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    GNPDA2 glucosamine-6-phosphate deaminase 2 [ Homo sapiens (human) ]

    Gene ID: 132789, updated on 27-Nov-2024

    Summary

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    Official Symbol
    GNPDA2provided by HGNC
    Official Full Name
    glucosamine-6-phosphate deaminase 2provided by HGNC
    Primary source
    HGNC:HGNC:21526
    See related
    Ensembl:ENSG00000163281 MIM:613222; AllianceGenome:HGNC:21526
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GNP2; SB52
    Summary
    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]
    Expression
    Ubiquitous expression in ovary (RPKM 8.8), thyroid (RPKM 8.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GNPDA2 in Genome Data Viewer
    Location:
    4p12
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (44701795..44726556, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (44668716..44693480, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (44703812..44728573, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Yip1 domain family member 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:44665473-44665974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:44665975-44666474 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:44679656-44680544 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15397 Neighboring gene GTP binding elongation factor GUF1 Neighboring gene Sharpr-MPRA regulatory region 4028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21527 Neighboring gene uncharacterized LOC105374439 Neighboring gene uncharacterized LOC112268465 Neighboring gene uncharacterized LOC105374440

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Studies of metabolic phenotypic correlates of 15 obesity associated gene variants. Sandholt CH, et al. PLoS One, 2011. PMID 21912638, Free PMC Article
    2. Genetic risk score does not correlate with body mass index of Latina women in a clinical trial. Coenen KR, et al. Clin Transl Sci, 2011 Oct. PMID 22029802, Free PMC Article
    3. Role of BMI-associated loci identified in GWAS meta-analyses in the context of common childhood obesity in European Americans. Zhao J, et al. Obesity (Silver Spring), 2011 Dec. PMID 21779088
    4. Adult obesity susceptibility variants are associated with greater childhood weight gain and a faster tempo of growth: the 1946 British Birth Cohort Study. Elks CE, et al. Am J Clin Nutr, 2012 May. PMID 22456663, Free PMC Article
    5. Susceptibility variants for obesity and colorectal cancer risk: the multiethnic cohort and PAGE studies. Lim U, et al. Int J Cancer, 2012 Sep 15. PMID 22511254, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GNPDA1 siRNA induced GFAT2 which was hardly measurable in these cells under standard culture conditions, GNPDA2 siRNA increased GFAT1, and GFAT1 siRNA increased the expression of hyaluronan synthase 2 (HAS2). Silencing of GFAT1 stimulated GNPDA1 and GDPDA2, and inhibited cell migration.
      Title: Hexosamine biosynthesis in keratinocytes: roles of GFAT and GNPDA enzymes in the maintenance of UDP-GlcNAc content and hyaluronan synthesis.
    2. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: MC4R variant is associated with BMI but not response to resistance training in young females.
    3. Data show that SNPs in SEC16B and TMEM18 were significantly associated with obesity, and the SNPs in GNPDA2, BDNF, FAIM2 and MC4R were marginally associated with obesity in Japanese.
      Title: Association between obesity and polymorphisms in SEC16B, TMEM18, GNPDA2, BDNF, FAIM2 and MC4R in a Japanese population.
    4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Evaluating the discriminative power of multi-trait genetic risk scores for type 2 diabetes in a northern Swedish population.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Associations of six single nucleotide polymorphisms in obesity-related genes with BMI and risk of obesity in Chinese children.
    6. Observational study, meta-analysis, and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry.
    EBI GWAS Catalog
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glucosamine-6-phosphate deaminase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glucosamine-6-phosphate deaminase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in N-acetylglucosamine catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in N-acetylneuraminate catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in UDP-N-acetylglucosamine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in UDP-N-acetylglucosamine biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glucosamine catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    glucosamine-6-phosphate isomerase 2
    Names
    glcN6P deaminase 2
    glucosamine-6-phosphate isomerase SB52
    NP_001257809.1
    NP_001257810.1
    NP_612208.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001270880.2 → NP_001257809.1  glucosamine-6-phosphate isomerase 2 isoform 2

      See identical proteins and their annotated locations for NP_001257809.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AC096586
      Consensus CDS
      CCDS59473.1
      UniProtKB/Swiss-Prot
      Q8TDQ7
      Related
      ENSP00000425868.1, ENST00000507917.5
      Conserved Domains (1) summary
      cl00339
      Location:1 → 219
      SugarP_isomerase; SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ...

    2. NM_001270881.2 → NP_001257810.1  glucosamine-6-phosphate isomerase 2 isoform 3

      See identical proteins and their annotated locations for NP_001257810.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' UTR and uses a downstream start codon compared to variant 1. It encodes isoform 3 which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC096586
      Consensus CDS
      CCDS59472.1
      UniProtKB/Swiss-Prot
      Q8TDQ7
      Related
      ENSP00000427423.1, ENST00000507534.5
      Conserved Domains (1) summary
      cl00339
      Location:1 → 183
      SugarP_isomerase; Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose ...

    3. NM_138335.3 → NP_612208.1  glucosamine-6-phosphate isomerase 2 isoform 1

      See identical proteins and their annotated locations for NP_612208.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC096586
      Consensus CDS
      CCDS3469.1
      UniProtKB/Swiss-Prot
      B4DJF3, Q2VYF1, Q59EA7, Q8NCZ8, Q8TDQ7, Q96BJ4, Q96NC6
      Related
      ENSP00000295448.3, ENST00000295448.8
      Conserved Domains (1) summary
      cl00339
      Location:1 → 253
      SugarP_isomerase; Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose ...

    RNA

    1. NR_073094.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks the first coding (AUG) exon and uses an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 3, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC096586

    2. NR_073095.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC096586

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      44701795..44726556 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_007096361.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      44668716..44693480 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_008486911.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TDQ7.1 GenPept UniProtKB/Swiss-Prot:Q8TDQ7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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