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    AFG1L AFG1 like ATPase [ Homo sapiens (human) ]

    Gene ID: 246269, updated on 28-Oct-2024

    Summary

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    Official Symbol
    AFG1Lprovided by HGNC
    Official Full Name
    AFG1 like ATPaseprovided by HGNC
    Primary source
    HGNC:HGNC:16411
    See related
    Ensembl:ENSG00000135537 MIM:617469; AllianceGenome:HGNC:16411
    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
    AFG1; LACE1; c222389
    Summary
    This gene encodes a mitochondrial integral membrane protein that plays a role in mitochondrial protein homeostasis. The protein contains a P-loop motif and a five-domain structure that is conserved in fly, yeast, and bacteria. It functions to mediate the degradation of nuclear-encoded complex IV subunits. Two conserved estrogen receptor binding sites are located within 2.5 kb of this gene. Polymorphisms in this gene have been associated with bipolar disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2016]
    Expression
    Broad expression in testis (RPKM 1.7), kidney (RPKM 1.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See AFG1L in Genome Data Viewer
    Location:
    6q21
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (108295054..108526001)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (109472456..109703353)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (108616258..108847204)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:108582429-108583264 Neighboring gene sorting nexin 3 Neighboring gene RNA, 5S ribosomal pseudogene 212 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:108603498-108603672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24912 Neighboring gene RNA, U6 small nuclear 1144, pseudogene Neighboring gene ribosomal protein L36a pseudogene 24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24913 Neighboring gene NANOG hESC enhancer GRCh37_chr6:108686579-108687121 Neighboring gene translocase of outer mitochondrial membrane 5 homolog (yeast) pseudogene Neighboring gene uncharacterized LOC124901371 Neighboring gene RNA, U6 small nuclear 770, pseudogene Neighboring gene MPRA-validated peak6014 silencer Neighboring gene uncharacterized LOC124901370 Neighboring gene uncharacterized LOC124901372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17454 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:108882597-108883097 Neighboring gene Sharpr-MPRA regulatory region 14072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24915 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:108908380-108908581 Neighboring gene forkhead box O3 Neighboring gene SUMO2 pseudogene 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. An investigation of candidate regions for association with bipolar disorder. Knight J, et al. Am J Med Genet B Neuropsychiatr Genet, 2010 Oct 5. PMID 20872768, Free PMC Article
    2. Single nucleotide polymorphism C/T(-13910), located upstream of the lactase gene, associated with adult-type hypolactasia: validation for clinical practice. Mattar R, et al. Clin Biochem, 2008 May. PMID 18237552
    3. LACE1 interacts with p53 and mediates its mitochondrial translocation and apoptosis. Cesnekova J, et al. Oncotarget, 2016 Jul 26. PMID 27323408, Free PMC Article
    4. Identification of FOXO3 and PRDM1 as tumor-suppressor gene candidates in NK-cell neoplasms by genomic and functional analyses. Karube K, et al. Blood, 2011 Sep 22. PMID 21690554
    5. Novel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce loci. Abrahams BS, et al. Genomics, 2002 Jul. PMID 12079282

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Increased expression of LACE1 partitions p53 to mitochondria, causes reduction in nuclear p53 content and induces apoptosis. Thus, LACE1 mediates mitochondrial translocation of p53 and its transcription-independent apoptosis.
      Title: LACE1 interacts with p53 and mediates its mitochondrial translocation and apoptosis.
    2. This study establishes LACE1 as a novel factor with a crucial role in mitochondrial protein homeostasis.
      Title: The mammalian homologue of yeast Afg1 ATPase (lactation elevated 1) mediates degradation of nuclear-encoded complex IV subunits.
    3. association between bipolar disorder and two SNPs in the gene LACE1
      Title: An investigation of candidate regions for association with bipolar disorder.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of genetic testing. (HuGE Navigator)
      Title: Single nucleotide polymorphism C/T(-13910), located upstream of the lactase gene, associated with adult-type hypolactasia: validation for clinical practice.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitochondrial electron transport, cytochrome c to oxygen IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    AFG1-like ATPase
    Names
    ATPase family gene 1 homolog
    CG8520 gene product
    lactation elevated 1
    lactation elevated protein 1

