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Gene

GM2A

ganglioside GM2 activator

Summary

Cytogenetic location
5q33.1
Coordinates
Chromosome 5: 151,253,185–151,270,440 (GRCh38)
Exons
4 exons across 17.3 kb
Protein
193 amino acids
Inheritance
Autosomal recessive
Also known as
SAP-3, GM2-AP, GM2AP
MANE Select transcript
ENST00000357164.4NM_000405.5
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

  • Sandhoff Disease and GM2 Activator Deficiency

    • GM2 activator deficiency (Tay-Sachs disease AB variant)Autosomal recessive

      A rare form clinically similar to infantile Tay-Sachs disease with normal hexosaminidase activity, caused by GM2A 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 GM2A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 5, with a bracket where GM2A sits. GM2A and 13 genes near it on chromosome 5, from 150,761,813 to 151,761,812.Chromosome 55q33.1p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3150.8 Mb151 Mb151.2 Mb151.4 Mb151.6 MbSMIM3: 150,777,883–150,796,736, forward strandSMIM3IRGM: 150,846,521–150,900,736, forward strandIRGMZNF300: 150,893,804–150,904,987, reverse strandZNF300GPX3: 151,020,585–151,030,769, forward strandGPX3TNIP1: 151,029,935–151,093,577, reverse strandTNIP1ANXA6: 151,100,706–151,157,979, reverse strandANXA6CCDC69: 151,181,049–151,224,156, reverse strandCCDC69GM2A: 151,253,185–151,270,440, forward strandGM2ASLC36A3: 151,276,358–151,303,766, reverse strandSLC36A3SLC36A2: 151,314,972–151,347,602, reverse strandSLC36A2SLC36A1: 151,437,046–151,525,119, forward strandSLC36A1FAT2: 151,504,092–151,591,331, reverse strandFAT2SPARC: 151,661,096–151,687,352, reverse strandSPARCATOX1: 151,728,919–151,772,532, reverse strandATOX1Diagram of GM2A: 4 exons on the forward strand of chromosome 5Exon 1: 1 known disease-causing siteExon 2: 3 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 1: 151,253,185–151,253,297, 113 basesExon 2: 151,259,755–151,259,916, 162 basesExon 3: 151,266,731–151,266,913, 183 basesExon 4: 151,267,296–151,270,440, 3,145 bases12345′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 3.6 kb of the gene's 17.3 kb; 582 of those bases code for the protein.

How a genome test reads GM2A

9

positions in GM2A 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 17.3 kb of GM2A, introns included, not only the 3.6 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.). GM2A gene: ganglioside GM2 activator. Retrieved 16 October 2026, from https://dantelabs.com/genes/gm2a

Vancouver

Dante Labs. GM2A gene: ganglioside GM2 activator [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/gm2a

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