LIPT1 (lipoyltransferase 1)

Gene

• Entrez ID: 51601
• Gene name: Lipoyltransferase 1
• Gene symbol: LIPT1
• Synonyms (NCBI Gene): LIPT1D
• Chromosome: 2
• Chromosome location: 2q11.2
• Summary: The process of transferring lipoic acid to proteins is a two-step process. The first step is the activation of lipoic acid by lipoate-activating enzyme to form lipoyl-AMP. For the second step, the protein encoded by this gene transfers the lipoyl moiety t

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32814053, 33961781
GO:0005737	Component	Cytoplasm	IBA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006629	Process	Lipid metabolic process	TAS	10103005
GO:0009249	Process	Protein lipoylation	IEA
GO:0009249	Process	Protein lipoylation	TAS
GO:0016410	Function	N-acyltransferase activity	IEA
GO:0016410	Function	N-acyltransferase activity	TAS
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0016747	Function	Acyltransferase activity, transferring groups other than amino-acyl groups	IEA
GO:0017118	Function	Lipoyltransferase activity	IBA
GO:0017118	Function	Lipoyltransferase activity	IEA
GO:0017118	Function	Lipoyltransferase activity	ISS
GO:0036211	Process	Protein modification process	TAS	10103005

Other IDs

• MIM: 610284
• HGNC: 29569
• e!Ensembl: ENSG00000144182

Protein

• UniProt ID: Q9Y234
• Protein name: Lipoyl amidotransferase LIPT1, mitochondrial (EC 2.3.1.200) (Lipoate biosynthesis protein) (Lipoate-protein ligase) (Lipoyl ligase) (Lipoyltransferase 1) (EC 2.3.1.-)
• Protein function: Lipoyl amidotransferase that catalyzes the transfer of lipoyl moieties from lipoyl-protein H of the glycine cleavage system (lipoyl-GCSH) to E2 subunits of the pyruvate dehydrogenase complex (PDCE2) (PubMed:29987032). Unable to catalyze the tran
• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in skeletal muscle and heart, moderately in kidney and pancreas, and detected at lower levels in liver, brain, placenta and lung. {ECO:0000269|PubMed:10103005}.
• Sequence:

  MLIPFSMKNCFQLLCNCQVPAAGFKKTVKNGLILQSISNDVYQNLAVEDWIHDHMNLEGK
  PILFFWQNSPSVVIGRHQNPWQECNLNLMREEGIKLARRRSGGGTVYHDMGNINLTFFTT
  KKKYDRMENLKLIVRALNAVQPQLDVQATKRFDLLLDGQFKISGTASKIGRTTAYHHCTL
  LCSTDGTFLSSLLKSPYQGIRSNATASIPSLVKNLLEKDPTLTCEVLMNAVATEYAAYHQ
  IDNHIHLINPTDETLFPGINSKAKELQTWEWIYGKTPKFSINTSFHVLYEQSHLEIKVFI
  DIKNGRIEICNIEAPDHWLPLEIRDKLNSSLIGSKFCPTETTMLTNILLRTCPQDHKLNS
  KWNILCEKIKGIM

• Sequence length: 373

Pathways

KEGG:

Lipoic acid metabolism
Metabolic pathways
Biosynthesis of cofactors

Reactome:

Glyoxylate metabolism and glycine degradation

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
Lipoyl transferase 1 deficiency	Pathogenic; Likely pathogenic	rs786205156, rs767568897, rs863224892, rs137891647, rs1468529365	RCV000170325 RCV000170326 RCV003389324 RCV000351422 RCV000680033	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Abnormal cardiovascular system morphology	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Abnormal optic nerve morphology	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Failure to thrive	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing impairment	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hypotonia	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Leigh syndrome	Conflicting classifications of pathogenicity	ClinVar ClinGen	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
LIPOYLTRANSFERASE 1 DEFICIENCY	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIPT1-related disorder	Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	36213577, 36312586	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36195876, 37124062	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	36826087	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Ischemic stroke	Pubtator	37983626	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	37773841	Associate	★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	BEFREE	28757203		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	37866660	Associate	★☆☆☆☆ Found in Text Mining only
Fabry Disease	Fabry disease	Pubtator	24341803	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	40355831	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glomerulonephritis IGA	Iga nephropathy	Pubtator	36329405	Associate	★☆☆☆☆ Found in Text Mining only
Heart Injuries	Cardiac injury	Pubtator	36988255	Associate	★☆☆☆☆ Found in Text Mining only
Hypertrichosis	HYPERTRICHOSIS	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Idiopathic pulmonary arterial hypertension	Pulmonary arterial hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	31042466		★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh Syndrome	BEFREE	24341803		★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh syndrome	Pubtator	24341803	Associate	★☆☆☆☆ Found in Text Mining only
Leigh syndrome with leukodystrophy	Leigh Syndrome With Leukodystrophy	Orphanet			★☆☆☆☆ Found in Text Mining only
Leukodystrophy	Leukodystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lipoyl transferase 1 deficiency	Lipoyltransferase deficiency	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
LIPOYLTRANSFERASE 1 DEFICIENCY	Lipoyltransferase deficiency	UNIPROT_DG	24256811, 24341803		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIPOYLTRANSFERASE 1 DEFICIENCY	Lipoyltransferase deficiency	CLINVAR_DG	24341803		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIPOYLTRANSFERASE 1 DEFICIENCY	Lipoyltransferase deficiency	ORPHANET_DG	24777537		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIPOYLTRANSFERASE 1 DEFICIENCY	Lipoyltransferase deficiency	GENOMICS_ENGLAND_DG	29681092		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIPOYLTRANSFERASE 1 DEFICIENCY	Lipoyltransferase deficiency	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mood swings	Mood swings	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nonketotic Hyperglycinemia	Nonketotic Hyperglycinemia	BEFREE	29681092		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteoarthritis	Osteoarthritis	Pubtator	36671512, 36817415	Stimulate	★☆☆☆☆ Found in Text Mining only
Osteoarthritis	Osteoarthritis	Pubtator	37809099	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	38497885, 40367233	Associate	★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Nervous System Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Progressive cerebellar ataxia	Cerebellar Ataxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary arterial hypertension	Pulmonary arterial hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	40255693	Associate	★☆☆☆☆ Found in Text Mining only
Pyruvate Dehydrogenase Complex Deficiency Disease	Pyruvate Dehydrogenase Complex Deficiency Disease	BEFREE	29681092		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	HPO_DG			★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic tetraparesis	Spastic tetraparesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37505170	Stimulate	★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Synovitis	Synovitis	Pubtator	36817415	Associate	★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
X-linked infantile spasms	Spasms X-Linked	BEFREE	29681092		★☆☆☆☆ Found in Text Mining only