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    AFG2B AFG2 AAA ATPase homolog B [ Homo sapiens (human) ]

    Gene ID: 79029, updated on 27-Nov-2024

    Summary

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    Official Symbol
    AFG2Bprovided by HGNC
    Official Full Name
    AFG2 AAA ATPase homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:28762
    See related
    Ensembl:ENSG00000171763 MIM:619578; AllianceGenome:HGNC:28762
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NEDHLS; DFNB119; SPATA5L1
    Summary
    Enables preribosome binding activity. Involved in ribosomal large subunit biogenesis. Located in cytoplasm and spindle. Implicated in autosomal recessive nonsyndromic deafness. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in esophagus (RPKM 2.7), bone marrow (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See AFG2B in Genome Data Viewer
    Location:
    15q21.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (45402336..45421415)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (43210511..43229587)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (45694534..45713613)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 953, pseudogene Neighboring gene glycine amidinotransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:45716799-45717298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6409 Neighboring gene uncharacterized LOC107987223 Neighboring gene chromosome 15 open reading frame 48 Neighboring gene microRNA 147b

    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. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss. Richard EM, et al. Am J Hum Genet, 2021 Oct 7. PMID 34626583, Free PMC Article
    2. Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly. Ni C, et al. Cell Rep, 2022 Mar 29. PMID 35354024, Free PMC Article
    3. Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate. Tin A, et al. J Hum Genet, 2013 Jul. PMID 23535967, Free PMC Article
    4. Multiple loci associated with indices of renal function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2009 Jun. PMID 19430482, Free PMC Article
    5. EML3 is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. Tegha-Dunghu J, et al. J Cell Sci, 2008 May 15. PMID 18445686

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss.
      Title: Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss.
    2. Observational study, meta-analysis, and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Multiple loci associated with indices of renal function and chronic kidney disease.
    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

    Associated conditions

    Description Tests
    Hearing loss, autosomal recessive 119
    MedGen: C5562023 OMIM: 619615 GeneReviews: Not available
    		Compare labs
    Neurodevelopmental disorder with hearing loss and spasticity
    MedGen: C5562024 OMIM: 619616 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Multiple loci associated with indices of renal function and chronic kidney disease.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog
    Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Interaction of HIV-1 Gag with spermatogenesis associated 5-like 1 (SPATA5L1) is identified in a series of six affinity purification/mass spectrometry screens PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC5347, FLJ12286

    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 polyubiquitin modification-dependent protein binding 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 autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic spindle disassembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde protein transport, ER to cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal large subunit biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of VCP-NPL4-UFD1 AAA ATPase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus 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 B
    Names
    ribosome biogenesis protein SPATA5L1
    spermatogenesis associated 5 like 1
    spermatogenesis-associated protein 5-like protein 1
    NP_001310569.1
    NP_076968.2

    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_001323640.2 → NP_001310569.1  ATPase family gene 2 protein homolog B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC025580
      Consensus CDS
      CCDS81877.1
      UniProtKB/Swiss-Prot
      Q9BVQ7
      Related
      ENSP00000436823.1, ENST00000531970.5
      Conserved Domains (3) summary
      smart00382
      Location:234 → 370
      AAA; ATPases associated with a variety of cellular activities
      COG1222
      Location:446 → 596
      RPT1; ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
      pfam00004
      Location:237 → 367
      AAA; ATPase family associated with various cellular activities (AAA)

    2. NM_024063.3 → NP_076968.2  ATPase family gene 2 protein homolog B isoform 1

      See identical proteins and their annotated locations for NP_076968.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
      Source sequence(s)
      AA451905, AC025580, AK225463, DC346759
      Consensus CDS
      CCDS10123.1
      UniProtKB/Swiss-Prot
      C9JHR5, Q9BVQ7, Q9H8W7, Q9HA41
      Related
      ENSP00000305494.6, ENST00000305560.11
      Conserved Domains (2) summary
      TIGR01243
      Location:22 → 746
      CDC48; AAA family ATPase, CDC48 subfamily
      pfam00004
      Location:501 → 651
      AAA; ATPase family associated with various cellular activities (AAA)

    RNA

    1. NR_027635.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA451905, AC025580, AK023232

    2. NR_136645.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025580

    3. NR_136646.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025580

    4. NR_136647.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025580

    5. NR_136648.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025580

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      45402336..45421415
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      43210511..43229587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BVQ7.2 GenPept UniProtKB/Swiss-Prot:Q9BVQ7

    Gene LinkOut

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

    Chemical Information
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