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Aliases for LETM1 Gene

Aliases for LETM1 Gene

  • Leucine Zipper And EF-Hand Containing Transmembrane Protein 1 2 3 5
  • Leucine Zipper-EF-Hand Containing Transmembrane Protein 1 2
  • Leucine Zipper-EF-Hand-Containing Transmembrane Protein 1 4
  • Mdm38 Homolog (Yeast) 2

External Ids for LETM1 Gene

Previous GeneCards Identifiers for LETM1 Gene

  • GC04M001807
  • GC04M001794
  • GC04M001776

Summaries for LETM1 Gene

Entrez Gene Summary for LETM1 Gene

  • This gene encodes a protein that is localized to the inner mitochondrial membrane. The protein functions to maintain the mitochondrial tubular shapes and is required for normal mitochondrial morphology and cellular viability. Mutations in this gene cause Wolf-Hirschhorn syndrome, a complex malformation syndrome caused by the deletion of parts of the distal short arm of chromosome 4. Related pseudogenes have been identified on chromosomes 8, 15 and 19. [provided by RefSeq, Oct 2009]

GeneCards Summary for LETM1 Gene

LETM1 (Leucine Zipper And EF-Hand Containing Transmembrane Protein 1) is a Protein Coding gene. Diseases associated with LETM1 include Wolf-Hirschhorn Syndrome and Chromosomal Deletion Syndrome. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is LETM2.

UniProtKB/Swiss-Prot for LETM1 Gene

  • Crucial for the maintenance of mitochondrial tubular networks and for the assembly of the supercomplexes of the respiratory chain. Required for the maintenance of the tubular shape and cristae organization.

Gene Wiki entry for LETM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LETM1 Gene

Genomics for LETM1 Gene

Regulatory Elements for LETM1 Gene

Enhancers for LETM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04F001882 1 ENCODE 12.5 -27.0 -27028 1.6 PKNOX1 ATF1 ARNT ELK1 GATA2 NCOA1 MBD2 MEF2D SMARCA4 PBX2 LETM1 GC04P001890 NSD2
GH04F001938 1.1 Ensembl ENCODE 10.9 -83.7 -83717 2.2 INSM2 FEZF1 ZNF2 ZNF335 ZNF366 SCRT2 FOS ZNF280D TSHZ1 ZEB2 MIR943 HAUS3 CRIPAK NELFA ENSG00000254094 LETM1 C4orf48 PIR46454 GC04P001890
GH04F001808 1 ENCODE 11.5 +46.5 46505 1.6 PKNOX1 ARID4B ZNF48 GTF3C2 GLIS2 CBX5 ZNF143 PAF1 ZNF263 SP5 CRIPAK MIR943 HAUS3 LETM1 ENSG00000254094 GC04M001809 GC04P001802
GH04F001878 0.8 Ensembl 12.5 -23.4 -23354 2.4 MAX ZNF384 RAD21 TEAD3 YY1 SCRT2 HNF4G PRDM10 SCRT1 SMARCA5 LETM1 NELFA NSD2 GC04P001890
GH04F001042 1.8 FANTOM5 Ensembl ENCODE 4.7 +812.1 812075 2.7 HDGF PKNOX1 ARNT SIN3A ZNF2 CBX5 FOS JUNB REST SMARCB1 ZNF141 MIR943 ZNF718 LOC100288172 ZNF732 PCGF3 FGFRL1 LETM1 GAK MAEA
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LETM1 on UCSC Golden Path with GeneCards custom track

Promoters for LETM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001234739 347 2601 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF207 ZNF143

Genomic Location for LETM1 Gene

Chromosome:
4
Start:
1,811,479 bp from pter
End:
1,856,247 bp from pter
Size:
44,769 bases
Orientation:
Minus strand

Genomic View for LETM1 Gene

Genes around LETM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LETM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LETM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LETM1 Gene

