This gene encodes a member of the EF-hand super family of calcium binding proteins, which are involved in a variety of cellular processes including mitosis, synaptic transmission, and cytoskeletal rearrangement. The protein encoded by this gene is composed of an N-terminal disordered region, proline-rich elements, two EF-hands, and a C-terminal coiled-coil domain. This protein ... See more...

Aliases for EFHD1 Gene

Aliases for EFHD1 Gene

  • EF-Hand Domain Family Member D1 2 3 5
  • Swiprosin-2 2 3 4
  • EF-Hand Domain-Containing Protein D1 3 4
  • EF-Hand Domain-Containing Protein 1 3 4
  • SWS2 3 4
  • EF Hand Domain Containing 1 2
  • FLJ13612 2
  • MSTP133 3
  • MST133 3
  • PP3051 3
  • EFHD1 5

External Ids for EFHD1 Gene

Previous GeneCards Identifiers for EFHD1 Gene

  • GC02P233700
  • GC02P233323
  • GC02P233206
  • GC02P233470
  • GC02P225321

Summaries for EFHD1 Gene

Entrez Gene Summary for EFHD1 Gene

  • This gene encodes a member of the EF-hand super family of calcium binding proteins, which are involved in a variety of cellular processes including mitosis, synaptic transmission, and cytoskeletal rearrangement. The protein encoded by this gene is composed of an N-terminal disordered region, proline-rich elements, two EF-hands, and a C-terminal coiled-coil domain. This protein has been shown to associate with the mitochondrial inner membrane, and in HeLa cells, acts as a novel mitochondrial calcium ion sensor for mitochondrial flash activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

GeneCards Summary for EFHD1 Gene

EFHD1 (EF-Hand Domain Family Member D1) is a Protein Coding gene. Diseases associated with EFHD1 include Colorblindness, Partial, Protan Series and Red-Green Color Blindness. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is EFHD2.

UniProtKB/Swiss-Prot Summary for EFHD1 Gene

  • Acts as a calcium sensor for mitochondrial flash (mitoflash) activation, an event characterized by stochastic bursts of superoxide production (PubMed:26975899). May play a role in neuronal differentiation (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EFHD1 Gene

Genomics for EFHD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for EFHD1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EFHD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EFHD1

Top Transcription factor binding sites by QIAGEN in the EFHD1 gene promoter:
  • ATF6
  • COUP
  • COUP-TF
  • COUP-TF1
  • Evi-1
  • HNF-4alpha1
  • HNF-4alpha2
  • HOXA3
  • RSRFC4

Genomic Locations for EFHD1 Gene

Genomic Locations for EFHD1 Gene
chr2:232,606,057-232,682,781
(GRCh38/hg38)
Size:
76,725 bases
Orientation:
Plus strand
chr2:233,470,767-233,547,491
(GRCh37/hg19)
Size:
76,725 bases
Orientation:
Plus strand

Genomic View for EFHD1 Gene

Genes around EFHD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFHD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFHD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFHD1 Gene

Proteins for EFHD1 Gene

  • Protein details for EFHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUP0-EFHD1_HUMAN
    Recommended name:
    EF-hand domain-containing protein D1
    Protein Accession:
    Q9BUP0
    Secondary Accessions:
    • B2RD83
    • E9PFH3
    • Q9BTF8
    • Q9H8I2
    • Q9HBQ0

    Protein attributes for EFHD1 Gene

    Size:
    239 amino acids
    Molecular mass:
    26928 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAG17248.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for EFHD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EFHD1 Gene

Post-translational modifications for EFHD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for EFHD1 Gene

Domains & Families for EFHD1 Gene

Gene Families for EFHD1 Gene

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

Protein Domains for EFHD1 Gene

Suggested Antigen Peptide Sequences for EFHD1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51583, highly similar to EF-hand domain-containing protein 1 (Swiprosin-2) (B4DEE0_HUMAN)
  • Swiprosin-2 (EFHD1_HUMAN)
  • MSTP133 (Q7Z2R5_HUMAN)
genes like me logo Genes that share domains with EFHD1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for EFHD1 Gene

Function for EFHD1 Gene

Molecular function for EFHD1 Gene

UniProtKB/Swiss-Prot Function:
Acts as a calcium sensor for mitochondrial flash (mitoflash) activation, an event characterized by stochastic bursts of superoxide production (PubMed:26975899). May play a role in neuronal differentiation (By similarity).

Phenotypes From GWAS Catalog for EFHD1 Gene

Gene Ontology (GO) - Molecular Function for EFHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0046872 metal ion binding IEA --
GO:0061891 calcium ion sensor activity IMP 26975899
genes like me logo Genes that share ontologies with EFHD1: view
genes like me logo Genes that share phenotypes with EFHD1: view

Animal Model Products

CRISPR Products

miRNA for EFHD1 Gene

miRTarBase miRNAs that target EFHD1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EFHD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EFHD1 Gene

Localization for EFHD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFHD1 Gene

Mitochondrion inner membrane.

