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LIPT1 Gene(Protein Coding)

Lipoyltransferase 1

GCID:
GC02P099155
GIFtS:
56
Genes Participants
UDN Logo

Aliases for LIPT1 Gene

Aliases for LIPT1 Gene

  • Lipoyltransferase 1 2 3 5
  • Lipoate Biosynthesis Protein 3 4
  • Lipoyl Ligase 3 4
  • Lipoyltransferase 1, Mitochondrial 3
  • Lipoate-Protein Ligase 4
  • EC 2.3.1.- 4
  • LIPT1D 3

External Ids for LIPT1 Gene

Previous GeneCards Identifiers for LIPT1 Gene

  • GC02P098224
  • GC02P099375
  • GC00U914350
  • GC02P099393
  • GC02P099229
  • GC02P099138
  • GC02P099139
  • GC02P099771
  • GC02P093537

Summaries for LIPT1 Gene

Entrez Gene Summary for LIPT1 Gene

  • 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 to apoproteins. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 13. Read-through transcription also exists between this gene and the neighboring downstream mitochondrial ribosomal protein L30 (MRPL30) gene. [provided by RefSeq, Mar 2011]

GeneCards Summary for LIPT1 Gene

LIPT1 (Lipoyltransferase 1) is a Protein Coding gene. Diseases associated with LIPT1 include Lipoyltransferase 1 Deficiency and Leigh Syndrome With Leukodystrophy. Among its related pathways are Glyoxylate metabolism and glycine degradation and Viral mRNA Translation. GO annotations related to this gene include transferase activity, transferring acyl groups.

UniProtKB/Swiss-Prot for LIPT1 Gene

  • Catalyzes the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIPT1 Gene

Genomics for LIPT1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for LIPT1 Gene

Enhancers for LIPT1 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
GH02G099179 1.2 ENCODE 11.7 +26.6 26582 3.4 MLX CREB3L1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC TBX21 TSGA10 MITD1 LIPT1 UNC50 ENSG00000241962 LYG1 MRPL30 LYG2
GH02G098606 1.4 ENCODE dbSUPER 9 -546.1 -546133 4.2 HNRNPUL1 PKNOX1 MLX CREB3L1 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 INPP4A RNU7-46P MRPL30 LIPT1 TSGA10 UNC50 PIR57027
GH02G099065 1 Ensembl ENCODE 10 -88.5 -88538 1.9 CTCF ARID4B ZNF644 RAD21 GATA3 ARID3A GATA2 POLR2A SMC3 ETV6 TSGA10 LIPT1 MRPL30 LOC550644 KIAA1211L
GH02G099479 1 Ensembl ENCODE 9.1 +326.2 326153 3.0 PKNOX1 RFX1 HLF ZNF843 ZSCAN21 ZFHX2 CTBP1 PRDM6 ZNF366 EGR1 TSGA10 MRPL30 LYG1 LIPT1 REV1 ENSG00000273306
GH02G099152 1.2 ENCODE 7.1 -0.8 -795 4.2 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC TSGA10 MRPL30 LIPT1 ENSG00000241962 C2orf15
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LIPT1 on UCSC Golden Path with GeneCards custom track

Promoters for LIPT1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000120538 345 1801 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC TBX21

Transcription factor binding sites by QIAGEN in the LIPT1 gene promoter:

Genomic Location for LIPT1 Gene

Chromosome:
2
Start:
99,154,955 bp from pter
End:
99,163,157 bp from pter
Size:
8,203 bases
Orientation:
Plus strand

Genomic View for LIPT1 Gene

Genes around LIPT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIPT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIPT1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LIPT1 Gene

Proteins for LIPT1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for LIPT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y234-LIPT_HUMAN
    Recommended name:
    Lipoyltransferase 1, mitochondrial
    Protein Accession:
    Q9Y234
    Secondary Accessions:
    • Q4ZFZ1

    Protein attributes for LIPT1 Gene

    Size:
    373 amino acids
    Molecular mass:
    42479 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LIPT1 Gene

Protein Expression for LIPT1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LIPT1 Gene

  • Ubiquitination at Lys131, posLast=150150, and posLast=264264
  • Modification sites at PhosphoSitePlus

Other Protein References for LIPT1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LIPT1 Gene

Domains & Families for LIPT1 Gene

Protein Domains for LIPT1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LIPT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y234

UniProtKB/Swiss-Prot:

LIPT_HUMAN :
  • Belongs to the LplA family.
Family:
  • Belongs to the LplA family.
genes like me logo Genes that share domains with LIPT1: view

No data available for Gene Families for LIPT1 Gene

Function for LIPT1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LIPT1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Lipoyl-AMP + protein = protein N(6)-(lipoyl)lysine + AMP.
UniProtKB/Swiss-Prot Function:
Catalyzes the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes.