Proteins for LETM1 Gene

  • Protein details for LETM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95202-LETM1_HUMAN
    Recommended name:
    LETM1 and EF-hand domain-containing protein 1, mitochondrial
    Protein Accession:
    O95202
    Secondary Accessions:
    • B4DED2
    • Q9UF65

    Protein attributes for LETM1 Gene

    Size:
    739 amino acids
    Molecular mass:
    83354 Da
    Quaternary structure:
    • Can form 2 complexes: a major (300 kDa) and a minor complex (500-600 kDa). Interacts with BCS1L.
    SequenceCaution:
    • Sequence=CAB63769.2; Type=Erroneous translation; Note=Incomplete prediction of CDS at the C-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for LETM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LETM1 Gene

Post-translational modifications for LETM1 Gene

  • Ubiquitination at Lys 292
  • Modification sites at PhosphoSitePlus

Other Protein References for LETM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LETM1 Gene

Domains & Families for LETM1 Gene

Gene Families for LETM1 Gene

Protein Domains for LETM1 Gene

Graphical View of Domain Structure for InterPro Entry

O95202

UniProtKB/Swiss-Prot:

LETM1_HUMAN :
  • Contains 1 EF-hand domain.
Domain:
  • Contains 1 EF-hand domain.
  • Contains 1 Letm1 RBD (ribosome-binding) domain.
genes like me logo Genes that share domains with LETM1: view

Function for LETM1 Gene

Molecular function for LETM1 Gene

GENATLAS Biochemistry:
putative EF-hand calcium binding protein,ubiquitously expressed,highly conserved,flanking the Wolf-Hirschhorn critical region and deleted in most patients with the syndrome and putative contributor to the phenotype
UniProtKB/Swiss-Prot Function:
Crucial for the maintenance of mitochondrial tubular networks and for the assembly of the supercomplexes of the respiratory chain. Required for the maintenance of the tubular shape and cristae organization.

Gene Ontology (GO) - Molecular Function for LETM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 18628306
GO:0043022 ribosome binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LETM1: view
genes like me logo Genes that share phenotypes with LETM1: view

Human Phenotype Ontology for LETM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LETM1 Gene

Localization for LETM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LETM1 Gene

Mitochondrion inner membrane; Single-pass membrane protein.

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 LETM1 gene
Compartment Confidence
mitochondrion 5
cytosol 2
nucleus 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for LETM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion ISS --
GO:0005743 mitochondrial inner membrane IDA 18628306
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LETM1: view

Pathways & Interactions for LETM1 Gene

SuperPathways for LETM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LETM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006875 cellular metal ion homeostasis IBA --
GO:0042407 cristae formation IMP 18628306
genes like me logo Genes that share ontologies with LETM1: view

No data available for Pathways by source and SIGNOR curated interactions for LETM1 Gene

Transcripts for LETM1 Gene

Unigene Clusters for LETM1 Gene

Leucine zipper-EF-hand containing transmembrane protein 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LETM1 Gene

No ASD Table

Relevant External Links for LETM1 Gene

GeneLoc Exon Structure for
LETM1
ECgene alternative splicing isoforms for
LETM1

Expression for LETM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LETM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LETM1 Gene

This gene is overexpressed in Brain (9.8) and Nasal epithelium (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LETM1 Gene



Protein tissue co-expression partners for LETM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LETM1 Gene:

LETM1

SOURCE GeneReport for Unigene cluster for LETM1 Gene:

Hs.120165
genes like me logo Genes that share expression patterns with LETM1: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for LETM1 Gene

