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Gene

NAGA

alpha-N-acetylgalactosaminidase

Summary

Cytogenetic location
22q13.2
Coordinates
Chromosome 22: 42,058,334–42,070,812 (GRCh38)
Exons
9 exons across 12.5 kb
Protein
411 amino acids
Inheritance
Autosomal recessive
Also known as
D22S674
MANE Select transcript
ENST00000396398.8NM_000262.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Alpha-Mannosidosis and Other Glycoproteinoses

    • Alpha-N-acetylgalactosaminidase deficiency (Schindler and Kanzaki disease)Autosomal recessive

      A spectrum from infantile neuroaxonal dystrophy to adult-onset angiokeratomas, caused by NAGA variants.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

Broader groupings

  • Lysosomal Storage Disease

    • Lysosomal storage disease (other and unspecified types)

      One of 59 genes linked to it

      Covers lysosomal storage diseases without a dedicated report, such as Farber disease and other ASAH1-related disorders, prosaposin (PSAP) deficiencies, multiple sulfatase deficiency, mucopolysaccharidosis types IX and X, and Dorfman-Chanarin disease; inheritance varies by subtype, most often autosomal recessive.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How NAGA is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 22, with a bracket where NAGA sits. NAGA and 23 genes near it on chromosome 22, from 41,564,573 to 42,564,572.Chromosome 2222q13.2p13p12p11.2p11.1q11.1q11.21q11.22q11.23q12.1q12.2q12.3q13.1q13.2q13.31q13.32q13.3341.6 Mb41.8 Mb42 Mb42.2 Mb42.4 MbCSDC2: 41,560,758–41,577,741, forward strandCSDC2PMM1: 41,576,886–41,595,275, reverse strandPMM1DESI1: 41,598,028–41,621,089, reverse strandDESI1XRCC6: 41,620,786–41,664,087, forward strandXRCC6SNU13: 41,666,627–41,690,504, reverse strandSNU13MEI1: 41,699,494–41,799,456, forward strandMEI1CCDC134: 41,800,321–41,832,178, forward strandCCDC134SREBF2: 41,833,029–41,907,308, forward strandSREBF2SHISA8: 41,906,316–41,915,129, reverse strandSHISA8TNFRSF13C: 41,922,032–41,926,806, reverse strandTNFRSF13CCENPM: 41,927,514–41,947,183, reverse strandCENPMSMIM45: 41,947,178–41,958,942, forward strandSMIM45SEPTIN3: 41,969,443–41,998,221, forward strandSEPTIN3WBP2NL: 41,998,725–42,058,456, forward strandNAGA: 42,058,334–42,070,812, reverse strandNAGAPHETA2: 42,073,789–42,079,439, forward strandPHETA2SMDT1: 42,079,564–42,090,033, forward strandSMDT1NDUFA6: 42,080,336–42,090,884, reverse strandNDUFA6CYP2D6: 42,120,962–42,131,727, reverse strandCYP2D6CYP2D7: 42,140,203–42,149,500, reverse strandCYP2D7TCF20: 42,160,013–42,343,616, reverse strandTCF20NFAM1: 42,380,407–42,432,425, reverse strandNFAM1RRP7A: 42,507,982–42,519,853, reverse strandRRP7ASERHL2: 42,553,617–42,574,387, forward strandSERHL2Diagram of NAGA: 9 exons on the reverse strand of chromosome 22Exon 9: 1 known disease-causing siteExon 8: 6 known disease-causing sitesExon 7: 9 known disease-causing sitesExon 6: 14 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 7 known disease-causing sitesExon 2: 4 known disease-causing sitesExon 9: 42,058,334–42,060,413, 2,080 basesExon 8: 42,060,924–42,061,067, 144 basesExon 7: 42,062,827–42,063,024, 198 basesExon 6: 42,065,738–42,065,899, 162 basesExon 5: 42,066,710–42,066,804, 95 basesExon 4: 42,067,113–42,067,290, 178 basesExon 3: 42,067,765–42,067,936, 172 basesExon 2: 42,068,439–42,068,574, 136 basesExon 1: 42,070,282–42,070,812, 531 bases9876543215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.7 kb of the gene's 12.5 kb; 1,236 of those bases code for the protein.

How a genome test reads NAGA

61

positions in NAGA where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 12.5 kb of NAGA, introns included, not only the 3.7 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). NAGA gene: alpha-N-acetylgalactosaminidase. Retrieved 16 October 2026, from https://dantelabs.com/genes/naga

Vancouver

Dante Labs. NAGA gene: alpha-N-acetylgalactosaminidase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/naga

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