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GALC galactosylceramidase [ Homo sapiens (human) ]

Gene ID: 2581, updated on 14-Nov-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
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Genomic context

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See GALC in Genome Data Viewer
Location:
14q31.3
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (87933014..87993667, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (82153629..82214299, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (88399358..88460011, 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 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. Adult onset globoid cell leukodystrophy (Krabbe disease): analysis of galactosylceramidase cDNA from four Japanese patients. Furuya H, et al. Hum Genet, 1997 Sep. PMID 9272171
  2. Galactocerebrosidase from human urine: purification and partial characterization. Chen YQ, et al. Biochim Biophys Acta, 1993 Sep 29. PMID 8399327
  3. Mutations in GALC cause late-onset Krabbe disease with predominant cerebellar ataxia. Shao YH, et al. Neurogenetics, 2016 Apr. PMID 26915362
  4. DNA promoter hypermethylation contributes to down-regulation of galactocerebrosidase gene in lung and head and neck cancers. Peng J, et al. Int J Clin Exp Pathol, 2015. PMID 26617822, Free PMC Article
  5. Molecular defects in Krabbe disease. Tatsumi N, et al. Hum Mol Genet, 1995 Oct. PMID 8595408

See all (86) 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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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)

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
  
located_in membrane IEA
Inferred from Electronic Annotation
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_2024_08

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

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