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TOMM40 translocase of outer mitochondrial membrane 40 [ Homo sapiens (human) ]

Gene ID: 10452, updated on 17-Jun-2019

Summary

Official Symbol
TOMM40provided by HGNC
Official Full Name
translocase of outer mitochondrial membrane 40provided by HGNC
Primary source
HGNC:HGNC:18001
See related
Ensembl:ENSG00000130204 MIM:608061
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
TOM40; PEREC1; C19orf1; PER-EC1; D19S1177E
Summary
The protein encoded by this gene is localized in the outer membrane of the mitochondria. It is the channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex that is essential for import of protein precursors into mitochondria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
Expression
Ubiquitous expression in colon (RPKM 13.7), esophagus (RPKM 12.2) and 25 other tissues See more
Orthologs

Genomic context

See TOMM40 in Genome Data Viewer
Location:
19q13.32
Exon count:
11
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (44891220..44903689)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (45394477..45406946)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene basal cell adhesion molecule (Lutheran blood group) Neighboring gene nectin cell adhesion molecule 2 Neighboring gene APOC1 promoter region Neighboring gene apolipoprotein E Neighboring gene apolipoprotein C1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome wide association study identifies common variants associated with lipid levels in the Chinese population.
NHGRI GWA Catalog
A genome-wide association study for late-onset Alzheimer's disease using DNA pooling.
NHGRI GWA Catalog
A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing.
NHGRI GWA Catalog
A genome-wide scan for common variants affecting the rate of age-related cognitive decline.
NHGRI GWA Catalog
ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology.
NHGRI GWA Catalog
APOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir PET genome-wide association study.
NHGRI GWA Catalog
Are C-reactive protein associated genetic variants associated with serum levels and retinal markers of microvascular pathology in Asian populations from Singapore?
NHGRI GWA Catalog
Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities.
NHGRI GWA Catalog
Examination of the current top candidate genes for AD in a genome-wide association study.
NHGRI GWA Catalog
Genetic susceptibility to accelerated cognitive decline in the US Health and Retirement Study.
NHGRI GWA Catalog
Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.
NHGRI GWA Catalog
Genome-wide analysis of genetic loci associated with Alzheimer disease.
NHGRI GWA Catalog
Genome-wide association analysis of age-at-onset in Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
NHGRI GWA Catalog
Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women.
NHGRI GWA Catalog
Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study.
NHGRI GWA Catalog
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
NHGRI GWA Catalog
Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited.
NHGRI GWA Catalog
Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3.
NHGRI GWA Catalog
Genome-wide association study of Alzheimer's disease with psychotic symptoms.
NHGRI GWA Catalog
Genome-wide association study of Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort.
NHGRI GWA Catalog
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.
NHGRI GWA Catalog
Genome-wide scan of copy number variation in late-onset Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.
NHGRI GWA Catalog
GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease.
NHGRI GWA Catalog
Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis.
NHGRI GWA Catalog
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
NHGRI GWA Catalog
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
NHGRI GWA Catalog
Overrepresentation of glutamate signaling in Alzheimer's disease: network-based pathway enrichment using meta-analysis of genome-wide association studies.
NHGRI GWA Catalog
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein.
NHGRI GWA Catalog
SORL1 is genetically associated with late-onset Alzheimer's disease in Japanese, Koreans and Caucasians.
NHGRI GWA Catalog
The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 encephalitis infection upregulates TOM20 and TOM40 protein levels in post-mortem brain samples PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 Env (gp120) upregulates TOM20 and TOM40 protein levels in transgenic mouse neurons PubMed
Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with translocase of outer mitochondrial membrane 40 homolog (TOMM40) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Amyotrophic lateral sclerosis (ALS), organism-specific biosystem (from KEGG)
    Amyotrophic lateral sclerosis (ALS), organism-specific biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Amyotrophic lateral sclerosis (ALS), organism-specific biosystem (from WikiPathways)
    Amyotrophic lateral sclerosis (ALS), organism-specific biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Amyotrophic lateral sclerosis (ALS), conserved biosystem (from KEGG)
    Amyotrophic lateral sclerosis (ALS), conserved biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Mitochondrial protein import, organism-specific biosystem (from REACTOME)
    Mitochondrial protein import, organism-specific biosystemA human mitochondrion contains about 1500 proteins, more than 99% of which are encoded in the nucleus, synthesized in the cytosol and imported into the mitochondrion. Proteins are targeted to four lo...
  • Mitophagy, organism-specific biosystem (from REACTOME)
    Mitophagy, organism-specific biosystemMitophagy is a specific form of autophagy where mitochondria are specifically targeted for degradation by autophagolysosomes.. In mammals there are a number of known mechanisms of mitophagy. One insu...
  • Pink/Parkin Mediated Mitophagy, organism-specific biosystem (from REACTOME)
    Pink/Parkin Mediated Mitophagy, organism-specific biosystemThis is the process of selective removal of damaged mitochondria by autophagosomes and subsequent catabolism by lysosomes. In healthy mitochondria, PINK1 is imported to the inner mitochondrial membra...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
porin activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
protein transmembrane transporter activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
ion transport IEA
Inferred from Electronic Annotation
more info
 
