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Gene

POMT1

protein O-mannosyltransferase 1

Summary

Cytogenetic location
9q34.13
Coordinates
Chromosome 9: 131,502,918–131,523,799 (GRCh38)
Exons
20 exons across 20.9 kb
Protein
725 amino acids
Inheritance
Autosomal recessive
Also known as
LGMD2K
MANE Select transcript
ENST00000402686.8NM_001077365.2
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

  • 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).

      • 5 GenCC submitters rate it definitive or strong

  • Congenital Disorders of Glycosylation

    • Alpha-DystroglycanopathiesAutosomal recessive

      Muscle diseases caused by faulty sugar attachment (O-mannosylation) to alpha-dystroglycan, ranging from severe congenital muscular dystrophy with brain and eye involvement to milder limb-girdle weakness; also covered in more detail in the Congenital Muscular Dystrophies report.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
    • Congenital Disorders of Glycosylation (CDG)

      One of 98 genes linked to it

      A large group of inherited conditions in which sugar chains (glycans) are not correctly built or attached to proteins and lipids, often affecting the brain, liver, blood clotting, growth and many other body systems. Most are autosomal recessive, but some are X-linked or autosomal dominant.

      • ClinGen rates the link definitive
      • 7 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 POMT1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 9, with a bracket where POMT1 sits. POMT1 and 12 genes near it on chromosome 9, from 131,013,359 to 132,013,358.Chromosome 99q34.13p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.3131.2 Mb131.4 Mb131.6 Mb131.8 Mb132 MbLAMC3: 131,008,878–131,094,473, forward strandLAMC3AIF1L: 131,096,446–131,123,243, forward strandAIF1LNUP214: 131,124,868–131,234,667, forward strandNUP214FAM78A: 131,258,076–131,278,194, reverse strandFAM78APLPP7: 131,289,459–131,359,022, forward strandPLPP7PRRC2B: 131,373,636–131,500,197, forward strandPRRC2B: 131,430,129–131,430,218, forward strand: 131,432,759–131,446,473, forward strandPOMT1: 131,502,918–131,523,799, forward strandPOMT1UCK1: 131,523,756–131,531,289, reverse strandUCK1PRRT1B: 131,545,520–131,560,893, forward strandPRRT1BRAPGEF1: 131,576,758–131,740,134, reverse strandRAPGEF1MED27: 131,842,105–132,079,896, reverse strandMED27Diagram of POMT1: 20 exons on the forward strand of chromosome 9Exon 2: 9 known disease-causing sitesExon 3: 10 known disease-causing sitesExon 4: 5 known disease-causing sitesExon 5: 8 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 7: 6 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 9: 8 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 11: 5 known disease-causing sitesExon 12: 7 known disease-causing sitesExon 13: 10 known disease-causing sitesExon 14: 7 known disease-causing sitesExon 15: 12 known disease-causing sitesExon 16: 3 known disease-causing sitesExon 17: 4 known disease-causing sitesExon 18: 9 known disease-causing sitesExon 19: 14 known disease-causing sitesExon 20: 13 known disease-causing sitesExon 1: 131,502,918–131,503,073, 156 basesExon 2: 131,504,189–131,504,340, 152 basesExon 3: 131,506,114–131,506,220, 107 basesExon 4: 131,506,403–131,506,453, 51 basesExon 5: 131,507,368–131,507,514, 147 basesExon 6: 131,508,911–131,509,022, 112 basesExon 7: 131,509,743–131,509,808, 66 basesExon 8: 131,509,903–131,509,996, 94 basesExon 9: 131,510,260–131,510,415, 156 basesExon 10: 131,511,337–131,511,467, 131 basesExon 11: 131,512,041–131,512,136, 96 basesExon 12: 131,513,239–131,513,331, 93 basesExon 13: 131,515,426–131,515,522, 97 basesExon 14: 131,518,445–131,518,537, 93 basesExon 15: 131,518,837–131,518,957, 121 basesExon 16: 131,519,389–131,519,486, 98 basesExon 17: 131,520,080–131,520,193, 114 basesExon 18: 131,521,346–131,521,472, 127 basesExon 19: 131,522,047–131,522,224, 178 basesExon 20: 131,522,932–131,523,799, 868 bases124681012141618205′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 3.1 kb of the gene's 20.9 kb; 2,178 of those bases code for the protein.

How a genome test reads POMT1

178

positions in POMT1 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 20.9 kb of POMT1, introns included, not only the 3.1 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.). POMT1 gene: protein O-mannosyltransferase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/pomt1

Vancouver

Dante Labs. POMT1 gene: protein O-mannosyltransferase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pomt1

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