Gene Gene information from NCBI Gene database.
Entrez ID 4668
Gene name Alpha-N-acetylgalactosaminidase
Gene symbol NAGA
Synonyms (NCBI Gene)
D22S674GALB
Chromosome 22
Chromosome location 22q13.2
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 Ka
SNPs SNP information provided by dbSNP.
5
SNP ID Visualize variation Clinical significance Consequence
rs73167107 C>T Conflicting-interpretations-of-pathogenicity, uncertain-significance Coding sequence variant, missense variant
rs121434529 C>T Pathogenic-likely-pathogenic, pathogenic Coding sequence variant, missense variant
rs121434530 G>A Pathogenic Coding sequence variant, missense variant
rs121434533 C>T Uncertain-significance, pathogenic Coding sequence variant, missense variant
rs140673721 C>T Likely-pathogenic Splice donor variant
miRNA miRNA information provided by mirtarbase database.
153
miRTarBase ID miRNA Experiments Reference
MIRT016604 hsa-miR-193b-3p Microarray 20304954
MIRT043313 hsa-miR-331-3p CLASH 23622248
MIRT1172991 hsa-miR-150 CLIP-seq
MIRT1172992 hsa-miR-2110 CLIP-seq
MIRT1172993 hsa-miR-3120-3p CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
19
GO ID Ontology Definition Evidence Reference
GO:0004553 Function Hydrolase activity, hydrolyzing O-glycosyl compounds IEA
GO:0004557 Function Alpha-galactosidase activity IBA
GO:0005737 Component Cytoplasm IBA
GO:0005764 Component Lysosome IEA
GO:0005975 Process Carbohydrate metabolic process IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
104170 7631 ENSG00000198951
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P17050
Protein name Alpha-N-acetylgalactosaminidase (EC 3.2.1.49) (Alpha-galactosidase B)
Protein function Removes terminal alpha-N-acetylgalactosamine residues from glycolipids and glycopeptides. Required for the breakdown of glycolipids.
PDB 3H53 , 3H54 , 3H55 , 3IGU , 4DO4 , 4DO5 , 4DO6
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF16499 Melibiase_2 25 308 Alpha galactosidase A Family
PF17450 Melibiase_2_C 311 394 Alpha galactosidase A C-terminal beta sandwich domain Domain
Sequence
Sequence length 411
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Glycosphingolipid biosynthesis - globo and isoglobo series
Metabolic pathways
Lysosome
 
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
19
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Alpha-N-acetylgalactosaminidase deficiency Pathogenic; Likely pathogenic rs2519056409, rs121434530, rs781137026 RCV005407263
RCV004767012
RCV005408755
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Alpha-N-acetylgalactosaminidase deficiency type 1 Likely pathogenic; Pathogenic rs779423223, rs1348362674, rs2519053484, rs2519065527, rs2519064379, rs2519053431, rs1926691614, rs182798205, rs2519061179, rs1435289617, rs2519053637, rs1461803502, rs1381519494, rs140673721, rs2519056669
View all (13 more)
RCV000192506
RCV003517887
RCV003517907
RCV003518241
RCV003518292
View all (24 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alpha-N-acetylgalactosaminidase deficiency type 2 Likely pathogenic; Pathogenic rs779423223, rs775099024, rs121434530, rs121434531, rs140673721, rs768761898 RCV002478678
RCV005030337
RCV000019793
RCV000019794
RCV005034291
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Malignant tumor of esophagus Likely pathogenic rs768761898 RCV005866848
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Alpha-N-acetylgalactosaminidase deficiency type 3 Conflicting classifications of pathogenicity; Uncertain significance ClinVar
GenCC
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Arthrogryposis multiplex congenita Uncertain significance ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial cancer of breast Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adult Neuroaxonal Dystrophy Neuroaxonal Dystrophy CTD_human_DG 2243144
★☆☆☆☆
Found in Text Mining only
Agenesis of corpus callosum Agenesis Of Corpus Callosum BEFREE 10359046
★☆☆☆☆
Found in Text Mining only
Alpha-N-acetylgalactosaminidase deficiency type 1 Alpha-N-Acetylgalactosaminidase Deficiency Orphanet
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alpha-N-acetylgalactosaminidase deficiency type 2 Alpha-N-Acetylgalactosaminidase Deficiency Orphanet
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alpha-N-acetylgalactosaminidase deficiency type 3 Alpha-N-Acetylgalactosaminidase Deficiency Orphanet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Aplasia Cutis Congenita Aplasia Cutis Congenita BEFREE 10359046
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism HPO_DG
★☆☆☆☆
Found in Text Mining only
Cardiomyopathies Cardiomyopathy LHGDN 17171432
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
Central visual impairment Central Visual Impairment HPO_DG
★☆☆☆☆
Found in Text Mining only