    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.

    mRNA and Protein(s)

    1. NM_001323005.2 → NP_001309934.1  AFG1-like ATPase isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AL139106, AL832793, BC018445, FN063830
      UniProtKB/Swiss-Prot
      Q8WV93
      Conserved Domains (1) summary
      COG1485
      Location:73 → 425
      YhcM; Predicted ATPase [General function prediction only]

    2. NM_145315.5 → NP_660358.2  AFG1-like ATPase isoform a

      See identical proteins and their annotated locations for NP_660358.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AL139106, BC018445, FN063830
      Consensus CDS
      CCDS5067.1
      UniProtKB/Swiss-Prot
      Q8N6A3, Q8WV93
      Related
      ENSP00000357973.3, ENST00000368977.9
      Conserved Domains (1) summary
      COG1485
      Location:73 → 472
      YhcM; Predicted ATPase [General function prediction only]

    RNA

    1. NR_136553.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks four internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL139106, AL356121, BC018445, BI754108, BP246728, FN063830

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      108295054..108526001
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535657.3 → XP_011533959.1  AFG1-like ATPase isoform X2

      Conserved Domains (2) summary
      COG1485
      Location:73 → 438
      YhcM; Predicted ATPase [General function prediction only]
      cl21455
      Location:75 → 438
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. XM_011535660.3 → XP_011533962.1  AFG1-like ATPase isoform X7

      Conserved Domains (1) summary
      cl21455
      Location:75 → 271
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    3. XM_011535659.4 → XP_011533961.1  AFG1-like ATPase isoform X6

      Conserved Domains (1) summary
      cl21455
      Location:75 → 269
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    4. XM_011535661.3 → XP_011533963.1  AFG1-like ATPase isoform X8

      See identical proteins and their annotated locations for XP_011533963.1

      Conserved Domains (1) summary
      cl21455
      Location:75 → 250
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    5. XM_047418557.1 → XP_047274513.1  AFG1-like ATPase isoform X3

    6. XM_005266885.4 → XP_005266942.1  AFG1-like ATPase isoform X1

      Conserved Domains (2) summary
      COG1485
      Location:40 → 439
      YhcM; Predicted ATPase [General function prediction only]
      cl21455
      Location:42 → 439
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    7. XM_047418559.1 → XP_047274515.1  AFG1-like ATPase isoform X5

    8. XM_047418558.1 → XP_047274514.1  AFG1-like ATPase isoform X4

      Related
      ENSP00000398225.1, ENST00000421954.5

    9. XM_017010648.2 → XP_016866137.1  AFG1-like ATPase isoform X4

      UniProtKB/TrEMBL
      H0Y5F4
      Conserved Domains (1) summary
      COG1485
      Location:1 → 329
      YhcM; Predicted ATPase [General function prediction only]

    RNA

    1. XR_007059229.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      109472456..109703353
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354995.1 → XP_054210970.1  AFG1-like ATPase isoform X2

    2. XM_054355000.1 → XP_054210975.1  AFG1-like ATPase isoform X6

    3. XM_054355001.1 → XP_054210976.1  AFG1-like ATPase isoform X8

    4. XM_054354996.1 → XP_054210971.1  AFG1-like ATPase isoform X3

    5. XM_054354994.1 → XP_054210969.1  AFG1-like ATPase isoform X1

    6. XM_054354999.1 → XP_054210974.1  AFG1-like ATPase isoform X5

    7. XM_054354998.1 → XP_054210973.1  AFG1-like ATPase isoform X4

    8. XM_054354997.1 → XP_054210972.1  AFG1-like ATPase isoform X4

    RNA

    1. XR_008487287.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WV93.2 GenPept UniProtKB/Swiss-Prot:Q8WV93

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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