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    GLB1 galactosidase beta 1 [ Homo sapiens (human) ]

    Gene ID: 2720, updated on 3-Nov-2024

    Summary

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    Official Symbol
    GLB1provided by HGNC
    Official Full Name
    galactosidase beta 1provided by HGNC
    Primary source
    HGNC:HGNC:4298
    See related
    Ensembl:ENSG00000170266 MIM:611458; AllianceGenome:HGNC:4298
    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
    EBP; ELNR1; MPS4B
    Summary
    This gene encodes a member of the glycosyl hydrolase 35 family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature lysosomal enzyme. This enzyme catalyzes the hydrolysis of a terminal beta-linked galactose residue from ganglioside substrates and other glycoconjugates. Mutations in this gene may result in GM1-gangliosidosis and Morquio B syndrome. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in thyroid (RPKM 28.5), placenta (RPKM 24.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GLB1 in Genome Data Viewer
    Location:
    3p22.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (32961108..33097146, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (32962888..33098917, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (33002600..33138638, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:32859949-32860530 Neighboring gene MPRA-validated peak4592 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:32877349-32877906 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32878590-32879187 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32879188-32879784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32880383-32880978 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:32885158-32885753 Neighboring gene tripartite motif containing 71 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32888797-32889377 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32895307-32895816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32897845-32898520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32902307-32902911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:32905556-32906320 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32910977-32911780 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:32914193-32914996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14179 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:32944496-32944651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14180 Neighboring gene MPRA-validated peak4594 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:32978284-32978481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:32981295-32981797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14181 Neighboring gene C-C motif chemokine receptor 4 Neighboring gene uncharacterized LOC107986072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19640 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:33038929-33039428 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:33076939-33078138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19641 Neighboring gene SEC13 homolog, nuclear pore and COPII coat complex component pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19644 Neighboring gene SUMO2 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14183 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:33156217-33157208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14184 Neighboring gene RNA, 7SL, cytoplasmic 296, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr3:33157792-33157940 Neighboring gene transmembrane protein with metallophosphoesterase domain Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19647 Neighboring gene cartilage associated protein

    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. Four novel mutations in patients from the Middle East with the infantile form of GM1-gangliosidosis. Georgiou T, et al. Hum Mutat, 2004 Oct. PMID 15365997
    2. Absence of senescence-associated beta-galactosidase activity in human melanocytic nevi in vivo. Cotter MA, et al. J Invest Dermatol, 2007 Oct. PMID 17522702, Free PMC Article
    3. Association of the GLB1 rs4678680 genetic variant with risk of HBV-related hepatocellular carcinoma. Wang WT, et al. Oncotarget, 2016 Aug 30. PMID 27489354, Free PMC Article
    4. Twenty-one novel mutations in the GLB1 gene identified in a large group of GM1-gangliosidosis and Morquio B patients: possible common origin for the prevalent p.R59H mutation among gypsies. Santamaria R, et al. Hum Mutat, 2006 Oct. PMID 16941474
    5. Senescence-associated beta-galactosidase is lysosomal beta-galactosidase. Lee BY, et al. Aging Cell, 2006 Apr. PMID 16626397

    See all (171) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. p53 Regulates Mitochondrial Dynamics in Vascular Smooth Muscle Cell Calcification.
      Title: p53 Regulates Mitochondrial Dynamics in Vascular Smooth Muscle Cell Calcification.
    2. Higher Oxidative Stress in Endometriotic Lesions Upregulates Senescence-Associated p16[ink4a] and beta-Galactosidase in Stromal Cells.
      Title: Higher Oxidative Stress in Endometriotic Lesions Upregulates Senescence-Associated p16(ink4a) and β-Galactosidase in Stromal Cells.
    3. Detection of GM1-gangliosidosis in newborn dried blood spots by enzyme activity and biomarker assays using tandem mass spectrometry.
      Title: Detection of GM1-gangliosidosis in newborn dried blood spots by enzyme activity and biomarker assays using tandem mass spectrometry.
    4. Senescence-associated beta-galactosidase reveals the abundance of senescent CD8+ T cells in aging humans.
      Title: Senescence-associated β-galactosidase reveals the abundance of senescent CD8+ T cells in aging humans.
    5. A computational approach to analyse the amino acid variants of GLB1 protein causing GM1 Gangliosidosis.
      Title: A computational approach to analyse the amino acid variants of GLB1 protein causing GM1 Gangliosidosis.
    6. Increased cellular senescence in the murine and human stenotic kidney: Effect of mesenchymal stem cells.
      Title: Increased cellular senescence in the murine and human stenotic kidney: Effect of mesenchymal stem cells.
    7. Reduction of senescence-associated beta-galactosidase activity by vitamin E in human fibroblasts depends on subjects' age and cell passage number.
      Title: Reduction of senescence-associated beta-galactosidase activity by vitamin E in human fibroblasts depends on subjects' age and cell passage number.
    8. Morquio B disease: From pathophysiology towards diagnosis.
      Title: Morquio B disease: From pathophysiology towards diagnosis.
    9. Different Stages of Quiescence, Senescence, and Cell Stress Identified by Molecular Algorithm Based on the Expression of Ki67, RPS6, and Beta-Galactosidase Activity.
      Title: Different Stages of Quiescence, Senescence, and Cell Stress Identified by Molecular Algorithm Based on the Expression of Ki67, RPS6, and Beta-Galactosidase Activity.
    10. Novel and deleterious variants in VPS53, GLB1, and MLC1, genes previously associated with variable neurodevelopmental anomalies, were found to segregate with intellectual disabilities in the three families.
      Title: Novel variants underlying autosomal recessive intellectual disability in Pakistani consanguineous families.
    Submit: New GeneRIF Correction See all GeneRIFs (62)

