GALNT2

Chr 1AR

polypeptide N-acetylgalactosaminyltransferase 2

Also known as: CDG2T, GalNAc-T2

NCBI Gene: 2590ENSG00000143641UniProt: Q10471

This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

Primary Disease Associations & Inheritance

Congenital disorder of glycosylation, type IItMIM #618885
AR
247
ClinVar variants
47
Pathogenic / LP
0.01
pLI score
0
Active trials
Clinical Summary— GALNT2
🧬
Gene-Disease Validity (ClinGen)
congenital disorder of glycosylation, type iit · ARStrong

Strong evidence — appropriate for clinical testing

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.29) despite low pLI — interpret in context.
📋
ClinVar Variants
47 Pathogenic / Likely Pathogenic· 91 VUS of 247 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.49LOEUF
pLI 0.008
Z-score 3.99
OE 0.29 (0.18–0.49)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.00Z-score
OE missense 0.70 (0.63–0.78)
243 obs / 348.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.29 (0.18–0.49)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.70 (0.63–0.78)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.03
0≤1.21.6
LoF obs/exp: 11 / 37.3Missense obs/exp: 243 / 348.1Syn Z: -0.24

ClinVar Variant Classifications

247 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic41
Likely Pathogenic6
VUS91
Likely Benign85
Benign21
Conflicting3
41
Pathogenic
6
Likely Pathogenic
91
VUS
85
Likely Benign
21
Benign
3
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
41
0
41
Likely Pathogenic
0
4
2
0
6
VUS
1
77
12
1
91
Likely Benign
0
2
41
42
85
Benign
0
1
10
10
21
Conflicting
—3
Total18410653247

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

View in ClinVar →

Protein Context — Lollipop Plot

GALNT2 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Congenital disorder of glycosylation, type IIt

MIM #618885

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Biological, clinical and population relevance of 95 loci for blood lipids.
Teslovich TM et al.·Nature
2010Meta-analysis
Diagnostic Yield and Novel Candidate Genes by Exome Sequencing in 152 Consanguineous Families With Neurodevelopmental Disorders.
Reuter MS et al.·JAMA Psychiatry
2017
Integrative single-cell analysis of LUAD: elucidating immune cell dynamics and prognostic modeling based on exhausted CD8+ T cells.
Zhang H et al.·Front Immunol
2024Functional
Air pollution exacerbates cardiovascular-kidney-metabolic syndrome and sarcopenia comorbidity via shared genetic-epigenetic mechanisms: A multi-omics and Mendelian Randomization study.
Wei S et al.·Metabolism
2026Functional
GALNT2 sustains glioma stem cells by promoting CD44 expression.
Liu Y et al.·Aging (Albany NY)
2023
GALNT2 effect on HDL-cholesterol and triglycerides levels in humans: Evidence of pleiotropy?
Di Paola R et al.·Nutr Metab Cardiovasc Dis
2017
circ-hnRNPU inhibits NONO-mediated c-Myc transactivation and mRNA stabilization essential for glycosylation and cancer progression.
Li H et al.·J Exp Clin Cancer Res
2023
GALNT2 rs4846914 SNP Is Associated with Obesity, Atherogenic Lipid Traits, and ANGPTL3 Plasma Level.
Qaddoumi M et al.·Genes (Basel)
2022
GALNT2 expression is associated with glucose control and serum metabolites in patients with type 2 diabetes.
Trischitta V et al.·Acta Diabetol
2024Cohort
Mucin O-glycosylating enzyme GALNT2 facilitates the malignant character of glioma by activating the EGFR/PI3K/Akt/mTOR axis.
Sun Z et al.·Clin Sci (Lond)
2019
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools