Human Gene EFHC1 (uc003pap.4) Description and Page Index
  Description: Homo sapiens EF-hand domain (C-terminal) containing 1 (EFHC1), transcript variant A, mRNA.
RefSeq Summary (NM_018100): 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].
Transcript (Including UTRs)
   Position: hg19 chr6:52,284,994-52,360,583 Size: 75,590 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr6:52,285,209-52,357,139 Size: 71,931 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:52,284,994-52,360,583)mRNA (may differ from genome)Protein (640 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: EFHC1_HUMAN
DESCRIPTION: RecName: Full=EF-hand domain-containing protein 1; AltName: Full=Myoclonin-1;
FUNCTION: May enhance calcium influx through CACNA1E and stimulate programmed cell death.
SUBUNIT: Interacts with the C-terminus of CACNA1E.
TISSUE SPECIFICITY: Widely expressed. Not detected in lymphocytes.
DISEASE: Defects in EFHC1 are the cause of juvenile myoclonic epilepsy type 1 (EJM1) [MIM:254770]. EJM1 is a subtype of idiopathic generalized epilepsy (IGE). 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.
DISEASE: Genetic variations in EFHC1 are the cause of susceptibility to juvenile absence epilepsy type 1 (JAE1) [MIM:607631]. JAE is 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.
SIMILARITY: Contains 3 DM10 domains.
SIMILARITY: Contains 1 EF-hand domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/Myoclonin1/EFHC1";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EFHC1
CDC HuGE Published Literature: EFHC1
Positive Disease Associations: Albuminuria , migraine , Respiratory Function Tests
Related Studies:
  1. Albuminuria
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
  2. migraine
    Suzuki, T. et al. 2004, Mutations in EFHC1 cause juvenile myoclonic epilepsy., Nature genetics. 2004 Aug;36(8):842-9. [PubMed 15258581]
    Mutation analyses identified five missense mutations in EFHC1 that cosegregated with epilepsy or EEG polyspike wave in affected members of six unrelated families with JME and did not occur in 382 control individuals
  3. Respiratory Function Tests
    Jemma B Wilk et al. BMC medical genetics 2007, Framingham Heart Study genome-wide association: results for pulmonary function measures., BMC medical genetics. [PubMed 17903307]
    GSTO2 and IL6R are credible candidate genes for association to pulmonary function identified by GWA. These and other observed associations warrant replication studies. This resource of GWA results for pulmonary function measures is publicly available at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: EFHC1
Diseases sorted by gene-association score: myoclonic epilepsy, juvenile 1* (1275), epilepsy, juvenile absence 1* (700), epilepsy, generalized, with febrile seizures plus, type 5* (340), efhc1-related juvenile myoclonic epilepsy* (100), epilepsy (25), juvenile absence epilepsy (25), idiopathic generalized epilepsy (23), adolescence-adult electroclinical syndrome (20), unverricht-lundborg syndrome (7), epilepsy with generalized tonic-clonic seizures (7), childhood electroclinical syndrome (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.70 RPKM in Pituitary
Total median expression: 211.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -98.42215-0.458 Picture PostScript Text
3' UTR -1121.383444-0.326 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010554 - DUF1126
IPR011992 - EF-hand-like_dom
IPR018249 - EF_HAND_2
IPR006602 - Uncharacterised_DM10

Pfam Domains:
PF06565 - DUF1126 PH-like domain

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on Q5JVL4
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0043014 alpha-tubulin binding

Biological Process:
GO:0000281 mitotic cytokinesis
GO:0007052 mitotic spindle organization
GO:0021795 cerebral cortex cell migration
GO:0051302 regulation of cell division

Cellular Component:
GO:0000922 spindle pole
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005819 spindle
GO:0005856 cytoskeleton
GO:0005930 axoneme
GO:0043025 neuronal cell body
GO:0072686 mitotic spindle