    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
    Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma.
    EBI GWAS Catalog
    Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese 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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-galactosidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables beta-galactosidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables beta-galactosidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables beta-galactosidase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables galactoside binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carbohydrate metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in galactose catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in galactose catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycosphingolipid catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in heparan sulfate proteoglycan catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in keratan sulfate catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in response to Thyroglobulin triiodothyronine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to cortisone IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in azurophil granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    beta-galactosidase
    Names
    acid beta-galactosidase
    elastin binding protein
    elastin receptor 1, 67kDa
    lactase
    NP_000395.3
    NP_001073279.2
    NP_001129074.2
    NP_001303969.2
    NP_001380509.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_009005.2 RefSeqGene

      Range
      5000..105529
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000404.4 → NP_000395.3  beta-galactosidase isoform a preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (a).
      Source sequence(s)
      AC112211
      Consensus CDS
      CCDS43061.1
      UniProtKB/Swiss-Prot
      B2R7H8, B7Z6B0, P16278, P16279
      Related
      ENSP00000306920.4, ENST00000307363.10
      Conserved Domains (2) summary
      pfam01301
      Location:40 → 354
      Glyco_hydro_35; Glycosyl hydrolases family 35
      pfam13364
      Location:551 → 619
      BetaGal_dom4_5; Beta-galactosidase jelly roll domain

    2. NM_001079811.3 → NP_001073279.2  beta-galactosidase isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream start site compared to variant 1. The encoded isoform (b) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform a.
      Source sequence(s)
      AC112211
      Consensus CDS
      CCDS43062.1
      UniProtKB/Swiss-Prot
      B2R7H8, B7Z6B0, P16278, P16279
      Related
      ENSP00000382333.2, ENST00000399402.7
      Conserved Domains (2) summary
      pfam01301
      Location:10 → 324
      Glyco_hydro_35; Glycosyl hydrolases family 35
      pfam13364
      Location:521 → 589
      BetaGal_dom4_5; Beta-galactosidase jelly roll domain

    3. NM_001135602.3 → NP_001129074.2  beta-galactosidase isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate exons in the coding region compared to variant 1. The encoded isoform (c) is shorter than isoform a. This isoform (c) may undergo proteolytic processing similar to isoform a.
      Source sequence(s)
      AC112211
      Consensus CDS
      CCDS46785.1
      UniProtKB/TrEMBL
      B7Z5H9, E7EQ29
      Related
      ENSP00000305920.8, ENST00000307377.12
      Conserved Domains (2) summary
      pfam13364
      Location:420 → 488
      BetaGal_dom4_5; Beta-galactosidase jelly roll domain
      cl38930
      Location:40 → 223
      AmyAc_family; Alpha amylase catalytic domain family

    4. NM_001317040.2 → NP_001303969.2  beta-galactosidase isoform d precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (d) is longer than isoform a. This isoform (d) may undergo proteolytic processing similar to isoform a.
      Source sequence(s)
      AC112211
      UniProtKB/TrEMBL
      B7Z6Q5
      Conserved Domains (2) summary
      pfam01301
      Location:88 → 402
      Glyco_hydro_35; Glycosyl hydrolases family 35
      pfam13364
      Location:599 → 667
      BetaGal_dom4_5; Beta-galactosidase jelly roll domain

    5. NM_001393580.1 → NP_001380509.1  beta-galactosidase isoform e precursor

      Status: REVIEWED

      Source sequence(s)
      AC112211, AC137560
      UniProtKB/Swiss-Prot
      B2R7H8, B7Z6B0, P16278, P16279
      Conserved Domains (1) summary
      PLN03059
      Location:34 → 389
      PLN03059; beta-galactosidase; Provisional

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      32961108..33097146 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      32962888..33098917 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P16278.2 GenPept UniProtKB/Swiss-Prot:P16278

    Gene LinkOut

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

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