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Protein

EF-hand domain-containing protein 1

Gene

EFHC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).2 Publications

GO - Molecular functioni

GO - Biological processi

  • cerebral cortex cell migration Source: UniProtKB
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
EF-hand domain-containing protein 1
Alternative name(s):
Myoclonin-1
Gene namesi
Name:EFHC1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:16406. EFHC1.

Subcellular locationi

GO - Cellular componenti

  • axoneme Source: UniProtKB
  • centrosome Source: UniProtKB
  • cytoplasm Source: UniProtKB-KW
  • mitotic spindle Source: UniProtKB
  • neuronal cell body Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

Pathology & Biotechi

Involvement in diseasei

Juvenile myoclonic epilepsy 1 (EJM1)4 Publications
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:254770
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02361977P → T in EJM1; associated with H-221; reduces substantially the cell death effect; reduces partly the calcium influx; binds to CACNA1E. 1 PublicationCorresponds to variant rs149055334dbSNPEnsembl.1
Natural variantiVAR_072108118R → C in EJM1. 1 PublicationCorresponds to variant rs764096785dbSNPEnsembl.1
Natural variantiVAR_072109153R → Q in EJM1; unknown pathological significance. 1 PublicationCorresponds to variant rs745600475dbSNPEnsembl.1
Natural variantiVAR_072110182R → C in EJM1; unknown pathological significance. 1 PublicationCorresponds to variant rs200191497dbSNPEnsembl.1
Natural variantiVAR_023622210D → N in EJM1; reduces substantially the cell death effect; reduces partly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 2 PublicationsCorresponds to variant rs137852777dbSNPEnsembl.1
Natural variantiVAR_023623221R → H in EJM1; associated with T-77; reduces substantially the cell death effect; reduces partly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 2 PublicationsCorresponds to variant rs79761183dbSNPEnsembl.1
Natural variantiVAR_023624229F → L in EJM1; uncertain pathological significance; also found at homozygosity in neonatal intractable epilepsy; reduces substantially the cell death effect; reduces significantly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 5 PublicationsCorresponds to variant rs137852776dbSNPEnsembl.1
Natural variantiVAR_023625253D → Y in EJM1; reduces substantially the cell death effect; reduces partly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 2 PublicationsCorresponds to variant rs137852778dbSNPEnsembl.1
Natural variantiVAR_043157353R → W in EJM1. 1 PublicationCorresponds to variant rs527295360dbSNPEnsembl.1
Juvenile absence epilepsy 1 (JAE1)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA subtype of idiopathic generalized epilepsy characterized by onset occurring around puberty, absence seizures, generalized tonic-clonic seizures (GTCS), GTCS on awakening, and myoclonic seizures.
See also OMIM:607631
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_043154174I → V Associated with susceptibility to JAE1. 1 PublicationCorresponds to variant rs137852779dbSNPEnsembl.1
Natural variantiVAR_043155259C → Y Associated with susceptibility to JAE1. 1 PublicationCorresponds to variant rs137852780dbSNPEnsembl.1

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.

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

DisGeNETi114327.
MalaCardsiEFHC1.
MIMi254770. phenotype.
607631. phenotype.
OpenTargetsiENSG00000096093.
Orphaneti1941. Juvenile absence epilepsy.
307. Juvenile myoclonic epilepsy.
PharmGKBiPA27654.

Polymorphism and mutation databases

BioMutaiEFHC1.
DMDMi74762202.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000738771 – 640EF-hand domain-containing protein 1Add BLAST640

Proteomic databases

EPDiQ5JVL4.
MaxQBiQ5JVL4.
PaxDbiQ5JVL4.
PeptideAtlasiQ5JVL4.
PRIDEiQ5JVL4.

PTM databases

iPTMnetiQ5JVL4.
PhosphoSitePlusiQ5JVL4.

Expressioni

Tissue specificityi

Widely expressed. Not detected in lymphocytes.1 Publication

Gene expression databases

BgeeiENSG00000096093.
CleanExiHS_EFHC1.
ExpressionAtlasiQ5JVL4. baseline and differential.
GenevisibleiQ5JVL4. HS.

Organism-specific databases

HPAiHPA035307.

Interactioni

Subunit structurei

Interacts with the C-terminus of CACNA1E.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
EIF4ENIF1Q9NRA86EBI-743105,EBI-301024
IKZF3Q9UKT97EBI-743105,EBI-747204
RELQ048646EBI-743105,EBI-307352
TCF4P158846EBI-743105,EBI-533224

GO - Molecular functioni

Protein-protein interaction databases

BioGridi125313. 12 interactors.
IntActiQ5JVL4. 26 interactors.
MINTiMINT-1484267.
STRINGi9606.ENSP00000360107.

