This gene encodes a mitochondrial translation elongation factor. The encoded protein is an enzyme that catalyzes the exchange of guanine nucleotides on the translation elongation factor Tu during the elongation step of mitchondrial protein translation. Mutations in this gene are associated with combined oxidative phosphorylation deficiency-3 syndrome. Alternate splicing results... See more...

Aliases for TSFM Gene

Aliases for TSFM Gene

  • Ts Translation Elongation Factor, Mitochondrial 2 3 5
  • Elongation Factor Ts, Mitochondrial 3 4
  • Mitochondrial Elongation Factor Ts 3
  • EF-Tsmt 2
  • EF-TsMt 4
  • EFTSMT 3
  • EF-TS 2
  • EF-Ts 4
  • EFTS 3
  • TSFM 5

External Ids for TSFM Gene

Previous GeneCards Identifiers for TSFM Gene

  • GC12P058319
  • GC12P057893
  • GC12P056462
  • GC12P058167
  • GC12P055213
  • GC12P058176

Summaries for TSFM Gene

Entrez Gene Summary for TSFM Gene

  • This gene encodes a mitochondrial translation elongation factor. The encoded protein is an enzyme that catalyzes the exchange of guanine nucleotides on the translation elongation factor Tu during the elongation step of mitchondrial protein translation. Mutations in this gene are associated with combined oxidative phosphorylation deficiency-3 syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010]

GeneCards Summary for TSFM Gene

TSFM (Ts Translation Elongation Factor, Mitochondrial) is a Protein Coding gene. Diseases associated with TSFM include Combined Oxidative Phosphorylation Deficiency 3 and Nephrotic Syndrome, Type 21. Among its related pathways are Mitochondrial translation and Organelle biogenesis and maintenance. Gene Ontology (GO) annotations related to this gene include translation elongation factor activity.

UniProtKB/Swiss-Prot Summary for TSFM Gene

  • Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.

Gene Wiki entry for TSFM Gene

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

Genomics for TSFM Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TSFM 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
GH12J057770 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 301.7 -10.1 -10058 4.2 BCLAF1 SP1 ZNF207 NCOR1 ZNF600 IKZF1 MYC JUND ZNF580 ZNF592 TSFM EEF1AKMT3 ENSG00000257921 HSALNG0091660 METTL1 NEMP1 MBD6 ZBTB39 HSALNG0091662 HSALNG0091661
GH12J057782 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 302.4 +0.4 366 2.1 BCLAF1 SP1 ZNF207 ZNF654 NCOR1 IKZF1 MYC ZNF600 SIX5 ZNF580 TSFM NEMP1 ENSG00000224713 CTDSP2 CDK4 MBD6 NAB2 EEF1AKMT3 ZBTB39 SLC26A10
GH12J057764 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 250.4 -16.8 -16752 3.3 EZH2 ZNF600 POLR2A NFIC ZIC2 ZNF341 CTCF ZNF148 SIN3A KMT2B CYP27B1 piR-56275 TSFM NEMP1 CTDSP2 ENSG00000224713 ARHGAP9 lnc-CYP27B1-1 CDK4 RF00017-1060
GH12J057780 Promoter/Enhancer 0.5 EPDnew ENCODE 303.4 -1.6 -1642 1.4 TSFM EEF1AKMT3 HSALNG0091661 ENSG00000257921 RF00017-1060
GH12J057737 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 59 -40.8 -40816 9.1 SP1 ZNF207 ZNF600 IKZF1 SSRP1 JUND ZNF580 ZMYM3 ATF2 POLR2A AGAP2 TSPAN31 TSFM NEMP1 ARHGAP9 CTDSP2 CDK4 ATP23 DDIT3 CYP27B1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the TSFM gene promoter:
  • C/EBPalpha
  • CREB
  • deltaCREB

Genomic Locations for TSFM Gene

Latest Assembly
chr12:57,782,761-57,808,071
(GRCh38/hg38)
Size:
25,311 bases
Orientation:
Plus strand

Previous Assembly
chr12:58,176,570-58,196,639
(GRCh37/hg19 by Entrez Gene)
Size:
20,070 bases
Orientation:
Plus strand

chr12:58,176,372-58,201,854
(GRCh37/hg19 by Ensembl)
Size:
25,483 bases
Orientation:
Plus strand

Genomic View for TSFM Gene

Genes around TSFM on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for TSFM Gene

Proteins for TSFM Gene

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

    Protein Symbol:
    P43897-EFTS_HUMAN
    Recommended name:
    Elongation factor Ts, mitochondrial
    Protein Accession:
    P43897
    Secondary Accessions:
    • B4E391
    • F5H2T7
    • Q561V7
    • Q8TBC2
    • Q9UQK0

    Protein attributes for TSFM Gene

    Size:
    325 amino acids
    Molecular mass:
    35391 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for TSFM Gene

    Alternative splice isoforms for TSFM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TSFM Gene

Post-translational modifications for TSFM Gene

  • Ubiquitination at Lys192
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TSFM Gene

Domains & Families for TSFM Gene

Gene Families for TSFM Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TSFM Gene

InterPro:
Blocks:
  • Translation elongation factor EFTs/EF1B, dimerisation

Suggested Antigen Peptide Sequences for TSFM Gene

GenScript: Design optimal peptide antigens:
  • Elongation factor Ts (B4E391_HUMAN)
  • Elongation factor Ts (C9JG32_HUMAN)
  • Elongation factor Ts (C9JT21_HUMAN)
  • Elongation factor Ts, mitochondrial (EFTS_HUMAN)
  • Elongation factor Ts (F5H2T7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P43897

UniProtKB/Swiss-Prot:

EFTS_HUMAN :
  • Belongs to the EF-Ts family.
Family:
  • Belongs to the EF-Ts family.
genes like me logo Genes that share domains with TSFM: view

Function for TSFM Gene

Molecular function for TSFM Gene

UniProtKB/Swiss-Prot Function:
Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.

Phenotypes From GWAS Catalog for TSFM Gene

Gene Ontology (GO) - Molecular Function for TSFM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0003746 translation elongation factor activity IEA,IBA 21873635
GO:0005515 protein binding IEA,IPI 25910212
genes like me logo Genes that share ontologies with TSFM: view
genes like me logo Genes that share phenotypes with TSFM: view

Human Phenotype Ontology for TSFM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TSFM Gene

MGI Knock Outs for TSFM:
  • Tsfm Tsfm<tm1a(EUCOMM)Wtsi>

miRNA for TSFM Gene

Inhibitory RNAs for research

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

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

Localization for TSFM Gene

Subcellular locations from UniProtKB/Swiss-Prot for TSFM Gene

Mitochondrion.

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 TSFM gene
Compartment Confidence
mitochondrion 5
nucleus 4
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TSFM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion TAS,IDA --
GO:0005759 mitochondrial matrix IBA 21873635
genes like me logo Genes that share ontologies with TSFM: view

Pathways & Interactions for TSFM Gene

genes like me logo Genes that share pathways with TSFM: view

Pathways by source for TSFM Gene

Gene Ontology (GO) - Biological Process for TSFM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation IEA --
GO:0006414 translational elongation IEA,IBA 21873635
GO:0032784 regulation of DNA-templated transcription, elongation TAS 7615523
GO:0070125 mitochondrial translational elongation IBA 21873635
GO:0070129 regulation of mitochondrial translation IDA 27677415
genes like me logo Genes that share ontologies with TSFM: view

No data available for SIGNOR curated interactions for TSFM Gene

Drugs & Compounds for TSFM Gene

(3) Drugs for TSFM Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0

(3) Additional Compounds for TSFM Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TSFM: view

Transcripts for TSFM Gene

mRNA/cDNA for TSFM Gene

4 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

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

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c
SP1: - - -
SP2: - - - -
SP3: -
SP4: - - -
SP5: - -

Relevant External Links for TSFM Gene

GeneLoc Exon Structure for
TSFM

Expression for TSFM Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TSFM Gene

This gene is overexpressed in Brain (9.1) and Peripheral blood mononuclear cells (6.5).

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



Protein tissue co-expression partners for TSFM Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for TSFM Gene:

Hs.632704

mRNA Expression by UniProt/SwissProt for TSFM Gene:

P43897-EFTS_HUMAN
Tissue specificity: Expressed in all tissues, with the highest levels of expression in skeletal muscle, liver and kidney.

Evidence on tissue expression from TISSUES for TSFM Gene

  • Nervous system(4.7)
  • Liver(4.4)
  • Bone marrow(4.2)
  • Muscle(2.2)
  • Skin(2.1)
  • Kidney(2.1)
  • Heart(2.1)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • nervous
  • respiratory
  • skeletal muscle
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
Thorax:
  • heart
  • heart valve
  • lung
Abdomen:
  • kidney
  • liver
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with TSFM: view

No data available for mRNA differential expression in normal tissues for TSFM Gene

Orthologs for TSFM Gene

This gene was present in the common ancestor of animals.

