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

Gene ID: 80303, updated on 5-Aug-2018

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; Vega:OTTHUMG00000133263
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

Genomic context

See EFHD1 in Genome Data Viewer
Location:
2q37.1
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (232606057..232682781)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (233470767..233547491)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene microRNA 5001 Neighboring gene eukaryotic translation initiation factor 4E family member 2 Neighboring gene tigger transposable element derived 1 Neighboring gene uncharacterized LOC105373929 Neighboring gene RNA, 7SL, cytoplasmic 359, pseudogene Neighboring gene GRB10 interacting GYF protein 2 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 7 Neighboring gene potassium voltage-gated channel subfamily J member 13

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: EIF4E2

Homology

Clone Names

  • FLJ13612, DKFZp781H0842

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
neuron projection development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5001..81725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243252.1NP_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, AW271276, BM677018, DB461847
    Consensus CDS
    CCDS58755.1
    UniProtKB/Swiss-Prot
    Q9BUP0
    Related
    ENSP00000386556.1, OTTHUMP00000203631, ENST00000409613.5, OTTHUMT00000330598
    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_001308395.1NP_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)
    AC073254, AK315442, AW271276, BI460146, BU731354, CR627385, DB570289, DC328084
    Consensus CDS
    CCDS82580.1
    UniProtKB/Swiss-Prot
    Q9BUP0
    UniProtKB/TrEMBL
    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_025202.3NP_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, DC328084
    Consensus CDS
    CCDS2497.1
    UniProtKB/Swiss-Prot
    Q9BUP0
    Related
    ENSP00000264059.3, OTTHUMP00000164362, ENST00000264059.7, OTTHUMT00000257040
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    232606057..232682781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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