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    GALC galactosylceramidase [ Homo sapiens (human) ]

    Gene ID: 2581, updated on 3-Apr-2024

    Summary

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    Official Symbol
    GALCprovided by HGNC
    Official Full Name
    galactosylceramidaseprovided by HGNC
    Primary source
    HGNC:HGNC:4115
    See related
    Ensembl:ENSG00000054983 MIM:606890; AllianceGenome:HGNC:4115
    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
    Summary
    This gene encodes a lysosomal protein which hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Mutations in this gene have been associated with Krabbe disease, also known as globoid cell leukodystrophy. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in small intestine (RPKM 14.9), duodenum (RPKM 14.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    14q31.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (87933014..87993667, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (82153629..82214299, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (88399358..88460009, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2296 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:87896478-87897677 Neighboring gene long intergenic non-protein coding RNA 2330 Neighboring gene NANOG hESC enhancer GRCh37_chr14:88228569-88229110 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:88263144-88263835 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:88296681-88297225 Neighboring gene Sharpr-MPRA regulatory region 1922 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38563 Neighboring gene uncharacterized LOC124903355 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38584 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:88459339-88459839 Neighboring gene shieldin complex subunit 2 pseudogene 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8834 Neighboring gene RNA, U6 small nuclear 835, pseudogene Neighboring gene G protein-coupled receptor 65

    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. A novel mutation in the GALC gene causes Krabbe disease accompanied with extensive Mongolian spots in a consanguineous family. Jia W, et al. Neurol Sci, 2023 Jul. PMID 36920572
    2. GALC variants affect galactosylceramidase enzymatic activity and risk of Parkinson's disease. Senkevich K, et al. Brain, 2023 May 2. PMID 36370000, Free PMC Article
    3. Galactosylceramidase deficiency and pathological abnormalities in cerebral white matter of Krabbe disease. Iacono D, et al. Neurobiol Dis, 2022 Nov. PMID 36113749, Free PMC Article
    4. β-Galactosidase is a target enzyme for detecting peritoneal metastasis of gastric cancer. Kubo H, et al. Sci Rep, 2021 May 21. PMID 34021168, Free PMC Article
    5. Two Cases of Female Chinese Adult-Onset Krabbe Disease with One Novel Mutation and a Review of Literature. Zhang C, et al. J Mol Neurosci, 2021 Jun. PMID 33190188

    See all (84) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel mutation in the GALC gene causes Krabbe disease accompanied with extensive Mongolian spots in a consanguineous family.
      Title: A novel mutation in the GALC gene causes Krabbe disease accompanied with extensive Mongolian spots in a consanguineous family.
    2. GALC variants affect galactosylceramidase enzymatic activity and risk of Parkinson's disease.
      Title: GALC variants affect galactosylceramidase enzymatic activity and risk of Parkinson's disease.
    3. Galactosylceramidase deficiency and pathological abnormalities in cerebral white matter of Krabbe disease.
      Title: Galactosylceramidase deficiency and pathological abnormalities in cerebral white matter of Krabbe disease.
    4. Two Cases of Female Chinese Adult-Onset Krabbe Disease with One Novel Mutation and a Review of Literature.
      Title: Two Cases of Female Chinese Adult-Onset Krabbe Disease with One Novel Mutation and a Review of Literature.
    5. beta-Galactosidase is a target enzyme for detecting peritoneal metastasis of gastric cancer.
      Title: β-Galactosidase is a target enzyme for detecting peritoneal metastasis of gastric cancer.
    6. Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe's disease.
      Title: Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe's disease.
    7. beta-Galactosylceramidase Promotes Melanoma Growth via Modulation of Ceramide Metabolism.
      Title: β-Galactosylceramidase Promotes Melanoma Growth via Modulation of Ceramide Metabolism.
    8. Brainstem development requires galactosylceramidase and is critical for pathogenesis in a model of Krabbe disease.
      Title: Brainstem development requires galactosylceramidase and is critical for pathogenesis in a model of Krabbe disease.
    9. This study generated information on the recessive allele frequency dynamics of GALC gene across 15 global populations.
      Title: Allele frequency analysis of GALC gene causing Krabbe disease in human and its codon usage.
    10. Self-association of beta-galactocerebrosidase (human GALC)decreases as the concentration of sodium chloride increases from 50 to 500 mM. This indicates that ionic interactions are involved in the association. These results indicate that GALC has the highest tendency for oligomerization at physiological ionic strength and pH (lysosomal lumen).
      Title: Self-association of human beta-galactocerebrosidase: Dependence on pH, salt, and surfactant.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    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
    Galactosylceramide beta-galactosidase deficiency
    MedGen: C0023521 OMIM: 245200 GeneReviews: Krabbe Disease
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study of breast cancer in women of African ancestry.
    EBI GWAS Catalog
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of galactosylceramidase (GALC) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat protein transduction domain increases expression of GALC fusion protein mainly through increased translation efficiency in 293T cells PubMed