Structurei

3D structure databases

ProteinModelPortaliQ5JVL4.
SMRiQ5JVL4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 198DM10 1PROSITE-ProRule annotationAdd BLAST106
Domaini239 – 359DM10 2PROSITE-ProRule annotationAdd BLAST121
Domaini416 – 520DM10 3PROSITE-ProRule annotationAdd BLAST105
Domaini574 – 609EF-handPROSITE-ProRule annotationAdd BLAST36

Sequence similaritiesi

Contains 3 DM10 domains.PROSITE-ProRule annotation
Contains 1 EF-hand domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0043. Eukaryota.
ENOG410XQCQ. LUCA.
GeneTreeiENSGT00530000063528.
HOGENOMiHOG000265451.
HOVERGENiHBG059646.
InParanoidiQ5JVL4.
OMAiRIRQVHI.
OrthoDBiEOG091G063X.
PhylomeDBiQ5JVL4.
TreeFamiTF314504.

Family and domain databases

CDDicd00051. EFh. 1 hit.
Gene3Di1.10.238.10. 1 hit.
InterProiIPR010554. DUF1126.
IPR011992. EF-hand-dom_pair.
IPR002048. EF_hand_dom.
IPR006602. Uncharacterised_DM10.
[Graphical view]
PfamiPF06565. DUF1126. 3 hits.
[Graphical view]
SMARTiSM00676. DM10. 3 hits.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
PROSITEiPS51336. DM10. 3 hits.
PS50222. EF_HAND_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5JVL4-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MVSNPVHGLP FLPGTSFKDS TKTAFHRSQT LSYRNGYAIV RRPTVGIGGD
60 70 80 90 100
RLQFNQLSQA ELDELASKAP VLTYGQPKQA PPADFIPAHV AFDKKVLKFD
110 120 130 140 150
AYFQEDVPMS TEEQYRIRQV NIYYYLEDDS MSVIEPVVEN SGILQGKLIK
160 170 180 190 200
RQRLAKNDRG DHYHWKDLNR GINITIYGKT FRVVDCDQFT QVFLESQGIE
210 220 230 240 250
LNPPEKMALD PYTELRKQPL RKYVTPSDFD QLKQFLTFDK QVLRFYAIWD
260 270 280 290 300
DTDSMYGECR TYIIHYYLMD DTVEIREVHE RNDGRDPFPL LMNRQRVPKV
310 320 330 340 350
LVENAKNFPQ CVLEISDQEV LEWYTAKDFI VGKSLTILGR TFFIYDCDPF
360 370 380 390 400
TRRYYKEKFG ITDLPRIDVS KREPPPVKQE LPPYNGFGLV EDSAQNCFAL
410 420 430 440 450
IPKAPKKDVI KMLVNDNKVL RYLAVLESPI PEDKDRRFVF SYFLATDMIS
460 470 480 490 500
IFEPPVRNSG IIGGKYLGRT KVVKPYSTVD NPVYYGPSDF FIGAVIEVFG
510 520 530 540 550
HRFIILDTDE YVLKYMESNA AQYSPEALAS IQNHVRKREA PAPEAESKQT
560 570 580 590 600
EKDPGVQELE ALIDTIQKQL KDHSCKDNIR EAFQIYDKEA SGYVDRDMFF
610 620 630 640
KICESLNVPV DDSLVKELIR MCSHGEGKIN YYNFVRAFSN
Length:640
Mass (Da):73,990
Last modified:February 15, 2005 - v1
Checksum:i08F9E8BFEC42FCF3
GO
Isoform 2 (identifier: Q5JVL4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     243-278: LRFYAIWDDTDSMYGECRTYIIHYYLMDDTVEIREV → SDIGTTIGLLISKCDLHLLAKGLGSCIGNYFETLQL
     279-640: Missing.

