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    GLYCTK glycerate kinase [ Homo sapiens (human) ]

    Gene ID: 132158, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GLYCTKprovided by HGNC
    Official Full Name
    glycerate kinaseprovided by HGNC
    Primary source
    HGNC:HGNC:24247
    See related
    Ensembl:ENSG00000168237 MIM:610516; AllianceGenome:HGNC:24247
    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
    HBEBP2; HBEBP4; HBeAgBP4A
    Summary
    This locus encodes a member of the glycerate kinase type-2 family. The encoded enzyme catalyzes the phosphorylation of (R)-glycerate and may be involved in serine degradation and fructose metabolism. Decreased activity of the encoded enzyme may be associated with the disease D-glyceric aciduria. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]
    Expression
    Broad expression in liver (RPKM 19.7), duodenum (RPKM 15.1) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GLYCTK in Genome Data Viewer
    Location:
    3p21.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52287828..52295257)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52320727..52349445)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52321844..52329273)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19934 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1M Neighboring gene WD repeat domain 82 Neighboring gene microRNA let-7g Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52311392-52312024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52312657-52313288 Neighboring gene uncharacterized LOC107986086 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:52321476-52322675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52324415-52324915 Neighboring gene GLYCTK antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52332967-52333837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52333838-52334707 Neighboring gene microRNA 135a-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52344635-52345552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52350849-52351787 Neighboring gene dynein axonemal heavy chain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52377569-52378070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52385639-52386434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52396307-52396860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14440 Neighboring gene protein phosphatase 2 regulatory subunit B'gamma pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443144-52443692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443693-52444241 Neighboring gene BRCA1 associated deubiquitinase 1

    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. D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK). Sass JO, et al. Hum Mutat, 2010 Dec. PMID 20949620
    2. D-glycerate kinase deficiency as a cause of D-glyceric aciduria. Van Schaftingen E. FEBS Lett, 1989 Jan 30. PMID 2537226
    3. Biochemical contribution to diagnosis and study of a new case of D-glyceric acidemia/aciduria. Fontaine M, et al. Clin Chem, 1989 Oct. PMID 2551543
    4. d-Glycerate kinase deficiency in a neuropediatric patient. Sass JO, et al. Brain Dev, 2020 Feb. PMID 31837836
    5. Isolation and characterization of the human D-glyceric acidemia related glycerate kinase gene GLYCTK1 and its alternatively splicing variant GLYCTK2. Guo JH, et al. DNA Seq, 2006 Feb. PMID 16753811

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mutations in the GLYCTK gene is the cause of D-glycerate kinase deficiency and D-glyceric aciduria.
      Title: D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK).
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    3. Identification of two variants of the human glycerate kinase gene-Glycerate kinase 1 (GLYCTK1), longer variant, and Glycerate kinase 2 (GLYCTK2), shorter variant.
      Title: Isolation and characterization of the human D-glyceric acidemia related glycerate kinase gene GLYCTK1 and its alternatively splicing variant GLYCTK2.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    D-Glyceric aciduria
    MedGen: C0342765 OMIM: 220120 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycerate kinase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables glycerate kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycerate kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    glycerate kinase
    Names
    HBeAg binding protein 4
    HBeAg-binding protein 2
    NP_001138423.1
    NP_660305.2
    XP_016861219.1
    XP_024309119.1
    XP_024309120.1
    XP_047303421.1
    XP_047303422.1
    XP_047303423.1
    XP_054201255.1
    XP_054201256.1
    XP_054201257.1

    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.

    Genomic

    1. NG_023246.1 RefSeqGene

      Range
      5009..12438
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001144951.2 → NP_001138423.1  glycerate kinase isoform 2

      See identical proteins and their annotated locations for NP_001138423.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2), also known as GLYCTK2, is shorter and contains a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC092045, AY295075, BC036862
      Consensus CDS
      CCDS46841.1
      UniProtKB/Swiss-Prot
      Q8IVS8
      Related
      ENSP00000301965.9, ENST00000305690.12
      Conserved Domains (1) summary
      cl26100
      Location:38 → 178
      DUF4147; Domain of unknown function (DUF4147)

    2. NM_145262.4 → NP_660305.2  glycerate kinase isoform 1

      See identical proteins and their annotated locations for NP_660305.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1), also known as GLYCTK1.
      Source sequence(s)
      AA100208, AC092045, AI380271, BC036862, BC042151, BM555864, DA586797
      Consensus CDS
      CCDS2852.1
      UniProtKB/Swiss-Prot
      Q0P630, Q2EZ43, Q6Y2K6, Q7Z6G5, Q86YR8, Q8IVS8, Q8TED2, Q8WTY2
      Related
      ENSP00000389175.2, ENST00000436784.7
      Conserved Domains (1) summary
      cl26100
      Location:38 → 514
      DUF4147; Domain of unknown function (DUF4147)

    RNA

    1. NR_026699.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA100208, AC092045, AI380271, BC036862, BM555864, DA586797

    2. NR_026700.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA100208, AC092045, AI380271, AK074215, BC036862, BM555864, DA586797, DQ352863

    3. NR_026701.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA100208, AC092045, AF448855, AI380271, BM555864, DA586797

    4. NR_026702.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start site renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA100208, AC092045, AI380271, AY172690, BM555864, DA586797

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      52287828..52295257
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453351.2 → XP_024309119.1  glycerate kinase isoform X1

      UniProtKB/Swiss-Prot
      Q0P630, Q2EZ43, Q6Y2K6, Q7Z6G5, Q86YR8, Q8IVS8, Q8TED2, Q8WTY2

    2. XM_024453352.2 → XP_024309120.1  glycerate kinase isoform X5

      Related
      ENSP00000419008.1, ENST00000477382.1
      Conserved Domains (1) summary
      cl26100
      Location:38 → 178
      DUF4147; Domain of unknown function (DUF4147)

    3. XM_017005730.2 → XP_016861219.1  glycerate kinase isoform X2

    4. XM_047447465.1 → XP_047303421.1  glycerate kinase isoform X3

    5. XM_047447466.1 → XP_047303422.1  glycerate kinase isoform X3

    6. XM_047447467.1 → XP_047303423.1  glycerate kinase isoform X4

      UniProtKB/TrEMBL
      C9JA32
      Related
      ENSP00000417526.1, ENST00000471180.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52320727..52349445
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345280.1 → XP_054201255.1  glycerate kinase isoform X1

      UniProtKB/Swiss-Prot
      Q0P630, Q2EZ43, Q6Y2K6, Q7Z6G5, Q86YR8, Q8IVS8, Q8TED2, Q8WTY2

    2. XM_054345281.1 → XP_054201256.1  glycerate kinase isoform X3

    3. XM_054345282.1 → XP_054201257.1  glycerate kinase isoform X4

      UniProtKB/TrEMBL
      C9JA32
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IVS8.1 GenPept UniProtKB/Swiss-Prot:Q8IVS8

    Gene LinkOut

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