-  Descriptions from all associated GenBank mRNAs
  AY608690 - Homo sapiens EFHC1 isoform (EFHC1) mRNA, complete cds.
AK225543 - Homo sapiens mRNA for EF-hand domain (C-terminal) containing 1 variant, clone: KDN02133.
AL122084 - Homo sapiens mRNA; cDNA DKFZp434K0172 (from clone DKFZp434K0172).
AK001328 - Homo sapiens cDNA FLJ10466 fis, clone NT2RP1001665.
EU520261 - Homo sapiens EF-hand domain containing 1 (EFHC1) mRNA, complete cds.
BC020210 - Homo sapiens EF-hand domain (C-terminal) containing 1, mRNA (cDNA clone MGC:31844 IMAGE:4586338), complete cds.
AK295064 - Homo sapiens cDNA FLJ51667 complete cds, highly similar to EF-hand domain-containing protein 1.
BC012921 - Homo sapiens cDNA clone IMAGE:4470949, containing frame-shift errors.
DQ892170 - Synthetic construct clone IMAGE:100004800; FLH183654.01X; RZPDo839F01142D EF-hand domain (C-terminal) containing 1 (EFHC1) gene, encodes complete protein.
DQ895364 - Synthetic construct Homo sapiens clone IMAGE:100009824; FLH183650.01L; RZPDo839F01141D EF-hand domain (C-terminal) containing 1 (EFHC1) gene, encodes complete protein.
CU676508 - Synthetic construct Homo sapiens gateway clone IMAGE:100019973 5' read EFHC1 mRNA.
KJ900001 - Synthetic construct Homo sapiens clone ccsbBroadEn_09395 EFHC1 gene, encodes complete protein.
KR710581 - Synthetic construct Homo sapiens clone CCSBHm_00014138 EFHC1 (EFHC1) mRNA, encodes complete protein.
KR710582 - Synthetic construct Homo sapiens clone CCSBHm_00014141 EFHC1 (EFHC1) mRNA, encodes complete protein.
KR710583 - Synthetic construct Homo sapiens clone CCSBHm_00014147 EFHC1 (EFHC1) mRNA, encodes complete protein.
KR710584 - Synthetic construct Homo sapiens clone CCSBHm_00014148 EFHC1 (EFHC1) mRNA, encodes complete protein.
KR712240 - Synthetic construct Homo sapiens clone CCSBHm_00900199 EFHC1 (EFHC1) mRNA, encodes complete protein.
KR712242 - Synthetic construct Homo sapiens clone CCSBHm_00900201 EFHC1 (EFHC1) mRNA, encodes complete protein.
AK297632 - Homo sapiens cDNA FLJ58592 complete cds, highly similar to EF-hand domain-containing protein 1.
JD129378 - Sequence 110402 from Patent EP1572962.
JD406556 - Sequence 387580 from Patent EP1572962.
DQ574352 - Homo sapiens piRNA piR-42464, complete sequence.
AY608689 - Homo sapiens EFHC1 (EFHC1) mRNA, partial cds.
JD513862 - Sequence 494886 from Patent EP1572962.
AK094609 - Homo sapiens cDNA FLJ37290 fis, clone BRAMY2014469.
JD223807 - Sequence 204831 from Patent EP1572962.
JD545189 - Sequence 526213 from Patent EP1572962.
JD182644 - Sequence 163668 from Patent EP1572962.
JD084176 - Sequence 65200 from Patent EP1572962.
JD246692 - Sequence 227716 from Patent EP1572962.
JD100420 - Sequence 81444 from Patent EP1572962.
JD057164 - Sequence 38188 from Patent EP1572962.
JD405266 - Sequence 386290 from Patent EP1572962.
JD189796 - Sequence 170820 from Patent EP1572962.
JD050852 - Sequence 31876 from Patent EP1572962.
JD318886 - Sequence 299910 from Patent EP1572962.
JD364618 - Sequence 345642 from Patent EP1572962.
JD381569 - Sequence 362593 from Patent EP1572962.
JD367565 - Sequence 348589 from Patent EP1572962.
JD367566 - Sequence 348590 from Patent EP1572962.
JD059761 - Sequence 40785 from Patent EP1572962.
JD059762 - Sequence 40786 from Patent EP1572962.
JD308303 - Sequence 289327 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: EFHC1_HUMAN, NM_018100, NP_060570, Q5JVL4, Q5XKM4, Q6E1U7, Q6E1U8, Q8WUL2, Q9NVW6
UCSC ID: uc003pap.4
RefSeq Accession: NM_018100
Protein: Q5JVL4 (aka EFHC1_HUMAN)
CCDS: CCDS55021.1, CCDS4942.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018100.3
exon count: 11CDS single in 3' UTR: no RNA size: 5596
ORF size: 1923CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3867.00frame shift in genome: no % Coverage: 99.75
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.