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

Gene ID: 4668, updated on 5-Mar-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
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Genomic context

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Location:
22q13.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42058334..42070842, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42537918..42550425, complement)
105.20220307 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
  • 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. Could low α-N-acetylgalactosaminidase plasma concentration cause schizophrenia? Yılmaz S, et al. World J Biol Psychiatry, 2023 Jan. PMID 35521802
  2. Silencing of α-N-acetylgalactosaminidase in the gastric cancer cells amplified cell death and attenuated migration, while the multidrug resistance remained unchanged. Jafari M, et al. Cell Biol Int, 2022 Feb. PMID 34816536
  3. A Novel Homozygous Missense Variant in the NAGA Gene with Extreme Intrafamilial Phenotypic Heterogeneity. Mohamed FE, et al. J Mol Neurosci, 2020 Jan. PMID 31468281
  4. Exploration of Structural and Functional Variations Owing to Point Mutations in α-NAGA. Meshach Paul D, et al. Interdiscip Sci, 2018 Mar. PMID 27138754
  5. 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

See all (48) 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_2023_10

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

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