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Aliases for LETM1 Gene

Aliases for LETM1 Gene

  • Leucine Zipper And EF-Hand Containing Transmembrane Protein 1 2 3 5
  • LETM1 And EF-Hand Domain-Containing Protein 1, Mitochondrial 3
  • Leucine Zipper-EF-Hand Containing Transmembrane Protein 1 3
  • Leucine Zipper-EF-Hand-Containing Transmembrane Protein 1 4
  • Mitochondrial Proton/Calcium Exchanger Protein 3
  • Mdm38 Homolog (Yeast) 2
  • Mdm38 Homolog 3
  • SLC55A1 3

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 Chromosome 4P Deletion and Wolf-Hirschhorn Syndrome. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is LETM2.

UniProtKB/Swiss-Prot for LETM1 Gene

  • Mitochondrial proton/calcium antiporter that mediates proton-dependent calcium efflux from mitochondrion (PubMed:19797662). Crucial for the maintenance of mitochondrial tubular networks and for the assembly of the supercomplexes of the respiratory chain (PubMed:18628306). Required for the maintenance of the tubular shape and cristae organization (PubMed:18628306). In contrast to SLC8B1/NCLX, does not constitute the major factor for mitochondrial calcium extrusion (PubMed:24898248).

Gene Wiki entry for LETM1 Gene

Additional gene information for LETM1 Gene

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

Genomics for LETM1 Gene

GeneHancer (GH) Regulatory Elements for LETM1 Gene

Promoters and enhancers for LETM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J001854 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.3 -324 3.8 HDGF ARNT ZFP64 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 ZNF207 LETM1 NSD2 FAM193A NELFA RNF4 HAUS3 ENSG00000270195 GC04P001850 GC04M001869
GH04J001882 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.5 -27.0 -27028 1.6 PKNOX1 SMAD1 ATF1 ARNT NCOA2 TCF12 ZNF766 GATA2 ATF7 NCOA1 LETM1 GC04P001890 NSD2
GH04J001808 Enhancer 1.1 ENCODE dbSUPER 11.5 +46.5 46504 1.6 HDGF PKNOX1 ARID4B SIN3A ZNF48 GTF3C2 POLR2B GLIS2 CBX5 ARID2 RNF4 CRIPAK MAEA NELFA FAM193A HAUS3 GAK ENSG00000270195 IDUA LETM1
GH04J001009 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 5.3 +845.0 845009 3.8 HDGF PKNOX1 ZFP64 ARID4B SIN3A ZNF48 YY1 GLIS2 CBX5 ZNF143 FGFRL1 DGKQ CRIPAK UVSSA LETM1 GAK GC04M001024
GH04J001938 Enhancer 1 Ensembl ENCODE 10.9 -83.7 -83717 2.2 INSM2 FEZF1 ZNF335 ZNF366 ZSCAN5C SCRT2 FOS KLF13 ZNF280D TSHZ1 PIR46454 NELFA LETM1 C4orf48 GC04P001890 NSD2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LETM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LETM1 gene promoter:

Genomic Locations for LETM1 Gene

Genomic Locations for LETM1 Gene
chr4:1,811,479-1,856,247
(GRCh38/hg38)
Size:
44,769 bases
Orientation:
Minus strand
chr4:1,813,206-1,857,974
(GRCh37/hg19)

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:
    Mitochondrial proton/calcium exchanger protein
    Protein Accession:
    O95202
    Secondary Accessions:
    • B4DED2
    • Q9UF65

    Protein attributes for LETM1 Gene

    Size:
    739 amino acids
    Molecular mass:
    83354 Da
    Quaternary structure:
    • Homohexamer (By similarity). Can form 2 complexes: a major (300 kDa) and a minor complex (500-600 kDa) (PubMed:18628306). Interacts with BCS1L (PubMed:18628306).
    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 posLast=292292
  • 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for LETM1 Gene

Graphical View of Domain Structure for InterPro Entry

O95202

UniProtKB/Swiss-Prot:

LETM1_HUMAN :
  • Belongs to the LETM1 family.
Family:
  • Belongs to the LETM1 family.
genes like me logo Genes that share domains with LETM1: view

