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    NAGA alpha-N-acetylgalactosaminidase [ Homo sapiens (human) ]

    Gene ID: 4668, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NAGAprovided by HGNC
    Official Full Name
    alpha-N-acetylgalactosaminidaseprovided by HGNC
    Primary source
    HGNC:HGNC:7631
    See related
    Ensembl:ENSG00000198951 MIM:104170; AllianceGenome:HGNC:7631
    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
    GALB; D22S674
    Summary
    NAGA encodes the lysosomal enzyme alpha-N-acetylgalactosaminidase, which cleaves alpha-N-acetylgalactosaminyl moieties from glycoconjugates. Mutations in NAGA have been identified as the cause of Schindler disease types I and II (type II also known as Kanzaki disease). [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in placenta (RPKM 20.0), appendix (RPKM 15.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NAGA in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42058334..42070842, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42537918..42550425, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42454338..42466846, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13816 Neighboring gene septin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42394342-42394858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42394859-42395373 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:42396708-42397907 Neighboring gene solute carrier family 25 member 5 pseudogene 1 Neighboring gene WBP2 N-terminal like Neighboring gene CYP2D6 downstream enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19152 Neighboring gene uncharacterized LOC107985551 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:42462918-42464117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19153 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42469572-42470304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42470305-42471035 Neighboring gene Sharpr-MPRA regulatory region 6008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42473646-42474208 Neighboring gene Sharpr-MPRA regulatory region 7943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42475449-42476221 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 1 Neighboring gene PH domain containing endocytic trafficking adaptor 2 Neighboring gene single-pass membrane protein with aspartate rich tail 1

    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. Structural organization and complete sequence of the human alpha-N-acetylgalactosaminidase gene: homology with the alpha-galactosidase A gene provides evidence for evolution from a common ancestral gene. Wang AM, et al. Genomics, 1991 May. PMID 1646157
    2. A new infantile case of alpha-N-acetylgalactosaminidase deficiency. Cardiomyopathy as a presenting symptom. Chabás A, et al. J Inherit Metab Dis, 2007 Feb. PMID 17171432
    3. Three dimensional structural studies of alpha-N-acetylgalactosaminidase (alpha-NAGA) in alpha-NAGA deficiency (Kanzaki disease): different gene mutations cause peculiar structural changes in alpha-NAGAs resulting in different substrate specificities and clinical phenotypes. Kanekura T, et al. J Dermatol Sci, 2005 Jan. PMID 15619430
    4. Tumor cell alpha-N-acetylgalactosaminidase activity and its involvement in GcMAF-related macrophage activation. Mohamad SB, et al. Comp Biochem Physiol A Mol Integr Physiol, 2002 May. PMID 12062184
    5. A new case of alpha-N-acetylgalactosaminidase deficiency with angiokeratoma corporis diffusum, with Ménière's syndrome and without mental retardation. Kodama K, et al. Br J Dermatol, 2001 Feb. PMID 11251574

