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Aliases for EFHC1 Gene

Aliases for EFHC1 Gene

  • EF-Hand Domain Containing 1 2 3 5
  • Myoclonin-1 2 3 4
  • EF-Hand Domain (C-Terminal) Containing 1 2 3
  • EF-Hand Domain-Containing Protein 1 3
  • Epilepsy, Juvenile Myoclonic 1 2
  • DJ304B14.2 3
  • EJM1 3

External Ids for EFHC1 Gene

Previous HGNC Symbols for EFHC1 Gene

  • EJM1
  • EJM

Previous GeneCards Identifiers for EFHC1 Gene

  • GC00U991099
  • GC06U900420
  • GC06P052331
  • GC06P052393
  • GC06P052116
  • GC06P052284
  • GC06P052420

Summaries for EFHC1 Gene

Entrez Gene Summary for EFHC1 Gene

  • This gene encodes an EF-hand-containing calcium binding protein. The encoded protein likely plays a role in calcium homeostasis. Mutations in this gene have been associated with susceptibility to juvenile myoclonic epilepsy and juvenile absence epilepsy. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

GeneCards Summary for EFHC1 Gene

EFHC1 (EF-Hand Domain Containing 1) is a Protein Coding gene. Diseases associated with EFHC1 include Myoclonic Epilepsy, Juvenile 1 and Epilepsy, Juvenile Absence 1. GO annotations related to this gene include calcium ion binding and protein C-terminus binding. An important paralog of this gene is EFHC2.

UniProtKB/Swiss-Prot for EFHC1 Gene

  • Necessary for radial and tangential cell migration during brain development, possibly acting as a regulator of cell morphology and process formation during migration (PubMed:22926142). May enhance calcium influx through CACNA1E and stimulate programmed cell death (PubMed:15258581).

Gene Wiki entry for EFHC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EFHC1 Gene

Genomics for EFHC1 Gene

Regulatory Elements for EFHC1 Gene

Enhancers for EFHC1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G052388 2.4 VISTA FANTOM5 Ensembl ENCODE dbSUPER 17.8 +28.1 28069 3.7 HDGF FOXA2 MLX ARID4B FEZF1 YY1 ZNF766 CBX5 FOS JUNB EFHC1 PAQR8 MCM3 SLC25A20P1 IL17F PIR61259
GH06G052396 1.7 FANTOM5 Ensembl ENCODE dbSUPER 18.5 +37.1 37102 4.8 FOXA2 ARID4B FEZF1 ZNF2 ZNF48 SLC30A9 ZNF143 REST TSHZ1 PPARG MCM3 EFHC1 PAQR8 SLC25A20P1 IL17F PIR61259
GH06G052393 1.3 FANTOM5 ENCODE dbSUPER 19.5 +32.2 32202 1.4 PKNOX1 USF1 WRNIP1 ZIC2 ZBTB40 RELA ARID3A POLR2A NFYB EED EFHC1 MCM3 PAQR8 PIR61259
GH06G052593 2 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +234.4 234378 6.0 HNRNPUL1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF766 ZNF143 EFHC1 LOC730101 TRAM2 PIR56752 TRAM2-AS1
GH06G052563 2 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +209.1 209096 14.5 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 TRAM2-AS1 EFHC1 MCM3 PAQR8 LOC730101 TRAM2 GC06P052544
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around EFHC1 on UCSC Golden Path with GeneCards custom track

Promoters for EFHC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000197873 377 1801 HDGF PKNOX1 AGO1 SIN3A DMAP1 SLC30A9 CBX5 ZNF143 ZNF207 FOS

Genomic Location for EFHC1 Gene

Chromosome:
6
Start:
52,362,123 bp from pter
End:
52,529,886 bp from pter
Size:
167,764 bases
Orientation:
Plus strand

Genomic View for EFHC1 Gene

Genes around EFHC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFHC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFHC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFHC1 Gene

Proteins for EFHC1 Gene

  • Protein details for EFHC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5JVL4-EFHC1_HUMAN
    Recommended name:
    EF-hand domain-containing protein 1
    Protein Accession:
    Q5JVL4
    Secondary Accessions:
    • B4DMU3
    • F5GZD8
    • Q5XKM4
    • Q6E1U7
    • Q6E1U8
    • Q8WUL2
    • Q9NVW6

    Protein attributes for EFHC1 Gene

    Size:
    640 amino acids
    Molecular mass:
    73990 Da
    Quaternary structure:
    • Interacts with the C-terminus of CACNA1E.

