TSFM (Ts translation elongation factor, mitochondrial)

Gene

• Entrez ID: 10102
• Gene name: Ts translation elongation factor, mitochondrial
• Gene symbol: TSFM
• Synonyms (NCBI Gene): EFTS, EFTSMT
• Chromosome: 12
• Chromosome location: 12q14.1
• Summary: 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. Mu

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121909485	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant, intron variant, 3 prime UTR variant
rs138534976	G>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, intron variant, coding sequence variant
rs201754030	C>T	Pathogenic, conflicting-interpretations-of-pathogenicity	3 prime UTR variant, intron variant, stop gained, coding sequence variant
rs376562033	C>G,T	Likely-pathogenic	Intron variant, missense variant, 3 prime UTR variant, coding sequence variant
rs587777688	G>A	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant, intron variant, 3 prime UTR variant
rs863224936	G>C	Likely-pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT029759	hsa-miR-26b-5p	Microarray	19088304
MIRT050350	hsa-miR-25-3p	CLASH	23622248
MIRT050350	hsa-miR-25-3p	CLASH	23622248
MIRT043452	hsa-miR-331-3p	CLASH	23622248
MIRT036967	hsa-miR-877-3p	CLASH	23622248
MIRT1458573	hsa-miR-1224-3p	CLIP-seq
MIRT1458574	hsa-miR-124	CLIP-seq
MIRT1458575	hsa-miR-1299	CLIP-seq
MIRT1458576	hsa-miR-1343	CLIP-seq
MIRT1458577	hsa-miR-198	CLIP-seq
MIRT1458578	hsa-miR-2054	CLIP-seq
MIRT1458579	hsa-miR-2964a-5p	CLIP-seq
MIRT1458580	hsa-miR-3148	CLIP-seq
MIRT1458581	hsa-miR-326	CLIP-seq
MIRT1458582	hsa-miR-330-5p	CLIP-seq
MIRT1458583	hsa-miR-3926	CLIP-seq
MIRT1458584	hsa-miR-4640-5p	CLIP-seq
MIRT1458585	hsa-miR-4691-5p	CLIP-seq
MIRT1458586	hsa-miR-4712-5p	CLIP-seq
MIRT1458587	hsa-miR-4726-5p	CLIP-seq
MIRT1458588	hsa-miR-4753-5p	CLIP-seq
MIRT1458589	hsa-miR-488	CLIP-seq
MIRT1458590	hsa-miR-506	CLIP-seq
MIRT1458591	hsa-miR-520a-5p	CLIP-seq
MIRT1458592	hsa-miR-525-5p	CLIP-seq
MIRT1458593	hsa-miR-548an	CLIP-seq
MIRT1458594	hsa-miR-548n	CLIP-seq
MIRT1458595	hsa-miR-548t	CLIP-seq
MIRT1458596	hsa-miR-593	CLIP-seq
MIRT1458597	hsa-miR-610	CLIP-seq
MIRT1458598	hsa-miR-770-5p	CLIP-seq
MIRT1458599	hsa-miR-875-3p	CLIP-seq
MIRT1458600	hsa-miR-3180-5p	CLIP-seq
MIRT1458601	hsa-miR-3925-5p	CLIP-seq
MIRT1458602	hsa-miR-4653-3p	CLIP-seq
MIRT1458603	hsa-miR-4694-3p	CLIP-seq
MIRT1458591	hsa-miR-520a-5p	CLIP-seq
MIRT1458592	hsa-miR-525-5p	CLIP-seq
MIRT1458604	hsa-miR-589	CLIP-seq
MIRT1458600	hsa-miR-3180-5p	CLIP-seq
MIRT1458601	hsa-miR-3925-5p	CLIP-seq
MIRT1458591	hsa-miR-520a-5p	CLIP-seq
MIRT1458592	hsa-miR-525-5p	CLIP-seq
MIRT1458604	hsa-miR-589	CLIP-seq
MIRT1458600	hsa-miR-3180-5p	CLIP-seq
MIRT1458601	hsa-miR-3925-5p	CLIP-seq
MIRT1458591	hsa-miR-520a-5p	CLIP-seq
MIRT1458592	hsa-miR-525-5p	CLIP-seq
MIRT1458604	hsa-miR-589	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003746	Function	Translation elongation factor activity	IBA
GO:0003746	Function	Translation elongation factor activity	IEA
GO:0005515	Function	Protein binding	IPI	25910212, 32296183
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	TAS	7615523
GO:0006412	Process	Translation	IEA
GO:0006414	Process	Translational elongation	IEA
GO:0070013	Component	Intracellular organelle lumen	IEA
GO:0070125	Process	Mitochondrial translational elongation	IBA
GO:0070125	Process	Mitochondrial translational elongation	IDA	27677415
GO:0070125	Process	Mitochondrial translational elongation	TAS	7615523

Other IDs

• MIM: 604723
• HGNC: 12367
• e!Ensembl: ENSG00000123297

Protein

• UniProt ID: P43897
• Protein name: Elongation factor Ts, mitochondrial (EF-Ts) (EF-TsMt)
• Protein 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. {ECO:0000255|HAMAP-Rule:MF_03135, ECO:0000269|PubMed:27677415}
• PDB: 2CP9
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00889	EF_TS	116 → 274	Elongation factor TS	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in all tissues, with the highest levels of expression in skeletal muscle, liver and kidney.
• Sequence:

