POMGNT2

Chr 3AR

protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)

Also known as: AGO61, C3orf39, GTDC2, MDDGA8, MDDGC8

NCBI Gene: 84892 ENSG00000144647 UniProt: Q8NAT1 OMIM: 614828

The encoded protein is an O-linked mannose beta-1,4-N-acetylglucosaminyltransferase that synthesizes phosphorylated O-mannosyl trisaccharides on alpha-dystroglycan, enabling high-affinity binding to laminin and other extracellular matrix proteins. Mutations cause autosomal recessive muscular dystrophy-dystroglycanopathy, ranging from severe congenital forms with brain and eye anomalies to milder limb-girdle presentations. The gene shows low constraint against loss-of-function variants, consistent with its recessive inheritance pattern.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 1.012 OMIM phenotypes

Clinical Summary— POMGNT2

🧬

Gene-Disease Validity (ClinGen)

myopathy caused by variation in POMGNT2 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡

Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

📋

ClinVar Variants

30 unique Pathogenic / Likely Pathogenic· 266 VUS of 498 total submissions

💊

Clinical Trials

2 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?

1.01LOEUF

pLI 0.000

Z-score 1.53

OE 0.61 (0.38–1.01)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.95Z-score

OE missense 0.86 (0.79–0.94)

323 obs / 375.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.61 (0.38–1.01)

0≤0.351.4

Missense OE?0.86 (0.79–0.94)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 11 / 18.0Missense obs/exp: 323 / 375.0Syn Z: -0.39

ClinVar Variant Classifications

498 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic21

Likely Pathogenic9

VUS266

Likely Benign175

Benign11

Conflicting16

Pathogenic

Likely Pathogenic

266

VUS

175

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	17	3	1	0	21
Likely Pathogenic	8	1	0	0	9
VUS	2	263	1	0	266
Likely Benign	0	7	3	165	175
Benign	0	0	9	2	11
Conflicting	—				16
Total	27	274	14	167	498

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

7 pathogenic / likely-pathogenic (of 9) ClinVar copy-number / structural variants overlap POMGNT2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →