EFHC2 Gene (Protein Coding)

EF-Hand Domain Containing 2

GC0XM044146
GIFtS:
35
This gene encodes a protein which contains three DM10 domains and three calcium-binding EF-hand motifs. A related protein is encoded by a gene on chromosome 6. It has been suggested that both proteins are involved in the development of epilepsy (PMID: 15258581, 16112844) and that this gene may be associated with fear recognition in individuals with Turner syndrome. [provided by... See more...

Aliases for EFHC2 Gene

Aliases for EFHC2 Gene

  • EF-Hand Domain Containing 2 2 3 5
  • EF-Hand Domain-Containing Family Member C2 3 4
  • EF-Hand Domain (C-Terminal) Containing 2 2 3
  • Mental Retardation, X-Linked 74 2 3
  • DJ1158H2.1 3
  • FLJ22843 2
  • MRX74 3
  • EFHC2 5

External Ids for EFHC2 Gene

Previous HGNC Symbols for EFHC2 Gene

  • MRX74

Previous GeneCards Identifiers for EFHC2 Gene

  • GC0XM043764
  • GC0XM043892
  • GC0XM044007
  • GC0XM041736

Summaries for EFHC2 Gene

Entrez Gene Summary for EFHC2 Gene

  • This gene encodes a protein which contains three DM10 domains and three calcium-binding EF-hand motifs. A related protein is encoded by a gene on chromosome 6. It has been suggested that both proteins are involved in the development of epilepsy (PMID: 15258581, 16112844) and that this gene may be associated with fear recognition in individuals with Turner syndrome. [provided by RefSeq, Aug 2011]

GeneCards Summary for EFHC2 Gene

EFHC2 (EF-Hand Domain Containing 2) is a Protein Coding gene. Diseases associated with EFHC2 include Turner Syndrome and Norrie Disease. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is EFHC1.

Additional gene information for EFHC2 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EFHC2 Gene

Genomics for EFHC2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for EFHC2 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
GH0XJ044342 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 654.9 -0.4 -395 2.5 RFX1 LEF1 PKNOX1 SOX6 FOXJ2 TCF12 EP300 GTF2E2 ZNF766 EGR1 EFHC2 RF00017-8349 RF00017-8348 FUNDC1
GH0XJ044343 Enhancer 0.2 Ensembl 600.7 +1.4 1371 0.2 EFHC2 RF00017-8349 RF00017-8350 RF00017-8348 NDP
GH0XJ044331 Enhancer 0.5 Ensembl ENCODE 42.9 +11.1 11136 1.6 BHLHE40 NANOG EFHC2 piR-57460-717 RF00017-8349 RF00017-8348 RRM2P3 NDP
GH0XJ044349 Enhancer 0.3 Ensembl ENCODE 51.4 -5.8 -5795 2.1 EFHC2 RF00017-8349 piR-57460-718 RF00017-8348 FUNDC1
GH0XJ044312 Enhancer 1.3 FANTOM5 Ensembl ENCODE 10.7 +29.4 29426 4.1 LEF1 IKZF1 JUND MTA2 PHF21A PKNOX1 ZNF24 REST BRD9 DPF2 EFHC2 KDM6A MAOB RRM2P3 RF00017-8348 piR-57460-717 NDP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EFHC2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EFHC2

Top Transcription factor binding sites by QIAGEN in the EFHC2 gene promoter:
  • CUTL1
  • MIF-1
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • POU2F1
  • POU2F1a
  • RFX1

Genomic Locations for EFHC2 Gene

Genomic Locations for EFHC2 Gene
chrX:44,146,254-44,343,672
(GRCh38/hg38)
Size:
197,419 bases
Orientation:
Minus strand
chrX:44,007,128-44,202,923
(GRCh37/hg19)
Size:
195,796 bases
Orientation:
Minus strand

Genomic View for EFHC2 Gene

Genes around EFHC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFHC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFHC2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for EFHC2 Gene

Proteins for EFHC2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for EFHC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5JST6-EFHC2_HUMAN
    Recommended name:
    EF-hand domain-containing family member C2
    Protein Accession:
    Q5JST6
    Secondary Accessions:
    • Q5JST8
    • Q68DK4
    • Q8NEI0
    • Q9H653

    Protein attributes for EFHC2 Gene

    Size:
    749 amino acids
    Molecular mass:
    87397 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for EFHC2 Gene

    Alternative splice isoforms for EFHC2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EFHC2 Gene

Protein Expression for EFHC2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for EFHC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EFHC2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EFHC2 Gene

Domains & Families for EFHC2 Gene

Gene Families for EFHC2 Gene

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

Protein Domains for EFHC2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EFHC2 Gene

GenScript: Design optimal peptide antigens:
  • EF-hand domain (C-terminal) containing 2 (B1AL25_HUMAN)
  • EF-hand domain-containing family member C2 (EFHC2_HUMAN)
genes like me logo Genes that share domains with EFHC2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for EFHC2 Gene

Function for EFHC2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for EFHC2 Gene

Gene Ontology (GO) - Molecular Function for EFHC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0043014 alpha-tubulin binding IBA 21873635
genes like me logo Genes that share ontologies with EFHC2: view
genes like me logo Genes that share phenotypes with EFHC2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EFHC2

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EFHC2 Gene

Localization for EFHC2 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 EFHC2 gene
Compartment Confidence
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EFHC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005874 colocalizes_with microtubule IBA 21873635
GO:0005930 axoneme IBA 21873635
GO:0072686 mitotic spindle IBA 21873635
genes like me logo Genes that share ontologies with EFHC2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for EFHC2 Gene