Orthologs for LETM1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LETM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LETM1 34 35
  • 98.76 (n)
dog
(Canis familiaris)
Mammalia LETM1 34 35
  • 84.55 (n)
cow
(Bos Taurus)
Mammalia LETM1 34 35
  • 84.38 (n)
mouse
(Mus musculus)
Mammalia Letm1 34 16 35
  • 82.77 (n)
rat
(Rattus norvegicus)
Mammalia Letm1 34
  • 81.98 (n)
oppossum
(Monodelphis domestica)
Mammalia LETM1 35
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LETM1 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves LETM1 34 35
  • 68.93 (n)
lizard
(Anolis carolinensis)
Reptilia LETM1 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia letm1 34
  • 65.35 (n)
Str.2394 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.13372 34
zebrafish
(Danio rerio)
Actinopterygii letm1 34 35
  • 67.89 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003296 34
  • 58.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4589 36
  • 40 (a)
Letm1 35
  • 24 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea letm-1 34 35
  • 48.56 (n)
F58G11.1a 36
  • 38 (a)
F58G11.1b 36
  • 38 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR032W 34
  • 51.56 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B11341g 34
  • 46.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YLH47 34 35
  • 43.23 (n)
MDM38 35 37
  • 28 (a)
ManyToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU03217 34
  • 51.53 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mdm28 34
  • 46.48 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 41 (a)
OneToMany
Species where no ortholog for LETM1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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 LETM1 Gene

ENSEMBL:
Gene Tree for LETM1 (if available)
TreeFam:
Gene Tree for LETM1 (if available)

Paralogs for LETM1 Gene

Paralogs for LETM1 Gene

(1) SIMAP similar genes for LETM1 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for LETM1 Gene

genes like me logo Genes that share paralogs with LETM1: view

Variants for LETM1 Gene

Sequence variations from dbSNP and Humsavar for LETM1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs10014663 -- 1,811,316(+) AGGGC(A/G)GCCCA downstream-variant-500B
rs10015420 -- 1,833,903(+) CTGGG(C/T)GGCCC intron-variant
rs10019772 -- 1,833,819(+) GACAC(A/G)ATTTC intron-variant
rs10020075 -- 1,818,336(+) Gggcc(A/G)ggcac intron-variant
rs10026782 -- 1,812,479(+) AGCTC(A/C)TGAAA utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LETM1 Gene

Variant ID Type Subtype PubMed ID
nsv949756 CNV deletion 24416366
nsv829836 CNV loss 17160897
nsv822440 CNV gain 20364138
nsv508989 CNV insertion 20534489
nsv428434 CNV gain 18775914
nsv1145018 CNV deletion 24896259
esv3396290 CNV duplication 20981092
esv3376119 CNV duplication 20981092
esv2759218 CNV gain 17122850
dgv8901n54 CNV loss 21841781

Variation tolerance for LETM1 Gene

Residual Variation Intolerance Score: 14.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.09; 69.02% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LETM1 Gene

Human Gene Mutation Database (HGMD)
LETM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LETM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LETM1 Gene

Disorders for LETM1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LETM1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
wolf-hirschhorn syndrome
  • 4p deletion syndrome
chromosomal deletion syndrome
chromosomal disease
  • chromosomal disorders
- elite association - COSMIC cancer census association via MalaCards
Search LETM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LETM1

Genetic Association Database (GAD)
LETM1
Human Genome Epidemiology (HuGE) Navigator
LETM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LETM1
genes like me logo Genes that share disorders with LETM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LETM1 Gene

Publications for LETM1 Gene

  1. LETM1, a novel gene encoding a putative EF-hand Ca(2+)-binding protein, flanks the Wolf-Hirschhorn syndrome (WHS) critical region and is deleted in most WHS patients. (PMID: 10486213) Endele S. … Winterpacht A. (Genomics 1999) 2 3 4 64
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  3. Regulation of OPA1-mediated mitochondrial fusion by leucine zipper/EF-hand-containing transmembrane protein-1 plays a role in apoptosis. (PMID: 19168126) Piao L. … Park J. (Cell. Signal. 2009) 3 22 64
  4. Characterization of the mitochondrial protein LETM1, which maintains the mitochondrial tubular shapes and interacts with the AAA-ATPase BCS1L. (PMID: 18628306) Tamai S. … Oka T. (J. Cell Sci. 2008) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LETM1 Gene

Sources for LETM1 Gene

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