GNPDA2 Gene (Protein Coding)

Glucosamine-6-Phosphate Deaminase 2

GC04M044684
GIFtS:
40
The protein encoded by this gene is an allosteric enzyme that catalyzes the reversible reaction converting D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium. Variations of this gene have been reported to be associated with influencing body mass index and susceptibility to obesity. A pseudogene of this gene is located on chromosome 9. Alternative splicing result... See more...

Aliases for GNPDA2 Gene

Aliases for GNPDA2 Gene

  • Glucosamine-6-Phosphate Deaminase 2 2 3 4 5
  • Glucosamine-6-Phosphate Isomerase SB52 3 4
  • Glucosamine-6-Phosphate Isomerase 2 3 4
  • GlcN6P Deaminase 2 3 4
  • EC 3.5.99.6 4 51
  • GNP2 3 4
  • SB52 2 3
  • Glucosamine-6-Phosphate Isomerase 2
  • GNPDA 2 4
  • GNPDA2 5

External Ids for GNPDA2 Gene

Previous GeneCards Identifiers for GNPDA2 Gene

  • GC04M044619
  • GC04M044545
  • GC04M044398
  • GC04M044704
  • GC04M044025

Summaries for GNPDA2 Gene

Entrez Gene Summary for GNPDA2 Gene

  • The protein encoded by this gene is an allosteric enzyme that catalyzes the reversible reaction converting D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium. Variations of this gene have been reported to be associated with influencing body mass index and susceptibility to obesity. A pseudogene of this gene is located on chromosome 9. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Aug 2012]

GeneCards Summary for GNPDA2 Gene

GNPDA2 (Glucosamine-6-Phosphate Deaminase 2) is a Protein Coding gene. Diseases associated with GNPDA2 include Amyotrophic Lateral Sclerosis-Parkinsonism/Dementia Complex 1 and Leptin Deficiency Or Dysfunction. Among its related pathways are Amino sugar and nucleotide sugar metabolism and Glycosaminoglycan metabolism. Gene Ontology (GO) annotations related to this gene include hydrolase activity and glucosamine-6-phosphate deaminase activity. An important paralog of this gene is GNPDA1.

Gene Wiki entry for GNPDA2 Gene

Additional gene information for GNPDA2 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GNPDA2 Gene

Genomics for GNPDA2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for GNPDA2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH04J044725 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 252.4 +0.5 533 2.6 TBP NR2C1 SMAD5 ZFP64 POLR2A CTCF ELF1 ZIC2 HOMEZ THAP11 GNPDA2 LOC105374439 lnc-GUF1-9 lnc-YIPF7-3 YIPF7 GUF1 KCTD8 ENSG00000272936
GH04J044677 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 63 +47.3 47333 4.2 TBP ZBTB10 MXD4 NR2C1 MNT IKZF1 SMAD5 ETS1 IRF2 MBD2 GUF1 YIPF7 lnc-YIPF7-2 GNPDA2 ENSG00000273369 lnc-GUF1-5
GH04J044662 Enhancer 0.5 Ensembl 62.1 +64.0 63981 1.1 FOXA2 SPI1 CEBPB HLF SOX13 HSALNG0034166 piR-46823-001 GNPDA2 GUF1 lnc-GUF1-5 YIPF7 lnc-YIPF7-2 KCTD8
GH04J044764 Enhancer 0.2 ENCODE 40 -38.8 -38778 1.2 LOC112268465 GNPDA2 GUF1 KCTD8 piR-48553-214 lnc-GUF1-9 LOC105374439 HSALNG0034179
GH04J044863 Enhancer 0.6 Ensembl ENCODE 5.3 -136.3 -136342 3.6 YY1 SP1 POU5F1 NANOG KDM1A piR-56497-118 GUF1 GNPDA2 LOC100419045 HSALNG0034179 lnc-GUF1-9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GNPDA2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GNPDA2

Top Transcription factor binding sites by QIAGEN in the GNPDA2 gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • Evi-1
  • GATA-3
  • LCR-F1
  • Lmo2
  • Pax-6
  • POU3F1

Genomic Locations for GNPDA2 Gene

Latest Assembly
chr4:44,682,200-44,726,634
(GRCh38/hg38)
Size:
44,435 bases
Orientation:
Minus strand

Previous Assembly
chr4:44,703,812-44,728,651
(GRCh37/hg19 by Entrez Gene)
Size:
24,840 bases
Orientation:
Minus strand

chr4:44,684,217-44,728,612
(GRCh37/hg19 by Ensembl)
Size:
44,396 bases
Orientation:
Minus strand

Genomic View for GNPDA2 Gene

Genes around GNPDA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GNPDA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GNPDA2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GNPDA2 Gene

Proteins for GNPDA2 Gene

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  • Protein details for GNPDA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TDQ7-GNPI2_HUMAN
    Recommended name:
    Glucosamine-6-phosphate isomerase 2
    Protein Accession:
    Q8TDQ7
    Secondary Accessions:
    • B4DJF3
    • Q2VYF1
    • Q59EA7
    • Q8NCZ8
    • Q96BJ4
    • Q96NC6

