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

Gene ID: 132789, updated on 2-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
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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 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)

Genotypes

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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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

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