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Could low alpha-N-acetylgalactosaminidase plasma concentration cause schizophrenia?
      Title: Could low α-N-acetylgalactosaminidase plasma concentration cause schizophrenia?
    2. Silencing of alpha-N-acetylgalactosaminidase in the gastric cancer cells amplified cell death and attenuated migration, while the multidrug resistance remained unchanged.
      Title: Silencing of α-N-acetylgalactosaminidase in the gastric cancer cells amplified cell death and attenuated migration, while the multidrug resistance remained unchanged.
    3. A missense variant in NDUFA6 confers schizophrenia risk by affecting YY1 binding and NAGA expression.
      Title: A missense variant in NDUFA6 confers schizophrenia risk by affecting YY1 binding and NAGA expression.
    4. A Novel Homozygous Missense Variant in the NAGA Gene with Extreme Intrafamilial Phenotypic Heterogeneity.
      Title: A Novel Homozygous Missense Variant in the NAGA Gene with Extreme Intrafamilial Phenotypic Heterogeneity.
    5. results demonstrate the utility of eQTL mapping in the identification of novel asthma genes and provide evidence for the importance of FADS2, NAGA, and F13A1 in the pathogenesis of asthma.
      Title: A genome-wide survey of CD4(+) lymphocyte regulatory genetic variants identifies novel asthma genes.
    6. the active sites of human lysosomal enzymes alpha-galactosidase and alpha-N-acetylgalactosaminidase have interconvertible specificites
      Title: Interconversion of the specificities of human lysosomal enzymes associated with Fabry and Schindler diseases.
    7. Use of a modified NAGA in the development of enzyme replacement therapy for Fabry disease is reported.
      Title: Use of a modified alpha-N-acetylgalactosaminidase in the development of enzyme replacement therapy for Fabry disease.
    8. The active site of human alpha-NAGAL has anomeric selectivity for its catalytic product and the structure reveals a novel active-site rearrangement upon hexose ligand binding.
      Title: The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.
    9. Specific enzymatic activity of serum alpha-N-acetylgalactosaminidase was significantly increased in stage III melanoma patients, but not in early stages.
      Title: Serum proteomic profile of cutaneous malignant melanoma and relation to cancer progression: association to tumor derived alpha-N-acetylgalactosaminidase activity.
    10. NAGA mutation p.D217N (c.649G>A) in exon 6 and mutation p.E325K (c.973G>A) in exon 8 may have roles in alpha-N-acetylgalactosaminidase deficiency with cardiomyopathy
      Title: A new infantile case of alpha-N-acetylgalactosaminidase deficiency. Cardiomyopathy as a presenting symptom.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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
    Alpha-N-acetylgalactosaminidase deficiency type 1
    MedGen: C1836544 OMIM: 609241 GeneReviews: Not available
    		Compare labs
    Alpha-N-acetylgalactosaminidase deficiency type 2
    MedGen: C1836522 OMIM: 609242 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    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

    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 alpha-N-acetylgalactosaminidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables alpha-galactosidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carbohydrate catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in glycolipid catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycoside catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in oligosaccharide metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in lysosome IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    alpha-N-acetylgalactosaminidase
    Names
    Acetylgalactosaminidase, alpha-N- (alpha-galactosidase B)
    N-acetylgalactosaminidase, alpha-
    alpha-galactosidase B
    NP_000253.1
    NP_001349777.1
    NP_001349779.1

    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_009247.1 RefSeqGene

      Range
      5031..17509
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000262.3 → NP_000253.1  alpha-N-acetylgalactosaminidase precursor

      See identical proteins and their annotated locations for NP_000253.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript variant. Variants 1-3 encode the same protein.
      Source sequence(s)
      BE734247, CB988165, M38083, Z99716
      Consensus CDS
      CCDS14030.1
      UniProtKB/Swiss-Prot
      P17050
      Related
      ENSP00000379680.3, ENST00000396398.8
      Conserved Domains (1) summary
      cl07893
      Location:25 → 394
      AmyAc_family; Alpha amylase catalytic domain family

    2. NM_001362848.1 → NP_001349777.1  alpha-N-acetylgalactosaminidase precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      Z99716
      Consensus CDS
      CCDS14030.1
      UniProtKB/Swiss-Prot
      P17050
      Related
      ENSP00000384603.1, ENST00000402937.1
      Conserved Domains (1) summary
      cl07893
      Location:25 → 394
      AmyAc_family; Alpha amylase catalytic domain family

    3. NM_001362850.1 → NP_001349779.1  alpha-N-acetylgalactosaminidase precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      Z99716
      Consensus CDS
      CCDS14030.1
      UniProtKB/Swiss-Prot
      P17050
      Related
      ENSP00000385283.1, ENST00000403363.5
      Conserved Domains (1) summary
      cl07893
      Location:25 → 394
      AmyAc_family; Alpha amylase catalytic domain family

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      42058334..42070842 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      42537918..42550425 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P17050.2 GenPept UniProtKB/Swiss-Prot:P17050

    Gene LinkOut

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

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