    Protein attributes for GNPDA2 Gene

    Size:
    276 amino acids
    Molecular mass:
    31085 Da
    Quaternary structure:
    • Homohexamer.
    SequenceCaution:
    • Sequence=BAD93141.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GNPDA2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GNPDA2 Gene

Protein Expression for GNPDA2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for GNPDA2 Gene

Q8TDQ7:
  • NFFKHIDI
  • ALTVGVGT
  • TFNMDEYV
  • GHIAFNEP
  • LASEWAAKYICN
  • TGSTPLG
  • VNHMWTVSA
  • KTLAMDTILANA
  • FNEPGSS
  • VKTVKYFKGLM
  • VHNKLVDPL
  • HILDGNA
  • DEDATLEL
  • LFVGGIGPDGH

Post-translational modifications for GNPDA2 Gene

  • Ubiquitination at Lys160 and Lys172
  • Modification sites at PhosphoSitePlus

Other Protein References for GNPDA2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for GNPDA2
  • Boster Bio Antibodies for GNPDA2

Domains & Families for GNPDA2 Gene

Gene Families for GNPDA2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for GNPDA2 Gene

InterPro:
Blocks:
  • Glucosamine-6-phosphate isomerase
ProtoNet:

Suggested Antigen Peptide Sequences for GNPDA2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60594, highly similar to Homo sapiens glucosamine-6-phosphate deaminase 2 (GNPDA2), mRNA (B4DJF3_HUMAN)
  • Glucosamine-6-phosphate isomerase SB52 (GNPI2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TDQ7

UniProtKB/Swiss-Prot:

GNPI2_HUMAN :
  • Belongs to the glucosamine/galactosamine-6-phosphate isomerase family.
Family:
  • Belongs to the glucosamine/galactosamine-6-phosphate isomerase family.
genes like me logo Genes that share domains with GNPDA2: view

Function for GNPDA2 Gene

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  6. Cell Lines for research

Molecular function for GNPDA2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+); Xref=Rhea:RHEA:12172, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938, ChEBI:CHEBI:57634, ChEBI:CHEBI:75989; EC=3.5.99.6;.

Enzyme Numbers (IUBMB) for GNPDA2 Gene

Phenotypes From GWAS Catalog for GNPDA2 Gene

Gene Ontology (GO) - Molecular Function for GNPDA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004342 glucosamine-6-phosphate deaminase activity IBA 21873635
GO:0005515 protein binding IPI 25416956
GO:0016787 hydrolase activity IEA --
GO:0042802 identical protein binding IBA 21873635
genes like me logo Genes that share ontologies with GNPDA2: view
genes like me logo Genes that share phenotypes with GNPDA2: view

Animal Models for GNPDA2 Gene

MGI Knock Outs for GNPDA2:
  • Gnpda2 Gnpda2<tm1.1(KOMP)Vlcg>

Animal Models for research

miRNA for GNPDA2 Gene

miRTarBase miRNAs that target GNPDA2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GNPDA2

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GNPDA2 Gene

Localization for GNPDA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GNPDA2 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GNPDA2 gene
Compartment Confidence
cytosol 5
nucleus 4
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GNPDA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA 21630459
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with GNPDA2: view

Pathways & Interactions for GNPDA2 Gene

genes like me logo Genes that share pathways with GNPDA2: view

Gene Ontology (GO) - Biological Process for GNPDA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IEA --
GO:0006043 glucosamine catabolic process TAS --
GO:0006044 N-acetylglucosamine metabolic process IEA --
GO:0006046 N-acetylglucosamine catabolic process IBA 21873635
GO:0006048 UDP-N-acetylglucosamine biosynthetic process IBA 21873635
genes like me logo Genes that share ontologies with GNPDA2: view

No data available for SIGNOR curated interactions for GNPDA2 Gene

Drugs & Compounds for GNPDA2 Gene

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(4) Drugs for GNPDA2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ammonia Approved Pharma 0
Water Approved Pharma 0
Fructose 6-phosphate Experimental Pharma 0
glucosamine 6-phosphate Experimental Pharma 0

(1) Additional Compounds for GNPDA2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N-Acetyl-D-Glucosamine 6-Phosphate
  • 2-Acetamido-2-deoxy-6-O-phosphono-D-glucopyranose
  • N-Acetyl-D-glucosamine 6-phosphoric acid
  • N-Acetyl-D-glucosamine-6-p
  • N-Acetyl-D-glucosamine-6-phosphate
  • N-Acetyl-glucosamine-6-p
 18191-20-3
genes like me logo Genes that share compounds with GNPDA2: view

Transcripts for GNPDA2 Gene

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mRNA/cDNA for GNPDA2 Gene

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GNPDA2

Alternative Splicing Database (ASD) splice patterns (SP) for GNPDA2 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b
SP1: - -
SP2:
SP3: - - - - -
SP4: - - - - - -
SP5: -

