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

Gene ID: 10767, updated on 3-Apr-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
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Genomic context

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Location:
6q23.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (134960378..135054822, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (136148628..136243073, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. 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
  5. A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans. Kalisiak K, et al. Nucleic Acids Res, 2017 Feb 28. PMID 28204585, Free PMC Article

See all (119) 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_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
    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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