    Go to the HIV-1, Human Interaction Database

    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 galactosylceramidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables galactosylceramidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables galactosylceramidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables galactosylceramidase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in galactosylceramide catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in galactosylceramide catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in galactosylceramide catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in glycosphingolipid catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in myelination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    galactocerebrosidase
    Names
    GALCERase
    galactocerebroside beta-galactosidase
    galactosylceramide beta-galactosidase
    galactosylceraminidase
    testis tissue sperm-binding protein Li 88E
    testis tissue sperm-binding protein Li 89A
    NP_000144.2
    NP_001188330.1
    NP_001188331.1
    NP_001411000.1
    NP_001411001.1
    NP_001411002.1
    NP_001411003.1
    NP_001411004.1
    NP_001411005.1
    NP_001411006.1
    XP_047287155.1
    XP_054231744.1

    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_011853.3 RefSeqGene

      Range
      5382..65550
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000153.4 → NP_000144.2  galactocerebrosidase isoform a precursor

      See identical proteins and their annotated locations for NP_000144.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AL136501, AL157955
      Consensus CDS
      CCDS9878.2
      UniProtKB/Swiss-Prot
      B4DKE8, B4DYN1, B4DZJ8, B7Z7Z2, J3KN25, J3KPP8, P54803, Q8J030
      UniProtKB/TrEMBL
      A0A0A0MQV0
      Related
      ENSP00000261304.2, ENST00000261304.7
      Conserved Domains (2) summary
      pfam02057
      Location:17 → 685
      Glyco_hydro_59; Glycosyl hydrolase family 59
      cl23815
      Location:138 → 358
      Glyco_hydro_30; O-Glycosyl hydrolase family 30

    2. NM_001201401.2 → NP_001188330.1  galactocerebrosidase isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a.
      Source sequence(s)
      AL136501, AL157955
      Consensus CDS
      CCDS55936.1
      Related
      ENSP00000377198.4, ENST00000393568.8
      Conserved Domains (2) summary
      pfam02057
      Location:17 → 662
      Glyco_hydro_59; Glycosyl hydrolase family 59
      cl23815
      Location:115 → 335
      Glyco_hydro_30; O-Glycosyl hydrolase family 30

    3. NM_001201402.2 → NP_001188331.1  galactocerebrosidase isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AL136501, AL157955
      Consensus CDS
      CCDS55937.1
      Related
      ENSP00000377199.2, ENST00000393569.6
      Conserved Domains (2) summary
      pfam02057
      Location:39 → 659
      Glyco_hydro_59; Glycosyl hydrolase family 59
      cl23815
      Location:112 → 332
      Glyco_hydro_30; O-Glycosyl hydrolase family 30

    4. NM_001424071.1 → NP_001411000.1  galactocerebrosidase isoform e

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955

    5. NM_001424072.1 → NP_001411001.1  galactocerebrosidase isoform e

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955

    6. NM_001424073.1 → NP_001411002.1  galactocerebrosidase isoform f

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955
      Related
      ENSP00000437513.2, ENST00000544807.6

    7. NM_001424074.1 → NP_001411003.1  galactocerebrosidase isoform g

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955

    8. NM_001424075.1 → NP_001411004.1  galactocerebrosidase isoform g

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955

    9. NM_001424076.1 → NP_001411005.1  galactocerebrosidase isoform h

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955

    10. NM_001424077.1 → NP_001411006.1  galactocerebrosidase isoform h

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955
      Related
      ENSP00000450472.1, ENST00000555000.5

    RNA

    1. NR_187582.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL136501, AL157955

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      87933014..87993667 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431199.1 → XP_047287155.1  galactocerebrosidase isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      82153629..82214299 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375769.1 → XP_054231744.1  galactocerebrosidase isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001037525.2: Suppressed sequence

      Description
      NM_001037525.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P54803.3 GenPept UniProtKB/Swiss-Prot:P54803

    Gene LinkOut

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

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