GNPDA1

Chr 5

glucosamine-6-phosphate deaminase 1

Also known as: GNP1, GNPDA, GNPI, GPI, HLN

NCBI Gene: 10007ENSG00000113552UniProt: P46926

Glucosamine-6-phosphate deaminase (EC 3.5.99.6) is an allosteric enzyme that catalyzes the reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium (Arreola et al., 2003 [PubMed 12965206]).[supplied by OMIM, Jan 2010]

0
Active trials
12
Pathogenic / LP
44
ClinVar variants
2
Pubs (1 yr)
1.8
Missense Z
1.50
LOEUF
Clinical Summary— GNPDA1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
12 Pathogenic / Likely Pathogenic· 31 VUS of 44 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.50LOEUF
pLI 0.000
Z-score 0.28
OE 0.91 (0.57–1.50)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
1.79Z-score
OE missense 0.61 (0.52–0.72)
104 obs / 169.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.91 (0.57–1.50)
0≤0.351.4
Missense OE0.61 (0.52–0.72)
0≤0.61.4
Synonymous OE1.08
0≤1.21.6
LoF obs/exp: 11 / 12.1Missense obs/exp: 104 / 169.4Syn Z: -0.55
DN
DN
0.6454th %ile
GOF
0.6249th %ile
LOF
0.3744th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction 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

44 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic12
VUS31
Likely Benign1
12
Pathogenic
31
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
12
0
12
Likely Pathogenic
0
0
0
0
0
VUS
0
28
3
0
31
Likely Benign
0
0
1
0
1
Benign
0
0
0
0
0
Total02816044

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

View in ClinVar →

GNPDA1 · 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
Prognostic value of a novel glycolysis-related gene expression signature for gastrointestinal cancer in the Asian population
Xia R et al.·Cancer Cell Int
2021
Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic beta cells
Zhang Y et al.·Bioengineered
2021
The Possible Roles of Glucosamine-6-Phosphate Deaminases in Ammonium Metabolism in Cancer.
Lara-Lemus R et al.·Int J Mol Sci
2024
Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC
Zhao Y et al.·Front Cell Dev Biol
2021
Development and Validation of a Novel Prognosis Model Based on a Panel of Three Immunogenic Cell Death-Related Genes for Non-Cirrhotic Hepatocellular Carcinoma
Gong J et al.·J Hepatocell Carcinoma
2023Functional
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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