macroautophagy TAS
Traceable Author Statement
more info
 
protein import into mitochondrial matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to mitochondrion IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein targeting to mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of mitochondrial outer membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial outer membrane TAS
Traceable Author Statement
more info
 
mitochondrial outer membrane translocase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial outer membrane translocase complex IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
 
NOT mitochondrion IMP
Inferred from Mutant Phenotype
more info
PubMed 
pore complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
mitochondrial import receptor subunit TOM40 homolog
Names
mitochondrial outer membrane protein
p38.5
protein Haymaker
translocase of outer membrane 40 kDa subunit homolog
translocase of outer mitochondrial membrane 40 homolog

NCBI Reference Sequences (RefSeq)

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

  1. NG_042854.1 RefSeqGene

    Range
    5001..17470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001128916.1NP_001122388.1  mitochondrial import receptor subunit TOM40 homolog

    See identical proteins and their annotated locations for NP_001122388.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    BC012134, BC017224, BP265648
    Consensus CDS
    CCDS12646.1
    UniProtKB/Swiss-Prot
    O96008
    Related
    ENSP00000385184.2, ENST00000405636.6
    Conserved Domains (1) summary
    cd07305
    Location:77361
    Porin3_Tom40; Translocase of outer mitochondrial membrane 40 (Tom40)
  2. NM_001128917.2NP_001122389.1  mitochondrial import receptor subunit TOM40 homolog

    See identical proteins and their annotated locations for NP_001122389.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1-3 encode the same protein.
    Source sequence(s)
    BC001779, BC017224, BP265648
    Consensus CDS
    CCDS12646.1
    UniProtKB/Swiss-Prot
    O96008
    Related
    ENSP00000410339.1, ENST00000426677.7
    Conserved Domains (1) summary
    cd07305
    Location:77361
    Porin3_Tom40; Translocase of outer mitochondrial membrane 40 (Tom40)
  3. NM_006114.3NP_006105.1  mitochondrial import receptor subunit TOM40 homolog

    See identical proteins and their annotated locations for NP_006105.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
    Source sequence(s)
    AF043250, BC017224
    Consensus CDS
    CCDS12646.1
    UniProtKB/Swiss-Prot
    O96008
    Related
    ENSP00000252487.4, ENST00000252487.9
    Conserved Domains (1) summary
    cd07305
    Location:77361
    Porin3_Tom40; Translocase of outer mitochondrial membrane 40 (Tom40)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    44891220..44903689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005258411.4XP_005258468.1  mitochondrial import receptor subunit TOM40 homolog isoform X1

    Conserved Domains (1) summary
    cd07305
    Location:77316
    Porin3_Tom40; Translocase of outer mitochondrial membrane 40 (Tom40)
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