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

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 Epilepsy, Myoclonic Juvenile and Epilepsy, Juvenile Absence 1. Gene Ontology (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

  • Microtubule-associated protein which regulates cell division and neuronal migration during cortical development. Necessary for mitotic spindle organization (PubMed:19734894, PubMed:28370826). 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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for EFHC1 Gene

Promoters and enhancers for EFHC1 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
GH06J052415 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 687.9 +56.9 56902 6.8 MLX YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 SP3 EFHC1 MCM3 IL17F LOC724104 RPL31P28 TRAM2 PAQR8 PIR61259 PIR35463
GH06J052359 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.3 -252 4.1 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 SLC30A9 ZNF143 ZNF207 SP3 PAQR8 EFHC1
GH06J052992 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 30.2 +632.9 632918 4.1 ZFP64 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC RN7SK GSTA4 GC06P052997 ENSG00000202198 MCM3 EFHC1 ICK TRAM2 GSTA3 GC06P052982
GH06J052563 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 21.2 +209.1 209096 14.5 HDGF FOXA2 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 TRAM2 MCM3 EFHC1 TRAM2-AS1 PAQR8 LOC730101 GC06P052544
GH06J053306 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 34.1 +948.3 948319 8.1 HDGF PKNOX1 FOXA2 FEZF1 DMAP1 IRF4 YY1 ZNF766 FOS JUNB EFHC1 ELOVL5 RPL31P28 TRAM2 FBXO9 PIR59384 RPS16P5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EFHC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EFHC1 gene promoter:
  • STAT3
  • ZIC2
  • USF1
  • USF-1
  • RFX1
  • GR
  • GR-alpha
  • AML1a
  • Nkx2-2
  • POU2F1

Genomic Locations for EFHC1 Gene

Genomic Locations for EFHC1 Gene
chr6:52,362,123-52,529,886
(GRCh38/hg38)
Size:
167,764 bases
Orientation:
Plus strand
chr6:52,284,994-52,387,892
(GRCh37/hg19)
Size:
102,899 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 (PubMed:15258581). Interacts with alpha-tubulin (PubMed:19734894).

    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

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

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:
Microtubule-associated protein which regulates cell division and neuronal migration during cortical development. Necessary for mitotic spindle organization (PubMed:19734894, PubMed:28370826). 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).

Phenotypes From GWAS Catalog for EFHC1 Gene

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 --
GO:0043014 alpha-tubulin binding IDA 19734894
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

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. Cytoplasm, cytoskeleton, spindle pole.

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

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for EFHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000922 spindle pole IEA,IDA 28370826
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 22926142
GO:0005815 microtubule organizing center IEA --
GO:0005819 spindle 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:0000281 mitotic cytokinesis IMP 28370826
GO:0007052 mitotic spindle organization IMP 19734894
GO:0021795 cerebral cortex cell migration IMP 22926142
GO:0051302 regulation of cell division IMP 19734894
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 Approved Nutra 0
genes like me logo Genes that share compounds with EFHC1: view

Transcripts for EFHC1 Gene

mRNA/cDNA for EFHC1 Gene

(2) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(202) Selected AceView cDNA sequences:
(39) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EFHC1 Gene

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

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 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
Regions:
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with EFHC1: view

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 33
  • 99.64 (n)
OneToOne
dog
(Canis familiaris)
Mammalia EFHC1 34 33
  • 89.11 (n)
OneToOne
cow
(Bos Taurus)
Mammalia EFHC1 34 33
  • 87.24 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Efhc1 16 34 33
  • 83.49 (n)
rat
(Rattus norvegicus)
Mammalia Efhc1 33
  • 83.07 (n)
oppossum
(Monodelphis domestica)
Mammalia EFHC1 34
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EFHC1 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves EFHC1 34 33
  • 67.24 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EFHC1 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia efhc1 33
  • 64.57 (n)
Str.9549 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.11087 33
zebrafish
(Danio rerio)
Actinopterygii efhc1 34 33
  • 55.6 (n)
OneToOne
zgc63931 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003805 33
  • 48.58 (n)
worm
(Caenorhabditis elegans)
Secernentea Y49A10A.1 34
  • 24 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for EFHC1: view image

Paralogs for EFHC1 Gene

Paralogs for EFHC1 Gene

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

  • EFHC1_HUMAN
  • B2CKC5_HUMAN
  • H7C4B1_HUMAN
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 Variation AA Info Type
rs1045298708 likely-benign, Epilepsy juvenile absence, Juvenile myoclonic epilepsy 52,490,314(+) G/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1060503381 uncertain-significance, Epilepsy juvenile absence, Juvenile myoclonic epilepsy 52,454,286(+) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1060504898 likely-benign, Epilepsy juvenile absence, Juvenile myoclonic epilepsy 52,452,792(+) A/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs112311115 uncertain-significance, Juvenile myoclonic epilepsy 52,493,237(+) C/A/T 3_prime_UTR_variant, non_coding_transcript_variant
rs115205076 benign, uncertain-significance, not specified, Juvenile myoclonic epilepsy, Epilepsy juvenile absence 52,454,258(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant

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

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

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)

Additional Variant Information for EFHC1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for EFHC1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
epilepsy, myoclonic juvenile
  • ejm
epilepsy, juvenile absence 1
  • epilepsy, juvenile absence, susceptibility to, 1
epilepsy, idiopathic generalized 10
  • ejm
juvenile absence epilepsy
  • childhood absence epilepsy
epilepsy
  • epilepsy syndrome
- 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 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, ECO:0000269 PubMed:28370826}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • 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.
  • 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}.

Additional Disease Information for EFHC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Nature genetics 2004) 2 3 4 44 58
  2. Mutational analysis of EFHC1 gene in Italian families with juvenile myoclonic epilepsy. (PMID: 17634063) Annesi F … Quattrone A (Epilepsia 2007) 3 4 22 58
  3. Mutations in the GABRA1 and EFHC1 genes are rare in familial juvenile myoclonic epilepsy. (PMID: 16839746) Ma S … Hedera P (Epilepsy research 2006) 3 22 44 58
  4. Microtubule-associated defects caused by EFHC1 mutations in juvenile myoclonic epilepsy. (PMID: 28370826) Raju PK … Anand A (Human mutation 2017) 3 4 58
  5. Mutations of EFHC1, linked to juvenile myoclonic epilepsy, disrupt radial and tangential migrations during brain development. (PMID: 22926142) de Nijs L … Lakaye B (Human molecular genetics 2012) 3 4 58

Products for EFHC1 Gene

Sources for EFHC1 Gene

Content
Loading form....