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AFG1L AFG1 like ATPase [ Homo sapiens (human) ]

Gene ID: 246269, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (108295054..108526001)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (109472456..109703353)
105.20220307 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
  • 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. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. Guffanti A, et al. BMC Genomics, 2009 Apr 20. PMID 19379481, Free PMC Article

See all (22) 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 
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_2023_10

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

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