Note: May be due to intron retention.
Show »
Length:278
Mass (Da):31,661
Checksum:i806C5C56F5E294F9
GO
Isoform 3 (identifier: Q5JVL4-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-21: MVSNPVHGLPFLPGTSFKDST → ML

Note: No experimental confirmation available.
Show »
Length:621
Mass (Da):72,021
Checksum:iC289DD7386FF510B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti140N → D in BAG60005 (PubMed:14702039).Curated1
Sequence conflicti399A → T in BAA91628 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02361977P → T in EJM1; associated with H-221; reduces substantially the cell death effect; reduces partly the calcium influx; binds to CACNA1E. 1 PublicationCorresponds to variant rs149055334dbSNPEnsembl.1
Natural variantiVAR_072108118R → C in EJM1. 1 PublicationCorresponds to variant rs764096785dbSNPEnsembl.1
Natural variantiVAR_072109153R → Q in EJM1; unknown pathological significance. 1 PublicationCorresponds to variant rs745600475dbSNPEnsembl.1
Natural variantiVAR_023620159R → W Polymorphism with no effect on cell death; binds to CACNA1E as the wild type protein; does not affect subcellular location. 3 PublicationsCorresponds to variant rs3804506dbSNPEnsembl.1
Natural variantiVAR_043154174I → V Associated with susceptibility to JAE1. 1 PublicationCorresponds to variant rs137852779dbSNPEnsembl.1
Natural variantiVAR_072110182R → C in EJM1; unknown pathological significance. 1 PublicationCorresponds to variant rs200191497dbSNPEnsembl.1
Natural variantiVAR_023621182R → H No effect on cell death; binds to CACNA1E. 3 PublicationsCorresponds to variant rs3804505dbSNPEnsembl.1
Natural variantiVAR_023622210D → N in EJM1; reduces substantially the cell death effect; reduces partly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 2 PublicationsCorresponds to variant rs137852777dbSNPEnsembl.1
Natural variantiVAR_023623221R → H in EJM1; associated with T-77; reduces substantially the cell death effect; reduces partly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 2 PublicationsCorresponds to variant rs79761183dbSNPEnsembl.1
Natural variantiVAR_023624229F → L in EJM1; uncertain pathological significance; also found at homozygosity in neonatal intractable epilepsy; reduces substantially the cell death effect; reduces significantly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 5 PublicationsCorresponds to variant rs137852776dbSNPEnsembl.1
Natural variantiVAR_023625253D → Y in EJM1; reduces substantially the cell death effect; reduces partly the calcium influx; normally binds to CACNA1E; does not affect subcellular location; results in impaired cell migration. 2 PublicationsCorresponds to variant rs137852778dbSNPEnsembl.1
Natural variantiVAR_043155259C → Y Associated with susceptibility to JAE1. 1 PublicationCorresponds to variant rs137852780dbSNPEnsembl.1
Natural variantiVAR_026531285R → I.1 PublicationCorresponds to variant rs17851771dbSNPEnsembl.1
Natural variantiVAR_043156294R → H.1 PublicationCorresponds to variant rs1570624dbSNPEnsembl.1
Natural variantiVAR_043157353R → W in EJM1. 1 PublicationCorresponds to variant rs527295360dbSNPEnsembl.1
Natural variantiVAR_048666357E → K.Corresponds to variant rs505760dbSNPEnsembl.1
Natural variantiVAR_043158394A → S in a sporadic case of unclassified epilepsy. 1 Publication1
Natural variantiVAR_043159448M → T.1 PublicationCorresponds to variant rs1266787dbSNPEnsembl.1
Natural variantiVAR_023626619I → L Polymorphism with no effect on cell death; normally binds to CACNA1E; does not affect subcellular location. 3 PublicationsCorresponds to variant rs17851770dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0461071 – 21MVSNP…FKDST → ML in isoform 3. 1 PublicationAdd BLAST21
Alternative sequenceiVSP_015894243 – 278LRFYA…EIREV → SDIGTTIGLLISKCDLHLLA KGLGSCIGNYFETLQL in isoform 2. 1 PublicationAdd BLAST36
Alternative sequenceiVSP_015895279 – 640Missing in isoform 2. 1 PublicationAdd BLAST362

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY608689 mRNA. Translation: AAT67418.1.
AY608690 mRNA. Translation: AAT67419.1.
AK001328 mRNA. Translation: BAA91628.1.
AK297632 mRNA. Translation: BAG60005.1.
AL049611, AL136125 Genomic DNA. Translation: CAI19693.1.
AL136125, AL049611 Genomic DNA. Translation: CAI20107.1.
BC020210 mRNA. Translation: AAH20210.1.
CCDSiCCDS4942.1. [Q5JVL4-1]
CCDS55021.1. [Q5JVL4-3]
RefSeqiNP_001165891.1. NM_001172420.1. [Q5JVL4-3]
NP_060570.2. NM_018100.3. [Q5JVL4-1]
UniGeneiHs.403171.

