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    HBS1L HBS1 like translational GTPase [ Homo sapiens (human) ]

    Gene ID: 10767, updated on 28-Oct-2024

    Summary

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    Official Symbol
    HBS1Lprovided by HGNC
    Official Full Name
    HBS1 like translational GTPaseprovided by HGNC
    Primary source
    HGNC:HGNC:4834
    See related
    Ensembl:ENSG00000112339 MIM:612450; AllianceGenome:HGNC:4834
    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
    ERFS; HBS1; EF-1a; eRF3c; HSPC276
    Summary
    This gene encodes a member of the GTP-binding elongation factor family. It is expressed in multiple tissues with the highest expression in heart and skeletal muscle. The intergenic region of this gene and the MYB gene has been identified to be a quantitative trait locus (QTL) controlling fetal hemoglobin level, and this region influnces erythrocyte, platelet, and monocyte counts as well as erythrocyte volume and hemoglobin content. DNA polymorphisms at this region associate with fetal hemoglobin levels and pain crises in sickle cell disease. A single nucleotide polymorphism in exon 1 of this gene is significantly associated with severity in beta-thalassemia/Hemoglobin E. Multiple alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, May 2009]
    Expression
    Ubiquitous expression in bone marrow (RPKM 6.5), brain (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HBS1L in Genome Data Viewer
    Location:
    6q23.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (134960378..135054822, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (136148628..136243073, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (135281516..135375960, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:135226183-135226682 Neighboring gene MEMO1 pseudogene 2 Neighboring gene aldehyde dehydrogenase 8 family member A1 Neighboring gene MPRA-validated peak6134 silencer Neighboring gene MPRA-validated peak6136 silencer Neighboring gene microRNA 3662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25096 Neighboring gene uncharacterized LOC124901405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25097 Neighboring gene uncharacterized LOC124901406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25099 Neighboring gene uncharacterized LOC105378010

    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. Intergenic variants of HBS1L-MYB are responsible for a major quantitative trait locus on chromosome 6q23 influencing fetal hemoglobin levels in adults. Thein SL, et al. Proc Natl Acad Sci U S A, 2007 Jul 3. PMID 17592125, Free PMC Article
    2. Induction of fetal hemoglobin: Lentiviral shRNA knockdown of HBS1L in β0-thalassemia/HbE erythroid cells. Chumchuen S, et al. PLoS One, 2023. PMID 36888630, Free PMC Article
    3. The product of the mammalian orthologue of the Saccharomyces cerevisiae HBS1 gene is phylogenetically related to eukaryotic release factor 3 (eRF3) but does not carry eRF3-like activity. Wallrapp C, et al. FEBS Lett, 1998 Dec 4. PMID 9872408
    4. Histamine releasing factor and elongation factor 1 alpha secreted via malaria parasites extracellular vesicles promote immune evasion by inhibiting specific T cell responses. Demarta-Gatsi C, et al. Cell Microbiol, 2019 Jul. PMID 30835870
    5. 2SNP heritability and effects of genetic variants for neutrophil-to-lymphocyte and platelet-to-lymphocyte ratio. Lin BD, et al. J Hum Genet, 2017 Nov. PMID 29066854, Free PMC Article

    See all (131) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Induction of fetal hemoglobin: Lentiviral shRNA knockdown of HBS1L in beta0-thalassemia/HbE erythroid cells.
      Title: Induction of fetal hemoglobin: Lentiviral shRNA knockdown of HBS1L in β0-thalassemia/HbE erythroid cells.
    2. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences.
      Title: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences.
    3. Histamine releasing factor and elongation factor 1 alpha secreted via malaria parasites extracellular vesicles promote immune evasion by inhibiting specific T cell responses.
      Title: Histamine releasing factor and elongation factor 1 alpha secreted via malaria parasites extracellular vesicles promote immune evasion by inhibiting specific T cell responses.
    4. Patients carrying Fetal Hemoglobin-boosting alleles of BCL11A and HMIP-2 ( (HBS1L-MYB) were associated with milder clinical phenotypes. Higher HbF concentration may underlie this effect.
      Title: Functional polymorphisms of BCL11A and HBS1L-MYB genes affect both fetal hemoglobin level and clinical outcomes in a cohort of children with sickle cell anemia.
    5. Identification of HBS1LV3, a short splicing isoform of HBS1L, as a linker between the human cytoplasmic exosome and the SKI complex.
      Title: A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans.
    6. genome-wide association analyses identified a new genome-wide significant locus on the HBS1L-MYB intergenic region for platelet-to-lymphocyte ratio
      Title: 2SNP heritability and effects of genetic variants for neutrophil-to-lymphocyte and platelet-to-lymphocyte ratio.
    7. Studied association of BCL11A single nucleotide polymorphisms(snps) and HBS1L-MYB Intergenic snps with Hereditary Persistence of Fetal Hemoglobin (HPFH) in a cohort of sickle cell patients.
      Title: Protective BCL11A and HBS1L-MYB polymorphisms in a cohort of 102 Congolese patients suffering from sickle cell anemia.
    8. Induction of ribosome rescue factors PELO and HBS1L is required to support protein synthesis when ABCE1 levels fall in platelets, including for hemoglobin production during blood cell development.
      Title: Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets.
    9. Knowledge of the interacting residues in the yeast complexes allowed identification of a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor.
      Title: Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.
    10. high-risk genotypes of six Hb F-associated SNPs, rs9376090, rs7776054, rs9399137, rs9389268, rs9402685 in the HBS1L-MYB intergenic region and rs189984760 in the BCL11A locus, showed association with high Hb F levels
      Title: Genetic Variants at BCL11A and HBS1L-MYB loci Influence Hb F Levels in Chinese Zhuang β-Thalassemia Intermedia Patients.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    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
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    EBI GWAS Catalog
    A genome-wide association identified the common genetic variants influence disease severity in beta0-thalassemia/hemoglobin E.
    EBI GWAS Catalog
    A genome-wide association study of red blood cell traits using the electronic medical record.
    EBI GWAS Catalog
    A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
    EBI GWAS Catalog
    A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans.
    EBI GWAS Catalog
    Genome wide association study of fetal hemoglobin in sickle cell anemia in Tanzania.
    EBI GWAS Catalog
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
    EBI GWAS Catalog
    HbA2 levels in normal adults are influenced by two distinct genetic mechanisms.
    EBI GWAS Catalog
    Identification of nine novel loci associated with white blood cell subtypes in a Japanese population.
    EBI GWAS Catalog
    Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
    EBI GWAS Catalog
    Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians.
    EBI GWAS Catalog
    New gene functions in megakaryopoiesis and platelet formation.
    EBI GWAS Catalog
    Sequence variants in three loci influence monocyte counts and erythrocyte volume.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    EBI GWAS Catalog
    Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin's lymphoma.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686L13262