Pathways & Interactions for EFHC2 Gene

PathCards logo

SuperPathways for EFHC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EFHC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000281 mitotic cytokinesis IBA 21873635
GO:0007052 mitotic spindle organization IBA 21873635
GO:0010975 regulation of neuron projection development IBA 21873635
GO:0060285 cilium-dependent cell motility IBA 21873635
GO:1990830 cellular response to leukemia inhibitory factor IEA --
genes like me logo Genes that share ontologies with EFHC2: view

No data available for Pathways by source and SIGNOR curated interactions for EFHC2 Gene

Drugs & Compounds for EFHC2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for EFHC2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for EFHC2 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EFHC2

Alternative Splicing Database (ASD) splice patterns (SP) for EFHC2 Gene

No ASD Table

Relevant External Links for EFHC2 Gene

GeneLoc Exon Structure for
EFHC2

Expression for EFHC2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EFHC2 Gene

mRNA expression in normal human tissues for EFHC2 Gene
mRNA expression by GTEx for EFHC2 GenemRNA expression by BioGPS for EFHC2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for EFHC2 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for EFHC2 Gene



Protein tissue co-expression partners for EFHC2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EFHC2

SOURCE GeneReport for Unigene cluster for EFHC2 Gene:

Hs.521953

Evidence on tissue expression from TISSUES for EFHC2 Gene

  • Intestine(4)
genes like me logo Genes that share expression patterns with EFHC2: 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 EFHC2 Gene

Orthologs for EFHC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for EFHC2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia EFHC2 30 31
  • 99.73 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia EFHC2 30 31
  • 84.29 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia EFHC2 30
  • 83.63 (n)
Rat
(Rattus norvegicus)
 Mammalia Efhc2 30
  • 81.3 (n)
Mouse
(Mus musculus)
 Mammalia Efhc2 30 17 31
  • 80.41 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 68 (a)
 OneToMany
-- 31
  • 57 (a)
 OneToMany
Oppossum
(Monodelphis domestica)
 Mammalia EFHC2 31
  • 58 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves EFHC2 30 31
  • 65.23 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia EFHC2 31
  • 55 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia efhc2 30
  • 62.48 (n)
Zebrafish
(Danio rerio)
 Actinopterygii efhc2 30 31
  • 59.72 (n)
 OneToOne
Dr.13820 30
Fruit Fly
(Drosophila melanogaster)
 Insecta Efhc1.2 30 31
  • 45.68 (n)
 OneToMany
Efhc1.1 31
  • 30 (a)
 OneToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP003339 30
  • 44.6 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.3980 31
  • 51 (a)
 OneToOne
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.1550 30
Species where no ortholog for EFHC2 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 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)
  • Worm (Caenorhabditis elegans)

Evolution for EFHC2 Gene

ENSEMBL:
Gene Tree for EFHC2 (if available)
TreeFam:
Gene Tree for EFHC2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EFHC2: view image

Paralogs for EFHC2 Gene

Paralogs for EFHC2 Gene

(1) SIMAP similar genes for EFHC2 Gene using alignment to 1 proteins:

  • EFHC2_HUMAN
genes like me logo Genes that share paralogs with EFHC2: view

Variants for EFHC2 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EFHC2 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
787518 Benign: not provided 44,312,629(-) C/T MISSENSE_VARIANT
rs201560745 Uncertain Significance: not provided 44,261,277(-) C/T MISSENSE_VARIANT
rs3747354 Benign: not specified. - 44,232,582(-) C/Gp.Glu507Gln MISSENSE_VARIANT
rs17146914 - p.Asn31Ser
rs2208592 - p.Ser430Tyr

Additional dbSNP identifiers (rs#s) for EFHC2 Gene

Structural Variations from Database of Genomic Variants (DGV) for EFHC2 Gene

Variant ID Type Subtype PubMed ID
esv33270 CNV gain 17666407

Variation tolerance for EFHC2 Gene

Residual Variation Intolerance Score: 91.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.14; 61.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFHC2 Gene

Human Gene Mutation Database (HGMD)
EFHC2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFHC2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFHC2 Gene

Disorders for EFHC2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for EFHC2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
turner syndrome
  • ts
norrie disease
  • nd
leukocoria
  • leucocoria
adolescence-adult electroclinical syndrome
epilepsy
  • epilepsy syndrome
- elite association - COSMIC cancer census association via MalaCards
Search EFHC2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EFHC2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with EFHC2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EFHC2 Gene

Publications for EFHC2 Gene

  1. Preliminary evidence of association between EFHC2, a gene implicated in fear recognition, and harm avoidance. (PMID: 19429002) Blaya C … Smoller JW (Neuroscience letters 2009) 3 41
  2. EFHC2 SNP rs7055196 is not associated with fear recognition in 45,X Turner syndrome. (PMID: 17948898) Zinn AR … Ross JL (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 41
  3. Mutation frequencies of X-linked mental retardation genes in families from the EuroMRX consortium. (PMID: 17221867) de Brouwer AP … Hamel BC (Human mutation 2007) 2 3
  4. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4
  5. A new EF-hand containing gene EFHC2 on Xp11.4: tentative evidence for association with juvenile myoclonic epilepsy. (PMID: 16112844) Gu W … Steinlein OK (Epilepsy research 2005) 3 4

ExternalLinks

View latest publications for EFHC2 gene in Mastermind

Products for EFHC2 Gene

  • Addgene plasmids for EFHC2

Sources for EFHC2 Gene