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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
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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 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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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
not available

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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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

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