  MSLLRSLRVFLVARTGSYPAGSLLRQSPQPRHTFYAGPRLSASASSKELLMKLRRKTGYS
  FVNCKKALETCGGDLKQAEIWLHKEAQKEGWSKAAKLQGRKTKEGLIGLLQEGNTTVLVE
  VNCETDFVSRNLKFQLLVQQVALGTMMHCQTLKDQPSAYSKGFLNSSELSGLPAGPDREG
  SLKDQLALAIGKLGENMILKRAAWVKVPSGFYVGSYVHGAMQSPSLHKLVLGKYGALVIC
  ETSEQKTNLEDVGRRLGQHVVGMAPLSVGSLDDEPGGEAETKMLSQPYLLDPSITLGQYV
  QPQGVSVVDFVRFECGEGEEAAETE

• Sequence length: 325

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3	Likely pathogenic; Pathogenic	rs768320625, rs774870834, rs2140413092, rs751169823, rs1955738689, rs750371292, rs372337739, rs2140412540, rs1403882425, rs201754030, rs587777688, rs1955739271, rs772810012, rs121909485, rs2540949104, rs1595137877, rs863224936, rs779144962, rs752852871, rs2540965587, rs753609161, rs2540965622, rs2540950814, rs2540942755, rs2540965002, rs2540943259, rs2540943285, rs2540942894, rs1412289052, rs35957924, rs1565823841, rs1399931138, rs2540943012, rs2540943113, rs1346981321, rs2540959796, rs1955600413, rs373811833, rs1491203033, rs1381664827	RCV001335749 RCV003463018 RCV003462986 RCV003463037 RCV001785093 RCV003471012 RCV004571443 RCV003464284 RCV003464386 RCV000143783 RCV000143784 RCV002470383 RCV003464572 RCV000005710 RCV003464625 RCV003464617 RCV005614387 RCV003155836 RCV003230786 RCV003464721 RCV003464722 RCV003464723 RCV003464724 RCV003464725 RCV003466475 RCV003466476 RCV003464727 RCV003464728 RCV003466477 RCV003466478 RCV003464730 RCV003464731 RCV003464732 RCV003466479 RCV004573792 RCV004573793 RCV003467806 RCV003462540 RCV001832514 RCV005005085	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Primary dilated cardiomyopathy	Likely pathogenic; Pathogenic	rs201754030	RCV000157550	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CARDIOMYOPATHY, DILATED	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Combined oxidative phosphorylation deficiency	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 3	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DISORDER OF SKELETAL MUSCLE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSKINESIAS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSKINETIC SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Encephalomyopathy with respiratory failure and lactic acidosis	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEIGH SYNDROME	—	ClinGen, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASE	—	CTD, ClinGen	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephrotic syndrome, type 21	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SARCOIDOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Skeletal myopathy	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STEROID-RESISTANT NEPHROTIC SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TSFM-related disorder	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Asthma	Asthma	BEFREE	24044605		★☆☆☆☆ Found in Text Mining only
Ataxia	Ataxia	Pubtator	25037205, 27677415	Associate	★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	25037205	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	29180379	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	BEFREE	25037205, 30911037		★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	Pubtator	25037205, 27677415, 30911037	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Hypertrophic	Hypertrophic cardiomyopathy	Pubtator	21741925, 27677415	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Combined Oxidative Phosphorylation Deficiency 3	Combined Oxidative Phosphorylation Deficiency	ORPHANET_DG	17033963		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Combined Oxidative Phosphorylation Deficiency 3	Combined Oxidative Phosphorylation Deficiency	UNIPROT_DG	17033963, 22499341, 27677415		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Combined Oxidative Phosphorylation Deficiency 3	Combined Oxidative Phosphorylation Deficiency	GENOMICS_ENGLAND_DG	21119709, 25037205, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Combined Oxidative Phosphorylation Deficiency 3	Combined Oxidative Phosphorylation Deficiency	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Combined Oxidative Phosphorylation Deficiency 3	Combined Oxidative Phosphorylation Deficiency	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Concentric hypertrophic cardiomyopathy	Concentric hypertrophic cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Congenital abnormalities	Pubtator	17033963	Associate	★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	BEFREE	25037205, 31267352		★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3	Fatal Mitochondrial Disease	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Foramen Ovale, Patent	Patent foramen ovale	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hereditary Motor And Sensory Neuropathy VI	Hereditary motor and sensory neuropathies	Pubtator	25037205	Associate	★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	29180379	Associate	★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh Syndrome	BEFREE	25037205		★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh syndrome	Pubtator	25037205	Associate	★☆☆☆☆ Found in Text Mining only
Liver Failure	Liver failure	Pubtator	21741925	Associate	★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	21169334, 21741925	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial Diseases	BEFREE	31267352		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Encephalomyopathies	Mitochondrial encephalomyopathy	Pubtator	21741925	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	20405052, 23160276, 24044605, 36405756, 36759259	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	GWASCAT_DG	24076602		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	BEFREE	31321514		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple System Atrophy	Multiple system atrophy	Pubtator	25037205	Associate	★☆☆☆☆ Found in Text Mining only
Neonatal Hypotonia	Hypotonia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic atrophy	Pubtator	25037205	Associate	★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Nervous System Diseases	BEFREE	25037205		★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Peripheral nervous system disease	Pubtator	25037205	Associate	★☆☆☆☆ Found in Text Mining only
Peripheral Neuropathy	Peripheral Neuropathy	BEFREE	25037205		★☆☆☆☆ Found in Text Mining only
Respiratory Failure	Respiratory Failure	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	31267352		★☆☆☆☆ Found in Text Mining only