POMGNT1

Chr 1

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: Q8WZA1

This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease and several congenital muscular dystrophies. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtMuscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A3
UniProtMuscular dystrophy-dystroglycanopathy congenital with impaired intellectual development B3
UniProtMuscular dystrophy-dystroglycanopathy limb-girdle C3
UniProtRetinitis pigmentosa 76

Clinical highlights

Gene-disease validity (ClinGen)
myopathy caused by variation in POMGNT1 · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
2
Active trials
12
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
1.04
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — POMGNT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

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 OE?0.79 (0.60–1.04)
0≤0.351.4
Missense OE?0.88 (0.81–0.96)
0≤0.61.4
Synonymous OE?1.02
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.

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