    Alternative splice isoforms for EFHC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EFHC1 Gene

Post-translational modifications for EFHC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for EFHC1 Gene

Domains & Families for EFHC1 Gene

Gene Families for EFHC1 Gene

Protein Domains for EFHC1 Gene

Suggested Antigen Peptide Sequences for EFHC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with EFHC1: view

No data available for UniProtKB/Swiss-Prot for EFHC1 Gene

Function for EFHC1 Gene

Molecular function for EFHC1 Gene

UniProtKB/Swiss-Prot Function:
Necessary for radial and tangential cell migration during brain development, possibly acting as a regulator of cell morphology and process formation during migration (PubMed:22926142). May enhance calcium influx through CACNA1E and stimulate programmed cell death (PubMed:15258581).

Gene Ontology (GO) - Molecular Function for EFHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0008022 protein C-terminus binding ISS --
genes like me logo Genes that share ontologies with EFHC1: view
genes like me logo Genes that share phenotypes with EFHC1: view

Human Phenotype Ontology for EFHC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for EFHC1 Gene

MGI Knock Outs for EFHC1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for EFHC1 Gene

Localization for EFHC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFHC1 Gene

Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cytoplasm, cytoskeleton, spindle.

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 EFHC1 gene
Compartment Confidence
cytoskeleton 5
plasma membrane 3
cytosol 3
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for EFHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 22926142
GO:0005815 microtubule organizing center IEA --
GO:0005819 spindle IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with EFHC1: view

Pathways & Interactions for EFHC1 Gene

SuperPathways for EFHC1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EFHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0021795 cerebral cortex cell migration IMP 22926142
genes like me logo Genes that share ontologies with EFHC1: view

No data available for Pathways by source and SIGNOR curated interactions for EFHC1 Gene

Drugs & Compounds for EFHC1 Gene

(1) Drugs for EFHC1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with EFHC1: view

Transcripts for EFHC1 Gene

Unigene Clusters for EFHC1 Gene

EF-hand domain (C-terminal) containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EFHC1 Gene

No ASD Table

Relevant External Links for EFHC1 Gene

GeneLoc Exon Structure for
EFHC1
ECgene alternative splicing isoforms for
EFHC1

Expression for EFHC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EFHC1 Gene

Protein differential expression in normal tissues from HIPED for EFHC1 Gene

This gene is overexpressed in Plasma (40.0) and Testis (23.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for EFHC1 Gene



Protein tissue co-expression partners for EFHC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EFHC1 Gene:

EFHC1

SOURCE GeneReport for Unigene cluster for EFHC1 Gene:

Hs.403171

mRNA Expression by UniProt/SwissProt for EFHC1 Gene:

Q5JVL4-EFHC1_HUMAN
Tissue specificity: Widely expressed. Not detected in lymphocytes.

Evidence on tissue expression from TISSUES for EFHC1 Gene

  • Nervous system(4.8)
  • Kidney(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for EFHC1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with EFHC1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for EFHC1 Gene

Orthologs for EFHC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for EFHC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EFHC1 34 35
  • 99.64 (n)
dog
(Canis familiaris)
Mammalia EFHC1 34 35
  • 89.11 (n)
cow
(Bos Taurus)
Mammalia EFHC1 34 35
  • 87.24 (n)
mouse
(Mus musculus)
Mammalia Efhc1 34 16 35
  • 83.49 (n)
rat
(Rattus norvegicus)
Mammalia Efhc1 34
  • 83.07 (n)
oppossum
(Monodelphis domestica)
Mammalia EFHC1 35
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EFHC1 35
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves EFHC1 34 35
  • 67.24 (n)
lizard
(Anolis carolinensis)
Reptilia EFHC1 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia efhc1 34
  • 64.57 (n)
Str.9549 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.11087 34
zebrafish
(Danio rerio)
Actinopterygii efhc1 34 35
  • 55.6 (n)
zgc63931 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003805 34
  • 48.58 (n)
worm
(Caenorhabditis elegans)
Secernentea Y49A10A.1 35
  • 24 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 58 (a)
OneToOne
Species where no ortholog for EFHC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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 EFHC1 Gene

ENSEMBL:
Gene Tree for EFHC1 (if available)
TreeFam:
Gene Tree for EFHC1 (if available)

Paralogs for EFHC1 Gene

Paralogs for EFHC1 Gene

(1) SIMAP similar genes for EFHC1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with EFHC1: view

Variants for EFHC1 Gene

Sequence variations from dbSNP and Humsavar for EFHC1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs137852776 other, Juvenile myoclonic epilepsy 1 (EJM1) [MIM:254770] 52,452,799(+) CAGAC(C/T)TTGAT nc-transcript-variant, reference, missense
rs137852777 other, Juvenile myoclonic epilepsy 1 (EJM1) [MIM:254770] 52,452,742(+) CTCTT(A/G)ATCCT nc-transcript-variant, reference, missense
rs137852778 other, Juvenile myoclonic epilepsy 1 (EJM1) [MIM:254770] 52,454,128(+) ATACA(A/G/T)ACAGC nc-transcript-variant, reference, missense
rs149055334 other, Juvenile myoclonic epilepsy 1 (EJM1) [MIM:254770] 52,424,111(+) GCCAA(A/C)CTAAA nc-transcript-variant, reference, missense
rs200191497 Juvenile myoclonic epilepsy 1 (EJM1) [MIM:254770] 52,438,562(+) CTTTC(C/T)GCGTT nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for EFHC1 Gene

Variant ID Type Subtype PubMed ID
esv3341940 CNV insertion 20981092
esv3608996 CNV gain 21293372
nsv1025395 CNV gain 25217958
nsv472897 CNV novel sequence insertion 20440878
nsv517935 CNV loss 19592680
nsv522674 CNV loss 19592680

Variation tolerance for EFHC1 Gene

Residual Variation Intolerance Score: 88.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.40; 77.08% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for EFHC1 Gene

Human Gene Mutation Database (HGMD)
EFHC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFHC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFHC1 Gene

Disorders for EFHC1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for EFHC1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
myoclonic epilepsy, juvenile 1
  • janz syndrome
epilepsy, juvenile absence 1
  • epilepsy, juvenile absence, susceptibility to, 1
efhc1-related juvenile myoclonic epilepsy
epilepsy, generalized, with febrile seizures plus, type 5
  • epilepsy, idiopathic generalized, 10
idiopathic generalized epilepsy
  • generalised epilepsy
- elite association - COSMIC cancer census association via MalaCards
Search EFHC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

EFHC1_HUMAN
  • Juvenile absence epilepsy 1 (JAE1) [MIM:607631]: A subtype of idiopathic generalized epilepsy characterized by onset occurring around puberty, absence seizures, generalized tonic-clonic seizures (GTCS), GTCS on awakening, and myoclonic seizures. {ECO:0000269 PubMed:17159113, ECO:0000305 PubMed:17159113}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Juvenile myoclonic epilepsy 1 (EJM1) [MIM:254770]: A subtype of idiopathic generalized epilepsy. Patients have afebrile seizures only, with onset in adolescence (rather than in childhood) and myoclonic jerks which usually occur after awakening and are triggered by sleep deprivation and fatigue. {ECO:0000269 PubMed:15258581, ECO:0000269 PubMed:17634063, ECO:0000269 PubMed:22690745, ECO:0000269 PubMed:22727576, ECO:0000269 PubMed:22926142}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Note=Mutation Leu-229 may be a cause of intractable epilepsy of infancy. Affected individuals have seizures of multiple type, manifested as tonic, clonic, and myoclonic seizures in the neonatal period, and as tonic seizures activated frequently by sleep, and repeated frequent myoclonic seizures in later infancy. The seizures are unresponsive to numerous antiepileptic drugs, and infants die in the first years of life. Although heterozygosity for Leu-229 has been associated with relatively benign forms of epilepsy in adolescence, homozygosity for the same mutation has much more severe consequences. {ECO:0000269 PubMed:22690745}.

Relevant External Links for EFHC1

Genetic Association Database (GAD)
EFHC1
Human Genome Epidemiology (HuGE) Navigator
EFHC1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
EFHC1
genes like me logo Genes that share disorders with EFHC1: view

No data available for Genatlas for EFHC1 Gene

Publications for EFHC1 Gene

  1. Mutations in EFHC1 cause juvenile myoclonic epilepsy. (PMID: 15258581) Suzuki T. … Yamakawa K. (Nat. Genet. 2004) 2 3 4 46 64
  2. Mutational analysis of EFHC1 gene in Italian families with juvenile myoclonic epilepsy. (PMID: 17634063) Annesi F. … Quattrone A. (Epilepsia 2007) 3 4 22 64
  3. Mutations in the GABRA1 and EFHC1 genes are rare in familial juvenile myoclonic epilepsy. (PMID: 16839746) Ma S. … Hedera P. (Epilepsy Res. 2006) 3 22 46 64
  4. Mutations of EFHC1, linked to juvenile myoclonic epilepsy, disrupt radial and tangential migrations during brain development. (PMID: 22926142) de Nijs L. … Lakaye B. (Hum. Mol. Genet. 2012) 3 4 64
  5. Novel Myoclonin1/EFHC1 mutations in Mexican patients with juvenile myoclonic epilepsy. (PMID: 22727576) Jara-Prado A. … Alonso M.E. (Seizure 2012) 3 4 64

Products for EFHC1 Gene

Sources for EFHC1 Gene

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