Gene
POMT2
protein O-mannosyltransferase 2
- HGNC 19743(opens in a new tab)
- Ensembl gene ENSG00000009830(opens in a new tab)
- NCBI Gene 29954(opens in a new tab)
Summary
- Cytogenetic location
- 14q24.3
- Coordinates
- Chromosome 14: 77,274,956–77,320,883 (GRCh38)
- Exons
- 21 exons across 45.9 kb
- Protein
- 750 amino acids
- Inheritance
- Autosomal recessive
- Also known as
- LGMD2N
- MANE Select transcript
- ENST00000261534.9NM_013382.7
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Read POMT2, and the rest of your genome, with one test.
From $449Free shipping · Results in 6–8 weeks
Get my Genome TestCurated 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).
- 3 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
- 5 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
- 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 POMT2 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 4.9 kb of the gene's 45.9 kb; 2,253 of those bases code for the protein.
How a genome test reads POMT2
132
positions in POMT2 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 45.9 kb of POMT2, introns included, not only the 4.9 kb of exons.
Traits linked to POMT2
The Human Phenotype Ontology lists these as features of the rare conditions POMT2 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Absent speech development
- Agyria
- Cerebellar vermis hypoplasia
- Decrease in size of the outer layer of the brain due to loss of brain cells
- Epilepsy
- Global developmental delay
- Inability to walk
- Intellectual disability, severe
Show 57 more traits
- Small brainstem
- Small cerebellum
- Too much cerebrospinal fluid in the brain
- Type II lissencephaly
- Abnormal cerebellar vermis morphology
- Abnormal cortical gyration
- Abnormal gait
- Abnormal speech pattern
- Abnormality of neuronal migration
- Absent reflexes
- Cognitive impairment
- Decreased reflex response
- EEG abnormality
- Fewer and broader ridges in brain
- Fewer or absent grooves in brain
- Intellectual disability
- More grooves in brain
- Specific learning disability
- Ventriculomegaly
- Abnormal pyramidal sign
- Abnormal shape of brain
- Abnormal shape of brainstem
- Abnormality of movement
- Abnormality of the cerebellum
- Absent septum pellucidum
- Agenesis of corpus callosum
- Delayed motor skills
- Diffuse white matter abnormalities
- Dilated fourth ventricle
- Gray matter heterotopia
- Kinked brainstem
- Motor delay
- Partial absence of cerebellar vermis
- Poor gross motor coordination
- Abnormal periventricular white matter morphology
- Abnormal pons morphology
- Abnormality of the nervous system
- Absent/small cerebellum
- Cerebellar cyst
- Clonus
- Decreased thalamic volume
- Diminished deep tendon reflex
- Frontal cortical atrophy
- Fusion of the cerebellar hemispheres
- Holoprosencephaly
- Hypoplasia of the pons
- Increased reflexes
- Intellectual disability, mild
- Loss of ability to walk
- Meningocele
- Olivopontocerebellar hypoplasia
- Paralysis or weakness of one side of body
- Poor speech
- Underdevelopment of part of brain called corpus callosum
- Cerebellar dysplasia
- Excessive daytime sleepiness
- IQ less than 20
Abnormality of the musculoskeletal system
- Generalized muscle weakness
- Increased skeletal muscle cells
- Increased variability in muscle fiber diameter
- Low muscle tone
- Low muscle tone, in neonatal onset
- Muscular dystrophy
- Proximal neurogenic muscle weakness
- Absent/small skeletal muscles
Show 25 more traits
- Decreased muscle tone in infant
- EMG abnormality
- Hypoglycosylation of alpha-dystroglycan
- Muscle degeneration
- Muscle tissue disease
- Muscle weakness
- Reduced muscle fiber alpha dystroglycan
- Difficulty walking up stairs
- Excessive inward curvature of lower spine
- Fatigable weakness of skeletal muscles
- Multiple joint contractures
- Spasticity and rigidity of muscles
- Wasting of muscles near the body
- Abnormality of connective tissue
- Axial muscle weakness
- Limited neck movement
- Neuropathic spinal arthropathy
- Scapuloperoneal amyotrophy
- Scoliosis
- Congenital contracture
- Flexed joint that cannot be straightened
- Generalized decreased muscle tone
- Prominent swayback
- Reduced spine movement
- Severely decreased muscle tone
Abnormality of the eye
- Abnormally small eyeball
- Clouding of the lens of the eye
- Corneal opacity
- Retinal dysplasia
- Breakdown of light-sensitive cells in back of eye
- Chorioretinal dysplasia
- Close sighted
- Cross-eyed
Show 20 more traits
- Glaucoma
- Optic atrophy
- Optic nerve issue
- Retinal detachment
- Visual impairment
- Absence of eyeballs
- Enlarged eyeball
- Persistent pupillary membrane
- Peters anomaly
- Abnormality of the eye
- Abnormality of the iris
- Cat eye
- Cornea of eye less than 10mm in diameter
- Enlarged cornea
- Notched pupil
- Optic nerve hypoplasia
- Pigmentary retinopathy
- Blindness
- Farsightedness
- Retinal atrophy
External links
Gene records
Transcript
Protein
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
Dante Labs. (n.d.). POMT2 gene: protein O-mannosyltransferase 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/pomt2
Dante Labs. POMT2 gene: protein O-mannosyltransferase 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pomt2
One test. A lifetime of answers.
From $449Free shipping · Results in 6–8 weeks