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Gene

HGSNAT

heparan-alpha-glucosaminide N-acetyltransferase

Summary

Cytogenetic location
8p11.21-p11.1
Coordinates
Chromosome 8: 43,140,464–43,202,855 (GRCh38)
Exons
18 exons across 62.4 kb
Protein
635 amino acids
Inheritance
Autosomal recessive
Also known as
FLJ32731, HGNAT
Previous symbols
TMEM76
MANE Select transcript
ENST00000379644.9NM_152419.3
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

  • Mucopolysaccharidosis Type III (Sanfilippo Syndrome)

    • Mucopolysaccharidosis type III (Sanfilippo syndrome types A, B, C and D)Autosomal recessive

      Deficiency of one of four enzymes that break down heparan sulfate (SGSH in type A, NAGLU in type B, HGSNAT in type C, GNS in type D) causes speech delay, hyperactivity, sleep problems and progressive loss of skills in childhood.

      • ClinGen rates the link definitive
      • 8 GenCC submitters rate it definitive or strong
      What knowing changes

      There is no approved disease-modifying therapy yet; a genetic diagnosis guides supportive care, family testing and eligibility for clinical trials.

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
      • 8 GenCC submitters rate it definitive or strong

  • Retinitis Pigmentosa

    • One of 77 genes linked to it

      A group of inherited retinal dystrophies with progressive loss of rod and then cone photoreceptors, causing night blindness and gradual loss of peripheral vision.

      • 2 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 HGSNAT is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 8, with a bracket where HGSNAT sits. HGSNAT and 9 genes near it on chromosome 8, from 42,671,660 to 43,671,659.Chromosome 88p11.21-p11.1p23.3p23.2p23.1p22p21.3p21.2p21.1p12p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12.1q12.2q12.3q13.1q13.2q13.3q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.342.8 Mb43 Mb43.2 Mb43.4 Mb43.6 MbCHRNB3: 42,697,341–42,738,553, forward strandCHRNB3CHRNA6: 42,752,620–42,796,392, reverse strandCHRNA6THAP1: 42,836,249–42,843,364, reverse strandTHAP1RNF170: 42,849,637–42,897,309, reverse strandRNF170HOOK3: 42,896,499–43,030,535, forward strandHOOK3: 43,018,424–43,077,334, forward strandFNTA: 43,034,194–43,085,793, forward strandFNTAPOMK: 43,093,498–43,132,733, forward strandPOMKHGSNAT: 43,140,464–43,202,855, forward strandHGSNATPOTEA: 43,292,483–43,363,518, forward strandPOTEADiagram of HGSNAT: 18 exons on the forward strand of chromosome 8Exon 1: 17 known disease-causing sitesExon 2: 9 known disease-causing sitesExon 3: 8 known disease-causing sitesExon 4: 9 known disease-causing sitesExon 5: 6 known disease-causing sitesExon 6: 6 known disease-causing sitesExon 7: 14 known disease-causing sitesExon 8: 9 known disease-causing sitesExon 9: 4 known disease-causing sitesExon 10: 13 known disease-causing sitesExon 11: 10 known disease-causing sitesExon 12: 8 known disease-causing sitesExon 13: 15 known disease-causing sitesExon 14: 7 known disease-causing sitesExon 15: 7 known disease-causing sitesExon 16: 9 known disease-causing sitesExon 17: 7 known disease-causing sitesExon 18: 3 known disease-causing sitesExon 1: 43,140,464–43,140,614, 151 basesExon 2: 43,146,948–43,147,063, 116 basesExon 3: 43,158,575–43,158,711, 137 basesExon 4: 43,158,923–43,159,044, 122 basesExon 5: 43,161,438–43,161,507, 70 basesExon 6: 43,169,173–43,169,242, 70 basesExon 7: 43,170,585–43,170,694, 110 basesExon 8: 43,172,310–43,172,386, 77 basesExon 9: 43,173,713–43,173,743, 31 basesExon 10: 43,178,074–43,178,234, 161 basesExon 11: 43,182,145–43,182,260, 116 basesExon 12: 43,191,474–43,191,595, 122 basesExon 13: 43,192,304–43,192,430, 127 basesExon 14: 43,193,757–43,193,843, 87 basesExon 15: 43,196,948–43,197,025, 78 basesExon 16: 43,197,672–43,197,742, 71 basesExon 17: 43,197,840–43,197,952, 113 basesExon 18: 43,199,388–43,202,855, 3,468 bases1246810121416185′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 5.2 kb of the gene's 62.4 kb; 1,908 of those bases code for the protein.

How a genome test reads HGSNAT

196

positions in HGSNAT 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 62.4 kb of HGSNAT, introns included, not only the 5.2 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.). HGSNAT gene: heparan-alpha-glucosaminide N-acetyltransferase. Retrieved 17 October 2026, from https://dantelabs.com/genes/hgsnat

Vancouver

Dante Labs. HGSNAT gene: heparan-alpha-glucosaminide N-acetyltransferase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/hgsnat

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