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables translation elongation factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in nuclear-transcribed mRNA catabolic process, no-go decay IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rescue of stalled ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ribosome disassembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of Dom34-Hbs1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in cytosolic ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    HBS1-like protein
    Names
    ERF3-similar protein
    Hsp70 subfamily B suppressor 1-like protein
    eRF3 family member

    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_012002.1 RefSeqGene

      Range
      5077..99521
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001145158.2 → NP_001138630.1  HBS1-like protein isoform 2

      See identical proteins and their annotated locations for NP_001138630.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
      Source sequence(s)
      AB028961, AJ459826, AK295545, AL445190, BC040849, DB051030
      Consensus CDS
      CCDS47479.1
      UniProtKB/TrEMBL
      A8K9E1, B3KNB9
      Related
      ENSP00000356800.2, ENST00000367826.6
      Conserved Domains (5) summary
      cd01883
      Location:220 → 439
      EF1_alpha; Elongation Factor 1-alpha (EF1-alpha) protein family
      COG5256
      Location:214 → 642
      TEF1; Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
      pfam08938
      Location:5 → 81
      HBS1_N; HBS1 N-terminus
      cd16267
      Location:445 → 527
      HBS1-like_II; Domain II of Hbs1-like proteins
      cd04093
      Location:532 → 640
      HBS1_C_III; C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1)

    2. NM_001145207.2 → NP_001138679.1  HBS1-like protein isoform 3

      See identical proteins and their annotated locations for NP_001138679.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate exon for its 3' coding region and 3' UTR, compared to variant (1). This results in a protein (isoform 3) with a much shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AJ459827
      Consensus CDS
      CCDS47480.1
      UniProtKB/Swiss-Prot
      Q9Y450
      Related
      ENSP00000356796.5, ENST00000367822.9
      Conserved Domains (1) summary
      pfam08938
      Location:54 → 123
      HBS1_N; HBS1 N-terminus

    3. NM_001363686.2 → NP_001350615.1  HBS1-like protein isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AL353596, AL445190
      Consensus CDS
      CCDS87443.1
      UniProtKB/TrEMBL
      B7Z524, H0YDX7
      Related
      ENSP00000436256.1, ENST00000527578.5
      Conserved Domains (1) summary
      COG5256
      Location:92 → 520
      TEF1; Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]

    4. NM_006620.4 → NP_006611.1  HBS1-like protein isoform 1

      See identical proteins and their annotated locations for NP_006611.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL445190, BC001465, DB051030
      Consensus CDS
      CCDS5173.1
      UniProtKB/Swiss-Prot
      B7Z365, Q4VX89, Q4VX90, Q5T7G3, Q8NDW9, Q9UPW3, Q9Y450
      UniProtKB/TrEMBL
      A8K9E1, B3KNB9, D9YZV0
      Related
      ENSP00000356811.5, ENST00000367837.10
      Conserved Domains (2) summary
      COG5256
      Location:256 → 684
      TEF1; Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
      pfam08938
      Location:54 → 129
      HBS1_N; HBS1 N-terminus

    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
      134960378..135054822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418093.1 → XP_047274049.1  HBS1-like protein isoform X1

    2. XM_017010192.2 → XP_016865681.1  HBS1-like protein isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      136148628..136243073 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354060.1 → XP_054210035.1  HBS1-like protein isoform X1

    2. XM_054354061.1 → XP_054210036.1  HBS1-like protein isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y450.1 GenPept UniProtKB/Swiss-Prot:Q9Y450

    Gene LinkOut

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

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