Relevant External Links for GNPDA2 Gene

GeneLoc Exon Structure for
GNPDA2

Expression for GNPDA2 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GNPDA2 Gene

mRNA expression in normal human tissues for GNPDA2 Gene
mRNA expression by GTEx for GNPDA2 GenemRNA expression by BioGPS for GNPDA2 Gene

Protein differential expression in normal tissues from HIPED for GNPDA2 Gene

This gene is overexpressed in Ovary (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GNPDA2 Gene



Protein tissue co-expression partners for GNPDA2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GNPDA2

SOURCE GeneReport for Unigene cluster for GNPDA2 Gene:

Hs.21398

Evidence on tissue expression from TISSUES for GNPDA2 Gene

  • Nervous system(4.9)
  • Kidney(4.3)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with GNPDA2: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GNPDA2 Gene

Orthologs for GNPDA2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GNPDA2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia GNPDA2 30 31
  • 99.88 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia GNPDA2 31
  • 96 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia GNPDA2 30 31
  • 95.17 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia GNPDA2 30 31
  • 93.36 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Gnpda2 30
  • 90.94 (n)
Mouse
(Mus musculus)
 Mammalia Gnpda2 30 17 31
  • 89.61 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 77 (a)
 ManyToMany
Chicken
(Gallus gallus)
 Aves GNPDA2 30 31
  • 85.28 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia GNPDA2 31
  • 95 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia gnpda2 30
  • 79.49 (n)
Str.8141 30
African clawed frog
(Xenopus laevis)
 Amphibia MGC68593 30
Zebrafish
(Danio rerio)
 Actinopterygii gnpda2 30 31
  • 74.45 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta Oscillin 30 31
  • 66.67 (n)
 OneToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta GNPI_ANOGA 30
  • 63.67 (n)
Worm
(Caenorhabditis elegans)
 Secernentea T03F6.3 31
  • 67 (a)
 OneToMany
CELE_T03F6.3 30
  • 62.14 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.10232 31
  • 78 (a)
 OneToMany
Bread mold
(Neurospora crassa)
 Ascomycetes NCU04727 30
  • 56.26 (n)
Species where no ortholog for GNPDA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for GNPDA2 Gene

ENSEMBL:
Gene Tree for GNPDA2 (if available)
TreeFam:
Gene Tree for GNPDA2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GNPDA2: view image

Paralogs for GNPDA2 Gene

Paralogs for GNPDA2 Gene

(1) SIMAP similar genes for GNPDA2 Gene using alignment to 3 proteins:

  • GNPI2_HUMAN
  • V9GYK3_HUMAN
  • V9GYW0_HUMAN

Pseudogenes.org Pseudogenes for GNPDA2 Gene

genes like me logo Genes that share paralogs with GNPDA2: view

Variants for GNPDA2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GNPDA2 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs141733877 Benign: not provided 44,722,112(-) G/A
NM_138335.3(GNPDA2):c.96C>T (p.Asp32=) 		SYNONYMOUS_VARIANT,INTRON
rs374535255 Likely Benign: not provided 44,717,198(-) G/A
NM_138335.3(GNPDA2):c.324C>T (p.Asp108=) 		NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs17851302 - p.Pro182Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for GNPDA2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for GNPDA2 Gene

Variant ID Type Subtype PubMed ID
nsv1013488 CNV loss 25217958
nsv4319 CNV deletion 18451855

Variation tolerance for GNPDA2 Gene

Residual Variation Intolerance Score: 32.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GNPDA2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GNPDA2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GNPDA2 Gene

Disorders for GNPDA2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for GNPDA2 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis-parkinsonism/dementia complex 1
  • amyotrophic lateral sclerosis-parkinsonism/dementia complex of guam
leptin deficiency or dysfunction
  • lepd
type 2 diabetes mellitus
  • t2d
body mass index quantitative trait locus 11
  • bmiq11
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for GNPDA2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with GNPDA2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GNPDA2 Gene

Publications for GNPDA2 Gene

  1. Association between obesity and polymorphisms in SEC16B, TMEM18, GNPDA2, BDNF, FAIM2 and MC4R in a Japanese population. (PMID: 19851340) Hotta K … Nakamura Y (Journal of human genetics 2009) 3 23 41
  2. Two mammalian glucosamine-6-phosphate deaminases: a structural and genetic study. (PMID: 12965206) Arreola R … Horjales E (FEBS letters 2003) 2 3 4
  3. Genetic markers of adult obesity risk are associated with greater early infancy weight gain and growth. (PMID: 20520848) Elks CE … Ong KK (PLoS medicine 2010) 3 41
  4. Evaluating the discriminative power of multi-trait genetic risk scores for type 2 diabetes in a northern Swedish population. (PMID: 20571754) Fontaine-Bisson B … Franks PW (Diabetologia 2010) 3 41
  5. Analyses of shared genetic factors between asthma and obesity in children. (PMID: 20816195) Melén E … Lasky-Su J (The Journal of allergy and clinical immunology 2010) 3 41

ExternalLinks

View latest publications for GNPDA2 gene in Mastermind

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