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GLB1 galactosidase beta 1 [ Homo sapiens (human) ]

Gene ID: 2720, updated on 5-Mar-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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Location:
3p22.3
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (32961108..33097146, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (32962888..33098917, complement)
105.20220307 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
  • 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. Senescence-associated β-galactosidase reveals the abundance of senescent CD8+ T cells in aging humans. Martínez-Zamudio RI, et al. Aging Cell, 2021 May. PMID 33939265, Free PMC Article
  2. Morquio B disease: From pathophysiology towards diagnosis. Caciotti A, et al. Mol Genet Metab, 2021 Mar. PMID 33558080
  3. A computational approach to analyse the amino acid variants of GLB1 protein causing GM1 Gangliosidosis. Priyanka K, et al. Metab Brain Dis, 2021 Mar. PMID 33394287
  4. Detection of GM1-gangliosidosis in newborn dried blood spots by enzyme activity and biomarker assays using tandem mass spectrometry. Su P, et al. J Inherit Metab Dis, 2021 Jan. PMID 32506457
  5. Reduction of senescence-associated beta-galactosidase activity by vitamin E in human fibroblasts depends on subjects' age and cell passage number. Ricciarelli R, et al. Biofactors, 2020 Jul. PMID 32479666

See all (164) 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 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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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_2023_10

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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