POMGNT1

Chr 1AR

protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)

Also known as: GNTI.2, GnT I.2, LGMD2O, LGMDR15, MEB, MGAT1.2, RP76, gnT-I.2

NCBI Gene: 55624ENSG00000085998UniProt: Q8WZA1OMIM: 606822

The encoded protein localizes to the Golgi apparatus and catalyzes O-mannosyl glycosylation by adding N-acetylglucosamine to alpha-linked terminal mannose residues on dystroglycan. Mutations cause autosomal recessive dystroglycanopathies ranging from severe congenital muscular dystrophy with brain and eye anomalies (muscle-eye-brain disease) to milder limb-girdle muscular dystrophy, as well as retinitis pigmentosa. The pathogenic mechanism involves defective glycosylation of alpha-dystroglycan, disrupting its binding to extracellular matrix proteins.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.044 OMIM phenotypes
Clinical Summary— POMGNT1
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Gene-Disease Validity (ClinGen)
myopathy caused by variation in POMGNT1 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.04LOEUF
pLI 0.000
Z-score 1.32
OE 0.79 (0.60–1.04)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.90Z-score
OE missense 0.88 (0.81–0.96)
373 obs / 425.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.79 (0.60–1.04)
0≤0.351.4
Missense OE0.88 (0.81–0.96)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 36 / 45.6Missense obs/exp: 373 / 425.2Syn Z: -0.24

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

POMGNT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Expression of Dystroglycanopathy-Related Enzymes, POMGNT2 and POMGNT1, in the Mammalian Retina and 661W Cone-like Cell Line.
Quereda C et al.·Biomedicines
2025Open Access
Variable Ophthalmologic Phenotypes Associated with Biallelic Loss-of-Function Variants in POMGNT1.
Ziccardi L et al.·Int J Mol Sci
2025Open Access
Case Series on Autosomal Recessive Non-Syndromic Retinitis Pigmentosa Caused by POMGNT1 Mutations with a Report of a New Variant.
Patel A et al.·J Clin Med
2023Open AccessCohort
Uniparental disomy for chromosome 1 with POMGNT1 splice-site variant causes muscle-eye-brain disease.
Liu YD et al.·Front Genet
2023Open Access
Compound variants of FKTN, POMGNT1, and LAMB1 gene identified by prenatal whole-exome sequencing in three fetuses with congenital hydrocephalus.
Li M et al.·J Obstet Gynaecol Res
2022Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients