LIPT1 lipoyltransferase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LIPT1provided by HGNC
Official Full Name: lipoyltransferase 1provided by HGNC
Primary source: HGNC:HGNC:29569
See related: Ensembl:ENSG00000144182 MIM:610284; AllianceGenome:HGNC:29569
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LIPT1D
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 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]
Expression: Ubiquitous expression in testis (RPKM 4.4), thyroid (RPKM 4.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q11.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (99154967..99163137)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (99613838..99622016)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (99771430..99779600)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Aberrant expression of cuproptosis-related gene LIPT1 is associated with metabolic dysregulation of fatty acid and prognosis in hepatocellular carcinoma.
Title: Aberrant expression of cuproptosis‑related gene LIPT1 is associated with metabolic dysregulation of fatty acid and prognosis in hepatocellular carcinoma.
System analysis based on the cuproptosis-related genes identifies LIPT1 as a novel therapy target for liver hepatocellular carcinoma.
Title: System analysis based on the cuproptosis-related genes identifies LIPT1 as a novel therapy target for liver hepatocellular carcinoma.
LIPT1 mutations impair 2KDH lipoylation and activity. LIPT1 deficiency increases 2-HG and depletes structural lipids in plasma. LIPT1 deficiency impedes lipogenesis but increases fatty acid oxidation.
Title: Functional Assessment of Lipoyltransferase-1 Deficiency in Cells, Mice, and Humans.
LIPT1 protein is required for lipoylation and activation of 2-ketoacid dehydrogenases in humans.
Title: Mutations in the lipoyltransferase LIPT1 gene cause a fatal disease associated with a specific lipoylation defect of the 2-ketoacid dehydrogenase complexes.
Data report a putative case of impaired free or H protein-derived lipoic acid attachment due to LIPT1 mutations as a cause of PDH and alpha-KGDH deficiencies.
Title: Mutations in human lipoyltransferase gene LIPT1 cause a Leigh disease with secondary deficiency for pyruvate and alpha-ketoglutarate dehydrogenase.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Lipoyl transferase 1 deficiency MedGen: C4225379 OMIM: 616299 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH79092 (e-PCR)
- UniSTS:2877

WI-18495 (e-PCR)
- UniSTS:8831

WI-18450 (e-PCR)
- UniSTS:8832

RH80012 (e-PCR)
- UniSTS:85945

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables acyltransferase activity	TAS Traceable Author Statement more info
enables lipoyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables lipoyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in carboxylic acid metabolic process	TAS Traceable Author Statement more info
involved_in lipid metabolic process	TAS Traceable Author Statement more info	PubMed
involved_in protein lipoylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein modification process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrial matrix	TAS Traceable Author Statement more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: lipoyl amidotransferase LIPT1, mitochondrial

Names: lipoate biosynthesis protein; lipoyl ligase; lipoyltransferase 1, mitochondrial

NP_001191759.1

EC 2.3.1.200

NP_057013.1

EC 2.3.1.200

NP_660198.1

EC 2.3.1.200

NP_660199.1

EC 2.3.1.200

NP_660200.1

EC 2.3.1.200

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_050665.1 RefSeqGene

Range

5013..13183

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001204830.2 → NP_001191759.1 lipoyl amidotransferase LIPT1, mitochondrial precursor

See identical proteins and their annotated locations for NP_001191759.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate 5'-most non-coding exon, compared to variant 1. Variants 1 and 3-6 all encode the same protein.

Source sequence(s)

BC009772, BG717409, BX100979, DA607268

Consensus CDS

CCDS2039.1

UniProtKB/Swiss-Prot

Q4ZFZ1, Q9Y234

Conserved Domains (1) summary

cd16443
Location:33 → 235

LplA; lipoate-protein ligase
NM_015929.4 → NP_057013.1 lipoyl amidotransferase LIPT1, mitochondrial precursor

See identical proteins and their annotated locations for NP_057013.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the same protein as variants 3-6.

Source sequence(s)

AB017566, BC070145

Consensus CDS

CCDS2039.1

UniProtKB/Swiss-Prot

Q4ZFZ1, Q9Y234

Related

ENSP00000377115.2, ENST00000393473.6

Conserved Domains (1) summary

cd16443
Location:33 → 235

LplA; lipoate-protein ligase
NM_145197.3 → NP_660198.1 lipoyl amidotransferase LIPT1, mitochondrial precursor

See identical proteins and their annotated locations for NP_660198.1

Status: REVIEWED

Description

Transcript Variant: This variant (3), also known as transcript C, contains an additional exon in the 5' UTR, compared to variant 1. Variants 1 and 3-6 all encode the same protein. There are no publicly available transcripts representing this variant; it is supported by data in PMID:10103005.

Source sequence(s)

AB017566, AC092587, BC070145

Consensus CDS

CCDS2039.1

UniProtKB/Swiss-Prot

Q4ZFZ1, Q9Y234

Conserved Domains (1) summary

cd16443
Location:33 → 235

LplA; lipoate-protein ligase
NM_145198.3 → NP_660199.1 lipoyl amidotransferase LIPT1, mitochondrial precursor

See identical proteins and their annotated locations for NP_660199.1

Status: REVIEWED

Description

Transcript Variant: This variant (4), also known as transcript D, contains an additional exon in the 5' UTR, compared to variant 1. Variants 1 and 3-6 all encode the same protein. There are no publicly available transcripts representing this variant; it is supported by data in PMID:10103005.

Source sequence(s)

AB017566, AC092587, BC070145

Consensus CDS

CCDS2039.1

UniProtKB/Swiss-Prot

Q4ZFZ1, Q9Y234

Conserved Domains (1) summary

cd16443
Location:33 → 235

LplA; lipoate-protein ligase
NM_145199.3 → NP_660200.1 lipoyl amidotransferase LIPT1, mitochondrial precursor

See identical proteins and their annotated locations for NP_660200.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an exon in the 5' UTR, compared to variant 1. Variants 1 and 3-6 all encode the same protein.

Source sequence(s)

AB017566, BC070145

Consensus CDS

CCDS2039.1

UniProtKB/Swiss-Prot

Q4ZFZ1, Q9Y234

Related

ENSP00000498546.1, ENST00000651691.1

Conserved Domains (1) summary

cd16443
Location:33 → 235

LplA; lipoate-protein ligase

RNA

NR_037935.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate 5'-most exon and contains an additional exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is expected to interfere with translation of the supported ORF, as found in variant 1.

Source sequence(s)

BC009772, BQ432795, BX100979, DA607268
NR_037936.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as transcript B, uses an alternate second exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is expected to interfere with translation of the supported ORF, as found in variant 1.

Source sequence(s)

AB017566, BC009772, BQ422048, BX100979

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

99154967..99163137

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

99613838..99622016

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_145196.2: Suppressed sequence

Description

NM_145196.2: This RefSeq was permanently suppressed because the annotated coding sequence is unlikely to be translated due to interference from an inhibitory upstream ORF.