Genome annotation databases

EnsembliENST00000371068; ENSP00000360107; ENSG00000096093. [Q5JVL4-1]
ENST00000538167; ENSP00000444521; ENSG00000096093. [Q5JVL4-3]
ENST00000636489; ENSP00000489998; ENSG00000096093. [Q5JVL4-3]
ENST00000636954; ENSP00000489966; ENSG00000096093. [Q5JVL4-3]
GeneIDi114327.
KEGGihsa:114327.
UCSCiuc003pap.5. human. [Q5JVL4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY608689 mRNA. Translation: AAT67418.1.
AY608690 mRNA. Translation: AAT67419.1.
AK001328 mRNA. Translation: BAA91628.1.
AK297632 mRNA. Translation: BAG60005.1.
AL049611, AL136125 Genomic DNA. Translation: CAI19693.1.
AL136125, AL049611 Genomic DNA. Translation: CAI20107.1.
BC020210 mRNA. Translation: AAH20210.1.
CCDSiCCDS4942.1. [Q5JVL4-1]
CCDS55021.1. [Q5JVL4-3]
RefSeqiNP_001165891.1. NM_001172420.1. [Q5JVL4-3]
NP_060570.2. NM_018100.3. [Q5JVL4-1]
UniGeneiHs.403171.

3D structure databases

ProteinModelPortaliQ5JVL4.
SMRiQ5JVL4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125313. 12 interactors.
IntActiQ5JVL4. 26 interactors.
MINTiMINT-1484267.
STRINGi9606.ENSP00000360107.

PTM databases

iPTMnetiQ5JVL4.
PhosphoSitePlusiQ5JVL4.

Polymorphism and mutation databases

BioMutaiEFHC1.
DMDMi74762202.

Proteomic databases

EPDiQ5JVL4.
MaxQBiQ5JVL4.
PaxDbiQ5JVL4.
PeptideAtlasiQ5JVL4.
PRIDEiQ5JVL4.

Protocols and materials databases

DNASUi114327.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000371068; ENSP00000360107; ENSG00000096093. [Q5JVL4-1]
ENST00000538167; ENSP00000444521; ENSG00000096093. [Q5JVL4-3]
ENST00000636489; ENSP00000489998; ENSG00000096093. [Q5JVL4-3]
ENST00000636954; ENSP00000489966; ENSG00000096093. [Q5JVL4-3]
GeneIDi114327.
KEGGihsa:114327.
UCSCiuc003pap.5. human. [Q5JVL4-1]

Organism-specific databases

CTDi114327.
DisGeNETi114327.
GeneCardsiEFHC1.
HGNCiHGNC:16406. EFHC1.
HPAiHPA035307.
MalaCardsiEFHC1.
MIMi254770. phenotype.
607631. phenotype.
608815. gene.
neXtProtiNX_Q5JVL4.
OpenTargetsiENSG00000096093.
Orphaneti1941. Juvenile absence epilepsy.
307. Juvenile myoclonic epilepsy.
PharmGKBiPA27654.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0043. Eukaryota.
ENOG410XQCQ. LUCA.
GeneTreeiENSGT00530000063528.
HOGENOMiHOG000265451.
HOVERGENiHBG059646.
InParanoidiQ5JVL4.
OMAiRIRQVHI.
OrthoDBiEOG091G063X.
PhylomeDBiQ5JVL4.
TreeFamiTF314504.

Miscellaneous databases

ChiTaRSiEFHC1. human.
GeneWikiiEFHC1.
GenomeRNAii114327.
PROiQ5JVL4.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000096093.
CleanExiHS_EFHC1.
ExpressionAtlasiQ5JVL4. baseline and differential.
GenevisibleiQ5JVL4. HS.

Family and domain databases

CDDicd00051. EFh. 1 hit.
Gene3Di1.10.238.10. 1 hit.
InterProiIPR010554. DUF1126.
IPR011992. EF-hand-dom_pair.
IPR002048. EF_hand_dom.
IPR006602. Uncharacterised_DM10.
[Graphical view]
PfamiPF06565. DUF1126. 3 hits.
[Graphical view]
SMARTiSM00676. DM10. 3 hits.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
PROSITEiPS51336. DM10. 3 hits.
PS50222. EF_HAND_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEFHC1_HUMAN
AccessioniPrimary (citable) accession number: Q5JVL4
Secondary accession number(s): B4DMU3
, F5GZD8, Q5XKM4, Q6E1U7, Q6E1U8, Q8WUL2, Q9NVW6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: February 15, 2005
Last modified: November 30, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.