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Gene

B3GALNT2

beta-1,3-N-acetylgalactosaminyltransferase 2

Summary

Cytogenetic location
1q42.3
Coordinates
Chromosome 1: 235,447,190–235,504,452 (GRCh38)
Exons
12 exons across 57.3 kb
Protein
500 amino acids
Also known as
MGC39558
MANE Select transcript
ENST00000366600.8NM_152490.5
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 report relevant to this gene

  • Congenital Muscular Dystrophies

    • Congenital muscular dystrophy

      A group of muscular dystrophies with onset at birth or in infancy, including dystroglycanopathies (such as FKRP, FKTN and POMT1/2-related forms).

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

How B3GALNT2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where B3GALNT2 sits. B3GALNT2 and 8 genes near it on chromosome 1, from 234,975,821 to 235,975,820.Chromosome 11q42.3p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44235 Mb235.2 Mb235.4 Mb235.6 Mb235.8 MbTOMM20: 235,109,337–235,128,962, reverse strandTOMM20RBM34: 235,131,183–235,161,627, reverse strandRBM34ARID4B: 235,131,634–235,328,800, reverse strandARID4BGGPS1: 235,327,350–235,344,544, forward strandGGPS1: 235,328,570–235,448,952, forward strandTBCE: 235,367,360–235,452,443, forward strandTBCEB3GALNT2: 235,447,190–235,504,452, reverse strandB3GALNT2GNG4: 235,547,685–235,651,096, reverse strandGNG4LYST: 235,661,041–235,883,724, reverse strandLYSTDiagram of B3GALNT2: 12 exons on the reverse strand of chromosome 1Exon 12: 2 known disease-causing sitesExon 11: 3 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 8: 5 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 4: 4 known disease-causing sitesExon 2: 5 known disease-causing sitesExon 1: 5 known disease-causing sitesExon 12: 235,447,190–235,450,340, 3,151 basesExon 11: 235,453,090–235,453,146, 57 basesExon 10: 235,454,156–235,454,315, 160 basesExon 9: 235,455,559–235,455,684, 126 basesExon 8: 235,458,603–235,458,786, 184 basesExon 7: 235,465,636–235,465,714, 79 basesExon 6: 235,470,850–235,470,960, 111 basesExon 5: 235,480,054–235,480,149, 96 basesExon 4: 235,484,322–235,484,515, 194 basesExon 3: 235,489,168–235,489,268, 101 basesExon 2: 235,494,681–235,494,828, 148 basesExon 1: 235,504,141–235,504,452, 312 bases1210864215′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 4.7 kb of the gene's 57.3 kb; 1,503 of those bases code for the protein.

How a genome test reads B3GALNT2

52

positions in B3GALNT2 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 57.3 kb of B3GALNT2, introns included, not only the 4.7 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.). B3GALNT2 gene: beta-1,3-N-acetylgalactosaminyltransferase 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/b3galnt2

Vancouver

Dante Labs. B3GALNT2 gene: beta-1,3-N-acetylgalactosaminyltransferase 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/b3galnt2

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