Function for LETM1 Gene

Molecular function for LETM1 Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial proton/calcium antiporter that mediates proton-dependent calcium efflux from mitochondrion (PubMed:19797662). Crucial for the maintenance of mitochondrial tubular networks and for the assembly of the supercomplexes of the respiratory chain (PubMed:18628306). Required for the maintenance of the tubular shape and cristae organization (PubMed:18628306). In contrast to SLC8B1/NCLX, does not constitute the major factor for mitochondrial calcium extrusion (PubMed:24898248).
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by ruthenium red or its derivative Ru360.
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

Phenotypes From GWAS Catalog for LETM1 Gene

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:0015297 antiporter activity IEA --
GO:0015369 calcium:proton antiporter activity IDA 19797662
GO:0043022 ribosome 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

miRNA for LETM1 Gene

miRTarBase miRNAs that target LETM1

Clone 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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LETM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA,IEA --
GO:0005743 mitochondrial inner membrane IEA,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:0006811 ion transport IEA --
GO:0006816 calcium ion transport IEA --
GO:0006851 mitochondrial calcium ion transmembrane transport IDA 19797662
GO:0006875 cellular metal ion homeostasis IBA --
GO:0034214 protein hexamerization IEA,ISS --
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

Drugs & Compounds for LETM1 Gene

No Compound Related Data Available

Transcripts for LETM1 Gene

mRNA/cDNA for LETM1 Gene

Unigene Clusters for LETM1 Gene

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

Clone 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 CGAP 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, 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

Evidence on tissue expression from TISSUES for LETM1 Gene

  • Nervous system(4.4)
  • Liver(4.3)
  • Skin(4.2)
  • Heart(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LETM1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • scalp
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • urethra
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
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 33
  • 98.76 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LETM1 34 33
  • 84.55 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LETM1 34 33
  • 84.38 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Letm1 16 34 33
  • 82.77 (n)
rat
(Rattus norvegicus)
Mammalia Letm1 33
  • 81.98 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LETM1 34
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LETM1 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves LETM1 34 33
  • 68.93 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LETM1 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia letm1 33
  • 65.35 (n)
Str.2394 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.13372 33
zebrafish
(Danio rerio)
Actinopterygii letm1 34 33
  • 67.89 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003296 33
  • 58.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4589 35
  • 40 (a)
Letm1 34
  • 24 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea letm-1 34 33
  • 48.56 (n)
OneToMany
F58G11.1a 35
  • 38 (a)
F58G11.1b 35
  • 38 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR032W 33
  • 51.56 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B11341g 33
  • 46.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YLH47 34 33
  • 43.23 (n)
ManyToMany
MDM38 36 34
  • 28 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU03217 33
  • 51.53 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mdm28 33
  • 46.48 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for LETM1: view image

Paralogs for LETM1 Gene

Paralogs for LETM1 Gene

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

  • LETM1_HUMAN
  • D3DVQ1_HUMAN

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 Variation AA Info Type
rs753905629 uncertain-significance, Ependymoma 1,841,655(-) C/G/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000058784 -- 1,813,423(-) C/T 3_prime_UTR_variant
rs1000179606 -- 1,835,993(-) T/C intron_variant
rs1000240556 -- 1,839,020(-) T/C intron_variant
rs1000272076 -- 1,848,829(-) C/T genic_upstream_transcript_variant, intron_variant

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

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

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)

Additional Variant Information for LETM1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LETM1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LETM1 Gene - From: HGMD, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
chromosome 4p deletion
  • 4p deletion
wolf-hirschhorn syndrome
  • whs
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

Additional Disease Information for LETM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  2. NCLX protein, but not LETM1, mediates mitochondrial Ca2+ extrusion, thereby limiting Ca2+-induced NAD(P)H production and modulating matrix redox state. (PMID: 24898248) De Marchi U … Demaurex N (The Journal of biological chemistry 2014) 3 4 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. Genome-wide RNAi screen identifies Letm1 as a mitochondrial Ca2+/H+ antiporter. (PMID: 19797662) Jiang D … Clapham DE (Science (New York, N.Y.) 2009) 3 4 58
  5. 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 (Cellular signalling 2009) 3 22 58

Products for LETM1 Gene

Sources for LETM1 Gene

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