GFPT2

Chr 5

glutamine--fructose-6-phosphate transaminase 2

Also known as: GFAT, GFAT 2, GFAT2

NCBI Gene: 9945ENSG00000131459UniProt: O94808

Enables glutamine-fructose-6-phosphate transaminase (isomerizing) activity. Involved in UDP-N-acetylglucosamine biosynthetic process and fructose 6-phosphate metabolic process. Predicted to be located in cytosol. Implicated in type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Jul 2025]

0
Active trials
0
Pathogenic / LP
0
ClinVar variants
7
Pubs (1 yr)
1.5
Missense Z
0.74
LOEUF
Clinical Summary— GFPT2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
0.74LOEUF
pLI 0.000
Z-score 2.85
OE 0.51 (0.36–0.74)
Tolerant

Typical tolerance to LoF variation

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.
1.55Z-score
OE missense 0.79 (0.72–0.86)
336 obs / 426.0 exp
Tolerant

Mild missense constraint

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.0.51 (0.36–0.74)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.79 (0.72–0.86)
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.1.06
0≤1.21.6
LoF obs/exp: 20 / 39.3Missense obs/exp: 336 / 426.0Syn Z: -0.65
DN
0.7130th %ile
GOF
0.6930th %ile
LOF
0.3165th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

GFPT2 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
The GFPT2-O-GlcNAcylation-YBX1 axis promotes IL-18 secretion to regulate the tumor immune microenvironment in pancreatic cancer.
Zhang HR et al.·Cell Death Dis
2024
Cancer-associated fibroblast expression of glutamine fructose-6-phosphate aminotransferase 2 (GFPT2) is a prognostic marker in gastric cancer.
Yang S et al.·J Pathol Clin Res
2023
GFPT2 expression is induced by gemcitabine administration and enhances invasion by activating the hexosamine biosynthetic pathway in pancreatic cancer.
Miyazaki K et al.·Clin Exp Metastasis
2024
The Prognostic Value and Immunotherapeutic Characteristics of GFPT2 in Pan-cancer.
Zhou Y et al.·Comb Chem High Throughput Screen
2025
Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2) Is Upregulated in Breast Epithelial-Mesenchymal Transition and Responds to Oxidative Stress.
Wang Q et al.·Mol Cell Proteomics
2022
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
GFPT2 drives sunitinib resistance of renal cell carcinoma via enzyme-dependent and -independent manners.
Wang S et al.·Int J Biol Sci
2026Open Access
Diagnostic potential of a novel immunohistochemical marker, GFPT2, in differentiating mesothelioma from its morphological mimics.
Wei J et al.·Histopathology
2026
Verbascoside attenuates angiotensin-induced hypertension by inhibiting endoplasmic reticulum stress via the Nur77/GFPT2/CHOP pathway.
Liu K et al.·Arch Physiol Biochem
2025
Phosphoproteomic insights into GFPT2-Associated cellular phospho-signaling networks.
Chakraborty S et al.·Biochem Biophys Rep
2025Open Access
"Heptadecanol" a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation.
Ravi L et al.·J Comput Aided Mol Des
2025
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