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    AFG2A AFG2 AAA ATPase homolog A [ Homo sapiens (human) ]

    Gene ID: 166378, updated on 3-Nov-2024

    Summary

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    Official Symbol
    AFG2Aprovided by HGNC
    Official Full Name
    AFG2 AAA ATPase homolog Aprovided by HGNC
    Primary source
    HGNC:HGNC:18119
    See related
    Ensembl:ENSG00000145375 MIM:613940; AllianceGenome:HGNC:18119
    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
    AFG2; SPAF; EHLMRS; NEDHSB; SPATA5
    Summary
    This gene encodes a member of the ATPase associated with diverse activities family, whose members are defined by a highly conserved ATPase domain. Members of this family participate in diverse cellular processes that include membrane fusion, DNA replication, microtubule severing, and protein degradation. The protein encoded by this gene has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Allelic variants in this gene have been associated with epilepsy, hearing loss, and cognitive disability syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See AFG2A in Genome Data Viewer
    Location:
    4q28.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (122923078..123319433)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (126227197..126623517)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (123844233..124240588)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900773 Neighboring gene fibroblast growth factor 2 Neighboring gene Sharpr-MPRA regulatory region 4593 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123843896-123844432 Neighboring gene nudix hydrolase 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123865949-123866476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123866477-123867003 Neighboring gene coilin pseudogene 2 Neighboring gene uncharacterized LOC105377404 Neighboring gene uncharacterized LOC124900772

    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. Genome-wide pooling approach identifies SPATA5 as a new susceptibility locus for alopecia areata. Forstbauer LM, et al. Eur J Hum Genet, 2012 Mar. PMID 22027810, Free PMC Article
    2. Isolated Hearing Impairment Caused by SPATA5 Mutations in a Family with Variable Phenotypic Expression. Szczałuba K, et al. Adv Exp Med Biol, 2017. PMID 28293831
    3. Characterization of SPATA5-related encephalopathy in early childhood. Kurata H, et al. Clin Genet, 2016 Nov. PMID 27246907
    4. SPAF, a new AAA-protein specific to early spermatogenesis and malignant conversion. Liu Y, et al. Oncogene, 2000 Mar 16. PMID 10734318
    5. A Genome-wide Association Study for Concussion Risk. Kim SK, et al. Med Sci Sports Exerc, 2021 Apr 1. PMID 33017352

    See all (93) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly.
      Title: Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly.
    2. A Genome-wide Association Study for Concussion Risk.
      Title: A Genome-wide Association Study for Concussion Risk.
    3. Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility.
      Title: Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility.
    4. SPATA5 defects may account for a fraction of isolated sensorineural hearing impairment cases.
      Title: Isolated Hearing Impairment Caused by SPATA5 Mutations in a Family with Variable Phenotypic Expression.
    5. Clinical delineation of the SPATA5-related encephalopathy should improve diagnosis, facilitating further clinical and molecular investigation
      Title: Characterization of SPATA5-related encephalopathy in early childhood.
    6. Mutations in SPATA5 Are Associated with Microcephaly, Intellectual Disability, Seizures, and Hearing Loss.
      Title: Mutations in SPATA5 Are Associated with Microcephaly, Intellectual Disability, Seizures, and Hearing Loss.
    7. SPATA5 locus is a new susceptibility locus for Alopecia areata (AA).
      Title: Genome-wide pooling approach identifies SPATA5 as a new susceptibility locus for alopecia areata.
    8. 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.
    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
    Genome-wide association study identifies two novel genomic regions in irritable bowel syndrome.
    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 preribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal large subunit biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in spermatogenesis 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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in spindle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ATPase family gene 2 protein homolog A
    Names
    ATPase family gene 2 homolog
    ATPase family protein 2 homolog
    ribosome biogenesis protein SPATA5
    spermatogenesis associated 5
    spermatogenesis associated factor SPAF
    spermatogenesis-associated factor protein
    spermatogenesis-associated protein 5
    NP_001304728.1
    NP_001332785.1
    NP_660208.2
    XP_011529980.1
    XP_011529981.1
    XP_016863314.1
    XP_016863316.1
    XP_016863318.1
    XP_016863319.1
    XP_047305646.1
    XP_047305647.1
    XP_047305648.1
    XP_047305649.1
    XP_047305650.1
    XP_047305651.1
    XP_047305652.1
    XP_047305653.1
    XP_054205046.1
    XP_054205047.1
    XP_054205048.1
    XP_054205049.1
    XP_054205050.1
    XP_054205051.1
    XP_054205052.1
    XP_054205053.1
    XP_054205054.1
    XP_054205055.1
    XP_054205056.1
    XP_054205057.1
    XP_054205058.1
    XP_054205059.1

    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.

    Genomic

    1. NG_051570.1 RefSeqGene

      Range
      5009..401364
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001317799.2 → NP_001304728.1  ATPase family gene 2 protein homolog A isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, lacks several exons in the 3' coding region and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC109357, AK091384, BC048217, DA619323
      UniProtKB/Swiss-Prot
      Q8NB90
      Conserved Domains (4) summary
      smart00382
      Location:386 → 524
      AAA; ATPases associated with a variety of cellular activities
      smart01073
      Location:46 → 132
      CDC48_N; Cell division protein 48 (CDC48) N-terminal domain
      pfam00004
      Location:389 → 522
      AAA; ATPase family associated with various cellular activities (AAA)
      cl21455
      Location:663 → 694
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. NM_001345856.2 → NP_001332785.1  ATPase family gene 2 protein homolog A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate, in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
      Source sequence(s)
      AC021205, AC026402, AC109357

