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    EFHD1 EF-hand domain family member D1 [ Homo sapiens (human) ]

    Gene ID: 80303, updated on 10-Dec-2024

    Summary

    Official Symbol
    EFHD1provided by HGNC
    Official Full Name
    EF-hand domain family member D1provided by HGNC
    Primary source
    HGNC:HGNC:29556
    See related
    Ensembl:ENSG00000115468 MIM:611617; AllianceGenome:HGNC:29556
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SWS2; MST133; PP3051; MSTP133
    Summary
    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]
    Expression
    Biased expression in kidney (RPKM 68.5), placenta (RPKM 36.8) and 12 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See EFHD1 in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (232606057..232682776)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233092814..233169537)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (233470767..233547486)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12460 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:233432608-233433807 Neighboring gene microRNA 5001 Neighboring gene tigger transposable element derived 1 Neighboring gene eukaryotic translation initiation factor 4E family member 2 Neighboring gene uncharacterized LOC105373929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233465129-233465628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12461 Neighboring gene Sharpr-MPRA regulatory region 9991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233526805-233527304 Neighboring gene RNA, 7SL, cytoplasmic 359, pseudogene Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233561848-233562544 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233562545-233563239 Neighboring gene GRB10 interacting GYF protein 2 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 7 Neighboring gene potassium inwardly rectifying channel subfamily J member 13

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: EIF4E2

    Clone Names

    • FLJ13612, DKFZp781H0842

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium ion sensor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium ion sensor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cellular hyperosmotic salinity response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrial inner membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    EF-hand domain-containing protein D1
    Names
    EF-hand domain-containing protein 1
    swiprosin-2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_051251.1 RefSeqGene

      Range
      32548..81720
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243252.2NP_001230181.1  EF-hand domain-containing protein D1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK310565, BM677018, DB461847
      Consensus CDS
      CCDS58755.1
      UniProtKB/TrEMBL
      Q53SA2
      Related
      ENSP00000386556.1, ENST00000409613.5
      Conserved Domains (1) summary
      cd00051
      Location:656
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    2. NM_001308395.2NP_001295324.1  EF-hand domain-containing protein D1 isoform 3

      See identical proteins and their annotated locations for NP_001295324.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in its 5' UTR compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (3) that has a significantly shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK315442, BI460146, BU731354, CR627385, DB570289, DC328084
      Consensus CDS
      CCDS82580.1
      UniProtKB/TrEMBL
      Q53SA2, Q8WYH2
      Related
      ENSP00000386243.1, ENST00000409708.5
      Conserved Domains (1) summary
      cl08302
      Location:240
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    3. NM_025202.4NP_079478.1  EF-hand domain-containing protein D1 isoform 1

      See identical proteins and their annotated locations for NP_079478.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC064852, AC073254, AF218006, BC002449
      Consensus CDS
      CCDS2497.1
      UniProtKB/Swiss-Prot
      B2RD83, E9PFH3, Q9BTF8, Q9BUP0, Q9H8I2, Q9HBQ0
      UniProtKB/TrEMBL
      Q59EU6
      Related
      ENSP00000264059.3, ENST00000264059.8
      Conserved Domains (1) summary
      cd00051
      Location:94152
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      232606057..232682776
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      233092814..233169537
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)