Orthologs for TSFM Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TSFM 29 30
  • 99.23 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TSFM 30
  • 88 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia TSFM 29 30
  • 87.97 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Tsfm 29 16 30
  • 84.72 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tsfm 29
  • 84.62 (n)
Oppossum
(Monodelphis domestica)
Mammalia TSFM 30
  • 71 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TSFM 30
  • 61 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tsfm 29
  • 63.28 (n)
Str.10593 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.16462 29
Zebrafish
(Danio rerio)
Actinopterygii tsfm 29 30
  • 56.9 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009234 29
  • 51.59 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG6412 29 30 31
  • 49.94 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea tsfm-1 29 30
  • 45.43 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 31 (a)
OneToOne
Species where no ortholog for TSFM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chicken (Gallus gallus)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • 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 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 TSFM Gene

ENSEMBL:
Gene Tree for TSFM (if available)
TreeFam:
Gene Tree for TSFM (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TSFM: view image
Alliance of Genome Resources:
Additional Orthologs for TSFM

Paralogs for TSFM Gene

No data available for Paralogs for TSFM Gene

Variants for TSFM Gene

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

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
1033357 Pathogenic: Combined oxidative phosphorylation deficiency 3 57,796,206(+) C/T
NM_005726.6(TSFM):c.601C>T (p.Arg201Ter)
NONSENSE,THREE_PRIME_UTR_VARIANT,INTRON
845374 Pathogenic: not provided 57,793,059(+) T/A
NM_005726.6(TSFM):c.557T>A (p.Leu186Ter)
NONSENSE,INTRON
852530 Likely Pathogenic: not provided 57,796,512(+) CAG/C
NM_005726.6(TSFM):c.908_909del (p.Gln303fs)
FRAMESHIFT_VARIANT,THREE_PRIME_UTR_VARIANT,INTRON
854965 Pathogenic: not provided 57,787,074(+) TA/T
NM_005726.6(TSFM):c.399del (p.Lys133fs)
FRAMESHIFT
882314 Uncertain Significance: Combined oxidative phosphorylation deficiency 3 57,796,392(+) A/T
NM_005726.6(TSFM):c.787A>T (p.Met263Leu)
MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TSFM Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
nsv470296 CNV loss 18288195
nsv470297 CNV gain 18288195
nsv510601 CNV deletion 20534489
nsv559046 CNV gain 21841781

Variation tolerance for TSFM Gene

Residual Variation Intolerance Score: 82.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.62; 45.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TSFM Gene

Human Gene Mutation Database (HGMD)
TSFM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TSFM
Leiden Open Variation Database (LOVD)
TSFM

SNP Genotyping and Copy Number Assays for research

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

Disorders for TSFM Gene

MalaCards: The human disease database

(15) MalaCards diseases for TSFM Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search TSFM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

EFTS_HUMAN
  • Combined oxidative phosphorylation deficiency 3 (COXPD3) [MIM:610505]: A mitochondrial disease resulting in severe metabolic acidosis with encephalomyopathy or with hypertrophic cardiomyopathy. Patients show a severe defect in mitochondrial translation leading to a failure to assemble adequate amounts of three of the oxidative phosphorylation complexes. {ECO:0000269 PubMed:17033963, ECO:0000269 PubMed:22499341, ECO:0000269 PubMed:27677415}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TSFM

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TSFM: view

No data available for Genatlas for TSFM Gene

Publications for TSFM Gene

  1. Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs. (PMID: 17033963) Smeitink JA … Shoubridge EA (American journal of human genetics 2006) 3 4 22 72
  2. Cloning and expression of mitochondrial translational elongation factor Ts from bovine and human liver. (PMID: 7615523) Xin H … Spremulli LL (The Journal of biological chemistry 1995) 2 3 4 22
  3. Molecular-genetic characterization and rescue of a TSFM mutation causing childhood-onset ataxia and nonobstructive cardiomyopathy. (PMID: 27677415) Emperador S … Montoya J (European journal of human genetics : EJHG 2016) 3 4
  4. Mitochondrial EFTs defects in juvenile-onset Leigh disease, ataxia, neuropathy, and optic atrophy. (PMID: 25037205) Ahola S … Suomalainen A (Neurology 2014) 3 72
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 40

Products for TSFM Gene

Sources for TSFM Gene