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 EFHD1 gene
Compartment Confidence
mitochondrion 5
nucleus 3
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
  • Nucleoli fibrillar center (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EFHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion TAS 26975899
GO:0005743 mitochondrial inner membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with EFHD1: view

Pathways & Interactions for EFHD1 Gene

PathCards logo

SuperPathways for EFHD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EFHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031175 neuron projection development IEA --
GO:1900069 regulation of cellular hyperosmotic salinity response IMP 26975899
genes like me logo Genes that share ontologies with EFHD1: view

No data available for Pathways by source and SIGNOR curated interactions for EFHD1 Gene

Drugs & Compounds for EFHD1 Gene

No Compound Related Data Available

Transcripts for EFHD1 Gene

mRNA/cDNA for EFHD1 Gene

3 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
7 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 EFHD1

Alternative Splicing Database (ASD) splice patterns (SP) for EFHD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c
SP1: - -
SP2: - - -
SP3: -
SP4:

Relevant External Links for EFHD1 Gene

GeneLoc Exon Structure for
EFHD1

Expression for EFHD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EFHD1 Gene

mRNA differential expression in normal tissues according to GTEx for EFHD1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.4) and Artery - Tibial (x4.3).

Protein differential expression in normal tissues from HIPED for EFHD1 Gene

This gene is overexpressed in Adrenal (15.5), Liver, secretome (8.7), and Breast (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EFHD1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EFHD1

SOURCE GeneReport for Unigene cluster for EFHD1 Gene:

Hs.516769

Evidence on tissue expression from TISSUES for EFHD1 Gene

  • Nervous system(4.7)
  • Eye(4.6)
  • Heart(4.4)
  • Liver(4.3)
  • Lung(4.2)
  • Kidney(2.8)
  • Muscle(2.1)
  • Skin(2)
genes like me logo Genes that share expression patterns with EFHD1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EFHD1 Gene

Orthologs for EFHD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for EFHD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia EFHD1 30 31
  • 99.72 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia EFHD1 30 31
  • 88.65 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia EFHD1 30 31
  • 88.42 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia EFHD1 31
  • 85 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Efhd1 30 17 31
  • 82.34 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Efhd1 30
  • 82.34 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 75 (a)
OneToMany
-- 31
  • 71 (a)
OneToMany
-- 31
  • 61 (a)
OneToMany
-- 31
  • 59 (a)
OneToMany
-- 31
  • 58 (a)
OneToMany
-- 31
  • 58 (a)
OneToMany
Chicken
(Gallus gallus)
Aves EFHD1 30 31
  • 82.2 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia EFHD1 31
  • 70 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia efhd1 30
  • 74.87 (n)
Zebrafish
(Danio rerio)
Actinopterygii efhd1 30 31
  • 70.63 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG10641 31
  • 53 (a)
ManyToMany
CG14861 31
  • 16 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea efhd-1 31
  • 15 (a)
OneToMany
Species where no ortholog for EFHD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 EFHD1 Gene

ENSEMBL:
Gene Tree for EFHD1 (if available)
TreeFam:
Gene Tree for EFHD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EFHD1: view image

Paralogs for EFHD1 Gene

Paralogs for EFHD1 Gene

(5) SIMAP similar genes for EFHD1 Gene using alignment to 3 proteins:

  • EFHD1_HUMAN
  • C9JTV4_HUMAN
  • H7C0I0_HUMAN
genes like me logo Genes that share paralogs with EFHD1: view

Variants for EFHD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EFHD1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs370357320 Likely Benign: Anophthalmia - microphthalmia 232,633,949(+) C/T MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
rs11550699 - p.Lys186Arg

Additional dbSNP identifiers (rs#s) for EFHD1 Gene

Structural Variations from Database of Genomic Variants (DGV) for EFHD1 Gene

Variant ID Type Subtype PubMed ID
esv3561158 CNV deletion 23714750
esv3594659 CNV gain 21293372
esv3594661 CNV gain 21293372
esv3594662 CNV loss 21293372
nsv1002306 CNV gain 25217958
nsv1123438 CNV deletion 24896259

Variation tolerance for EFHD1 Gene

Residual Variation Intolerance Score: 80.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.20; 84.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFHD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFHD1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFHD1 Gene

Disorders for EFHD1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for EFHD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
colorblindness, partial, protan series
  • cbp
red-green color blindness
  • colorblindness, partial, deutan series
acromelic frontonasal dysostosis
  • afnd
muckle-wells syndrome
  • mws
- elite association - COSMIC cancer census association via MalaCards
Search EFHD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EFHD1

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 EFHD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EFHD1 Gene

Publications for EFHD1 Gene

  1. Identification of EFHD1 as a novel Ca(2+) sensor for mitoflash activation. (PMID: 26975899) Hou T … Wang X (Cell calcium 2016) 3 4
  2. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. (PMID: 22001757) Chambers JC … Kooner JS (Nature genetics 2011) 3 41
  3. Fraternal twins: Swiprosin-1/EFhd2 and Swiprosin-2/EFhd1, two homologous EF-hand containing calcium binding adaptor proteins with distinct functions. (PMID: 21244694) Dütting S … Mielenz D (Cell communication and signaling : CCS 2011) 2 3
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for EFHD1 Gene

Sources for EFHD1 Gene