFCAB3

Top Transcription factor binding sites by QIAGEN in the EFCAB3 gene promoter:
  • c-Myb
  • FOXJ2
  • FOXJ2 (long isoform)
  • Lhx3a
  • LHX3b
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4

Genomic Locations for EFCAB3 Gene

Latest Assembly
chr17:62,343,941-62,416,480
(GRCh38/hg38)
Size:
72,540 bases
Orientation:
Plus strand

Previous Assembly
chr17:60,447,579-60,493,841
(GRCh37/hg19 by Entrez Gene)
Size:
46,263 bases
Orientation:
Plus strand

chr17:60,447,579-60,493,837
(GRCh37/hg19 by Ensembl)
Size:
46,259 bases
Orientation:
Plus strand

Genomic View for EFCAB3 Gene

Genes around EFCAB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFCAB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFCAB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFCAB3 Gene

Proteins for EFCAB3 Gene

  • Protein details for EFCAB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N7B9-EFCB3_HUMAN
    Recommended name:
    EF-hand calcium-binding domain-containing protein 3
    Protein Accession:
    Q8N7B9
    Secondary Accessions:
    • J3KQM8

    Protein attributes for EFCAB3 Gene

    Size:
    438 amino acids
    Molecular mass:
    50147 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for EFCAB3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EFCAB3 Gene

Post-translational modifications for EFCAB3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EFCAB3 Gene

No data available for DME Specific Peptides for EFCAB3 Gene

Domains & Families for EFCAB3 Gene

Gene Families for EFCAB3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for EFCAB3 Gene

Suggested Antigen Peptide Sequences for EFCAB3 Gene

GenScript: Design optimal peptide antigens:
  • EF-hand calcium-binding domain-containing protein 3 (EFCB3_HUMAN)
genes like me logo Genes that share domains with EFCAB3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for EFCAB3 Gene

Function for EFCAB3 Gene

Phenotypes From GWAS Catalog for EFCAB3 Gene

Gene Ontology (GO) - Molecular Function for EFCAB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with EFCAB3: view
genes like me logo Genes that share phenotypes with EFCAB3: view

Animal Models for EFCAB3 Gene

MGI Knock Outs for EFCAB3:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EFCAB3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for EFCAB3 Gene

Localization for EFCAB3 Gene

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 EFCAB3 gene
Compartment Confidence
nucleus 2
cytosol 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for EFCAB3 Gene

Pathways & Interactions for EFCAB3 Gene

PathCards logo

SuperPathways for EFCAB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EFCAB3 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for EFCAB3 Gene

Drugs & Compounds for EFCAB3 Gene

No Compound Related Data Available

Transcripts for EFCAB3 Gene

mRNA/cDNA for EFCAB3 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
6 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 EFCAB3

Alternative Splicing Database (ASD) splice patterns (SP) for EFCAB3 Gene

No ASD Table

Relevant External Links for EFCAB3 Gene

GeneLoc Exon Structure for
EFCAB3

Expression for EFCAB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EFCAB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for EFCAB3 Gene

This gene is overexpressed in Testis (x50.3).

Protein differential expression in normal tissues from HIPED for EFCAB3 Gene

This gene is overexpressed in Cerebrospinal fluid (68.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for EFCAB3 Gene



Protein tissue co-expression partners for EFCAB3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EFCAB3

SOURCE GeneReport for Unigene cluster for EFCAB3 Gene:

Hs.152670

Evidence on tissue expression from TISSUES for EFCAB3 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with EFCAB3: 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 EFCAB3 Gene

Orthologs for EFCAB3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for EFCAB3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia EFCAB3 29 30
  • 99.39 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia EFCAB3 29 30
  • 87.15 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia EFCAB3 29 30
  • 86.91 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Efcab3 29
  • 76.85 (n)
Mouse
(Mus musculus)
Mammalia Efcab3 29 16 30
  • 76.39 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia EFCAB3 30
  • 33 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia EFCAB3 30
  • 5 (a)
OneToOne
Chicken
(Gallus gallus)
Aves EFCAB3 29
  • 47.59 (n)
-- 30
  • 31 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 40 (a)
OneToMany
Species where no ortholog for EFCAB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for EFCAB3 Gene

ENSEMBL:
Gene Tree for EFCAB3 (if available)
TreeFam:
Gene Tree for EFCAB3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EFCAB3: view image
Alliance of Genome Resources:
Additional Orthologs for EFCAB3

Paralogs for EFCAB3 Gene

(1) SIMAP similar genes for EFCAB3 Gene using alignment to 3 proteins:

  • EFCB3_HUMAN
  • E5RHB1_HUMAN
  • E5RJB7_HUMAN

Pseudogenes.org Pseudogenes for EFCAB3 Gene

genes like me logo Genes that share paralogs with EFCAB3: view

Variants for EFCAB3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EFCAB3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs115800066 Benign: not provided 62,416,121(+) C/T
NM_173503.4(EFCAB3):c.1109C>T (p.Ser370Phe)
MISSENSE
rs116377137 Benign: not provided 62,370,328(+) G/T
NM_001144933.1(EFCAB3):c.34+6G>T
INTRON
rs147289901 Likely Benign: not provided 62,391,835(+) C/T
NM_173503.4(EFCAB3):c.165C>T (p.Ala55=)
SYNONYMOUS
rs61751980 Benign: not provided 62,391,965(+) C/T
NM_173503.4(EFCAB3):c.295C>T (p.Arg99Ter)
NONSENSE
rs6504103 Benign: not provided 62,373,824(+) G/C
NM_001144933.1(EFCAB3):c.45G>C (p.Lys15Asn)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for EFCAB3 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 EFCAB3 Gene

Variant ID Type Subtype PubMed ID
dgv561e199 CNV deletion 23128226
esv2674408 CNV deletion 23128226
esv2758701 CNV gain+loss 17122850
esv3573775 CNV gain 25503493
esv3640971 CNV loss 21293372
esv3640972 CNV loss 21293372
esv3640974 CNV gain 21293372
nsv1109099 CNV deletion 24896259
nsv428350 CNV gain 18775914
nsv476233 CNV novel sequence insertion 20440878
nsv575845 CNV loss 21841781
nsv833508 CNV gain+loss 17160897
nsv962358 CNV duplication 23825009

Variation tolerance for EFCAB3 Gene

Residual Variation Intolerance Score: 71.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.28; 81.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFCAB3 Gene

Human Gene Mutation Database (HGMD)
EFCAB3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFCAB3
Leiden Open Variation Database (LOVD)
EFCAB3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFCAB3 Gene

Disorders for EFCAB3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for EFCAB3 Gene - From: COP

Disorder Aliases PubMed IDs
koolen-de vries syndrome
  • kdvs
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for EFCAB3

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 EFCAB3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EFCAB3 Gene

Publications for EFCAB3 Gene

  1. 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 40
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for EFCAB3 Gene

Sources for EFCAB3 Gene