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GLYCTK glycerate kinase [ Homo sapiens (human) ]

Gene ID: 132158, updated on 24-Nov-2020

Summary

Official Symbol
GLYCTKprovided by HGNC
Official Full Name
glycerate kinaseprovided by HGNC
Primary source
HGNC:HGNC:24247
See related
Ensembl:ENSG00000168237 MIM:610516
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

Genomic context

See GLYCTK in Genome Data Viewer
Location:
3p21.2
Exon count:
5
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (52287558..52295257)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52321836..52329272)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1M Neighboring gene WD repeat domain 82 Neighboring gene microRNA let-7g Neighboring gene uncharacterized LOC107986086 Neighboring gene GLYCTK antisense RNA 1 Neighboring gene microRNA 135a-1 Neighboring gene dynein axonemal heavy chain 1 Neighboring gene protein phosphatase 2 regulatory subunit B'gamma pseudogene Neighboring gene BRCA1 associated protein 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deficiency of glycerate kinase
MedGen: C1291386 OMIM: 220120 GeneReviews: Not available
Compare labs
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
GeneReviews: Not available
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
glycerate kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycerate kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
glycerate kinase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate TAS
Traceable Author Statement
more info
 
protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001144951.2NP_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:38178
    DUF4147; Domain of unknown function (DUF4147)
  2. NM_145262.4NP_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
    Q8IVS8
    UniProtKB/TrEMBL
    A0A024R302
    Related
    ENSP00000389175.2, ENST00000436784.7
    Conserved Domains (1) summary
    cl26100
    Location:38514
    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: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    52287558..52295257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005730.1XP_016861219.1  glycerate kinase isoform X2

  2. XM_024453352.1XP_024309120.1  glycerate kinase isoform X3

    Related
    ENSP00000419008.1, ENST00000477382.1
    Conserved Domains (1) summary
    cl26100
    Location:38178
    DUF4147; Domain of unknown function (DUF4147)
  3. XM_024453351.1XP_024309119.1  glycerate kinase isoform X1

RNA

  1. XR_245095.4 RNA Sequence

  2. XR_001740023.2 RNA Sequence

  3. XR_001740022.2 RNA Sequence

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