Enzyme Numbers (IUBMB) for LIPT1 Gene

Gene Ontology (GO) - Molecular Function for LIPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups TAS --
GO:0016979 lipoate-protein ligase activity IBA --
genes like me logo Genes that share ontologies with LIPT1: view
genes like me logo Genes that share phenotypes with LIPT1: view

Human Phenotype Ontology for LIPT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LIPT1 Gene

Localization for LIPT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIPT1 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 LIPT1 gene
Compartment Confidence
mitochondrion 5
cytosol 3
nucleus 2

Gene Ontology (GO) - Cellular Components for LIPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with LIPT1: view

Pathways & Interactions for LIPT1 Gene

genes like me logo Genes that share pathways with LIPT1: view

Pathways by source for LIPT1 Gene

2 BioSystems pathways for LIPT1 Gene
2 KEGG pathways for LIPT1 Gene

UniProtKB/Swiss-Prot Q9Y234-LIPT_HUMAN

  • Pathway: Protein modification; protein lipoylation via exogenous pathway; protein N(6)-(lipoyl)lysine from lipoate: step 2/2.

Interacting Proteins for LIPT1 Gene

Selected Interacting proteins: Q9Y234-LIPT_HUMAN for LIPT1 Gene via IID

Gene Ontology (GO) - Biological Process for LIPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process TAS 10103005
GO:0006629 lipid metabolic process TAS 10103005
GO:0009249 protein lipoylation IBA --
GO:0034641 cellular nitrogen compound metabolic process TAS --
GO:0046487 glyoxylate metabolic process TAS --
genes like me logo Genes that share ontologies with LIPT1: view

No data available for SIGNOR curated interactions for LIPT1 Gene

Drugs & Compounds for LIPT1 Gene

Products:

  1. Drug

(2) Drugs for LIPT1 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lipoic Acid Approved Nutra Target 0
Adenosine monophosphate Approved Nutra 0

(3) Additional Compounds for LIPT1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
(R)-lipoic acid
  • (+)-alpha-Lipoic acid
  • (R)-(+)-lipoic acid
  • (R)-1,2-Dithiolane-3-pentanoic acid
  • (R)-1,2-dithiolane-3-valeric acid
  • (R)-6,8-thioctic acid
 1200-22-2
(S)-lipoic acid
  • (S)-(−)-lipoic acid
  • (S)-1,2-dithiolane-3-pentanoic acid
  • (S)-alpha-lipoic acid
  • L-1,2-dithiolane 3-valeric acid
  • L-6,8-thioctic acid
 1077-27-6
Lipoyl-AMP
genes like me logo Genes that share compounds with LIPT1: view

Transcripts for LIPT1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LIPT1 Gene

(6) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(317) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LIPT1 Gene

Lipoyltransferase 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIPT1 Gene

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

Relevant External Links for LIPT1 Gene

GeneLoc Exon Structure for
LIPT1
ECgene alternative splicing isoforms for
LIPT1

Expression for LIPT1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIPT1 Gene

mRNA expression in normal human tissues for LIPT1 Gene
mRNA expression by BioGPS for LIPT1 GenemRNA expression by GTEx for LIPT1 Gene

mRNA differential expression in normal tissues according to GTEx for LIPT1 Gene

This gene is overexpressed in Testis (x4.2).

Protein differential expression in normal tissues from HIPED for LIPT1 Gene

This gene is overexpressed in CD8 Tcells (68.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIPT1 Gene



Protein tissue co-expression partners for LIPT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LIPT1 Gene:

LIPT1

SOURCE GeneReport for Unigene cluster for LIPT1 Gene:

Hs.719172

mRNA Expression by UniProt/SwissProt for LIPT1 Gene:

Q9Y234-LIPT_HUMAN
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.

Evidence on tissue expression from TISSUES for LIPT1 Gene

  • Bone marrow(4.1)
  • Liver(4.1)
  • Lung(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LIPT1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • meninges
  • neck
Thorax:
  • lung
Abdomen:
  • liver
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with LIPT1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for LIPT1 Gene