    3. NM_145207.3 → NP_660208.2  ATPase family gene 2 protein homolog A isoform 1

      See identical proteins and their annotated locations for NP_660208.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC026402, AK091384, AL832175, DA619323
      Consensus CDS
      CCDS3730.1
      UniProtKB/Swiss-Prot
      C9JT97, Q86XW1, Q8NB90, Q8NI20, Q8TDL7
      Related
      ENSP00000274008.3, ENST00000274008.5
      Conserved Domains (3) summary
      COG0464
      Location:370 → 882
      SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
      pfam00004
      Location:664 → 796
      AAA; ATPase family associated with various cellular activities (AAA)
      cl21693
      Location:65 → 133
      CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      122923078..123319433
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007825.2 → XP_016863314.1  ATPase family gene 2 protein homolog A isoform X1

      Conserved Domains (2) summary
      TIGR01243
      Location:323 → 913
      CDC48; AAA family ATPase, CDC48 subfamily
      cl21693
      Location:65 → 133
      CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

    2. XM_011531678.3 → XP_011529980.1  ATPase family gene 2 protein homolog A isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PGU6
      Related
      ENSP00000502453.1, ENST00000675612.1
      Conserved Domains (2) summary
      smart01073
      Location:46 → 132
      CDC48_N; Cell division protein 48 (CDC48) N-terminal domain
      TIGR01243
      Location:322 → 912
      CDC48; AAA family ATPase, CDC48 subfamily

    3. XM_047449690.1 → XP_047305646.1  ATPase family gene 2 protein homolog A isoform X3

    4. XM_047449691.1 → XP_047305647.1  ATPase family gene 2 protein homolog A isoform X4

    5. XM_047449696.1 → XP_047305652.1  ATPase family gene 2 protein homolog A isoform X10

    6. XM_047449695.1 → XP_047305651.1  ATPase family gene 2 protein homolog A isoform X9

    7. XM_017007827.3 → XP_016863316.1  ATPase family gene 2 protein homolog A isoform X5

      Conserved Domains (2) summary
      TIGR01243
      Location:323 → 803
      CDC48; AAA family ATPase, CDC48 subfamily
      cl21693
      Location:65 → 133
      CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

    8. XM_047449692.1 → XP_047305648.1  ATPase family gene 2 protein homolog A isoform X6

    9. XM_047449693.1 → XP_047305649.1  ATPase family gene 2 protein homolog A isoform X7

    10. XM_011531679.4 → XP_011529981.1  ATPase family gene 2 protein homolog A isoform X11

      UniProtKB/Swiss-Prot
      Q8NB90
      Related
      ENST00000422835.2
      Conserved Domains (2) summary
      TIGR01243
      Location:323 → 779
      CDC48; AAA family ATPase, CDC48 subfamily
      cl21693
      Location:65 → 133
      CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

    11. XM_047449694.1 → XP_047305650.1  ATPase family gene 2 protein homolog A isoform X8

    12. XM_047449697.1 → XP_047305653.1  ATPase family gene 2 protein homolog A isoform X12

    13. XM_017007830.2 → XP_016863319.1  ATPase family gene 2 protein homolog A isoform X14

      Conserved Domains (2) summary
      TIGR01243
      Location:323 → 583
      CDC48; AAA family ATPase, CDC48 subfamily
      cl21693
      Location:65 → 133
      CDC48_N; Cell division protein 48 (CDC48), N-terminal domain

    14. XM_017007829.2 → XP_016863318.1  ATPase family gene 2 protein homolog A isoform X13

      Conserved Domains (1) summary
      TIGR01243
      Location:171 → 761
      CDC48; AAA family ATPase, CDC48 subfamily

    RNA

    1. XR_007096375.1 RNA Sequence

    2. XR_007096376.1 RNA Sequence

    3. XR_007096377.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      126227197..126623517
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349071.1 → XP_054205046.1  ATPase family gene 2 protein homolog A isoform X1

    2. XM_054349072.1 → XP_054205047.1  ATPase family gene 2 protein homolog A isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PGU6

    3. XM_054349073.1 → XP_054205048.1  ATPase family gene 2 protein homolog A isoform X3

    4. XM_054349074.1 → XP_054205049.1  ATPase family gene 2 protein homolog A isoform X4

    5. XM_054349080.1 → XP_054205055.1  ATPase family gene 2 protein homolog A isoform X10

    6. XM_054349075.1 → XP_054205050.1  ATPase family gene 2 protein homolog A isoform X5

    7. XM_054349076.1 → XP_054205051.1  ATPase family gene 2 protein homolog A isoform X6

    8. XM_054349077.1 → XP_054205052.1  ATPase family gene 2 protein homolog A isoform X7

    9. XM_054349081.1 → XP_054205056.1  ATPase family gene 2 protein homolog A isoform X11

    10. XM_054349079.1 → XP_054205054.1  ATPase family gene 2 protein homolog A isoform X9

    11. XM_054349078.1 → XP_054205053.1  ATPase family gene 2 protein homolog A isoform X8

    12. XM_054349082.1 → XP_054205057.1  ATPase family gene 2 protein homolog A isoform X12

    13. XM_054349084.1 → XP_054205059.1  ATPase family gene 2 protein homolog A isoform X14

    14. XM_054349083.1 → XP_054205058.1  ATPase family gene 2 protein homolog A isoform X13

    RNA

    1. XR_008486940.1 RNA Sequence

    2. XR_008486941.1 RNA Sequence

    3. XR_008486942.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NB90.3 GenPept UniProtKB/Swiss-Prot:Q8NB90

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