GLYCTK glycerate kinase [Homo sapiens (human)] - Gene

Summary

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

Location:: 3p21.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (52287828..52295257)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (52320727..52349445)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (52321844..52329273)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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).
Observational study of gene-disease association. (HuGE Navigator)
Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
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.

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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 EBI GWAS CatalogPubMed
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-17518 (e-PCR)
- UniSTS:77858

RH78133 (e-PCR)
- UniSTS:30762

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	IBA Inferred from Biological aspect of Ancestor 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	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: glycerate kinase

Names: HBeAg binding protein 4; HBeAg-binding protein 2

NP_001138423.1

EC 2.7.1.31

NP_660305.2

EC 2.7.1.31

XP_016861219.1

EC 2.7.1.31

XP_024309119.1

EC 2.7.1.31

XP_024309120.1

EC 2.7.1.31

XP_047303421.1

EC 2.7.1.31

XP_047303422.1

EC 2.7.1.31

XP_047303423.1

EC 2.7.1.31

XP_054201255.1

EC 2.7.1.31

XP_054201256.1

EC 2.7.1.31

XP_054201257.1

EC 2.7.1.31

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

NG_023246.1 RefSeqGene

Range

5009..12438

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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

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
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
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
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