Orthologs for LIPT1 Gene

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

Orthologs for LIPT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia LIPT1 34 35
  • 99.55 (n)
dog
(Canis familiaris)
 Mammalia LIPT1 34 35
  • 91.33 (n)
cow
(Bos Taurus)
 Mammalia LIPT1 34 35
  • 88.56 (n)
rat
(Rattus norvegicus)
 Mammalia Lipt1 34
  • 80.95 (n)
mouse
(Mus musculus)
 Mammalia Lipt1 34 16 35
  • 80.34 (n)
oppossum
(Monodelphis domestica)
 Mammalia LIPT1 35
  • 78 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LIPT1 34 35
  • 67.47 (n)
lizard
(Anolis carolinensis)
 Reptilia LIPT1 35
  • 66 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia lipt1 34
  • 63.35 (n)
Str.12049 34
zebrafish
(Danio rerio)
 Actinopterygii lipt1 34 35
  • 57.98 (n)
Dr.6188 34
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.7358 34
fruit fly
(Drosophila melanogaster)
 Insecta CG8446 34 35
  • 49.43 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP012186 34
  • 49.2 (n)
worm
(Caenorhabditis elegans)
 Secernentea C45G3.3 34 35
  • 49.26 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes AIM22 35
  • 23 (a)
 OneToOne
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes aim22 34
  • 47.13 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU05421 34
  • 46.43 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 41 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.8499 34
Species where no ortholog for LIPT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • 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 LIPT1 Gene

ENSEMBL:
Gene Tree for LIPT1 (if available)
TreeFam:
Gene Tree for LIPT1 (if available)

Paralogs for LIPT1 Gene

Pseudogenes.org Pseudogenes for LIPT1 Gene

genes like me logo Genes that share paralogs with LIPT1: view

No data available for Paralogs for LIPT1 Gene

Variants for LIPT1 Gene

Sequence variations from dbSNP and Humsavar for LIPT1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs137973334 Pathogenic, Lipoyltransferase 1 deficiency (LIPT1D) [MIM:616299] 99,162,249(+) TGGCT(C/G/T)GGAGA intron-variant, nc-transcript-variant, reference, missense
rs767568897 Pathogenic, Lipoyltransferase 1 deficiency (LIPT1D) [MIM:616299] 99,162,169(+) TCCCT(C/G/T)TGTTG intron-variant, nc-transcript-variant, reference, missense
rs786205156 Pathogenic, Lipoyltransferase 1 deficiency (LIPT1D) [MIM:616299] 99,162,492(+) ATTGC(A/G)CTTTA intron-variant, nc-transcript-variant, reference, missense
rs137891647 Pathogenic 99,162,832(+) ACAGT(C/G)ACACT intron-variant, nc-transcript-variant, reference, stop-gained
rs863224892 Pathogenic 99,162,763(+) AACTT(A/G)GGAGT intron-variant, nc-transcript-variant, reference, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for LIPT1 Gene

Variant ID Type Subtype PubMed ID
esv3591732 CNV gain 21293372

Variation tolerance for LIPT1 Gene

Residual Variation Intolerance Score: 37.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.12; 38.62% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LIPT1 Gene

Human Gene Mutation Database (HGMD)
LIPT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIPT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIPT1 Gene

Disorders for LIPT1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LIPT1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
lipoyltransferase 1 deficiency
  • lipt1d
leigh syndrome with leukodystrophy
  • infantile subacute necrotizing encephalopathy with leukodystrophy
glycine encephalopathy
  • non-ketotic hyperglycinemia
leigh syndrome
  • leigh syndrome due to mitochondrial complex i deficiency
- elite association - COSMIC cancer census association via MalaCards
Search LIPT1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LIPT_HUMAN
  • Lipoyltransferase 1 deficiency (LIPT1D) [MIM:616299]: A disorder due to a defect in lipoic acid metabolism, resulting in severe lactic acidosis and metabolic decompensation. Variable clinical manifestations include delayed psychomotor development, severe hypotonia, dystonia, loss of head control, coma, bradycardia, and pulmonary hypertension. {ECO:0000269 PubMed:24256811, ECO:0000269 PubMed:24341803}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LIPT1

Genetic Association Database (GAD)
LIPT1
Human Genome Epidemiology (HuGE) Navigator
LIPT1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIPT1
genes like me logo Genes that share disorders with LIPT1: view

No data available for Genatlas for LIPT1 Gene

Publications for LIPT1 Gene

  1. Molecular cloning, structural characterization and chromosomal localization of human lipoyltransferase gene. (PMID: 10103005) Fujiwara K. … Motokawa Y. (Eur. J. Biochem. 1999) 2 3 4 64
  2. Mutations in the lipoyltransferase LIPT1 gene cause a fatal disease associated with a specific lipoylation defect of the 2-ketoacid dehydrogenase complexes. (PMID: 24256811) Tort F. … Ribes A. (Hum. Mol. Genet. 2014) 3 4 64
  3. Mutations in human lipoyltransferase gene LIPT1 cause a Leigh disease with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase. (PMID: 24341803) Soreze Y. … de Lonlay P. (Orphanet J Rare Dis 2013) 3 4 64
  4. 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
  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 LIPT1 Gene

Sources for LIPT1 Gene

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