PGK2 phosphoglycerate kinase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PGK2provided by HGNC
Official Full Name: phosphoglycerate kinase 2provided by HGNC
Primary source: HGNC:HGNC:8898
See related: Ensembl:ENSG00000170950 MIM:172270; AllianceGenome:HGNC:8898
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: PGKB; PGKPS; HEL-S-272; dJ417L20.2
Summary: This gene is intronless, arose via retrotransposition of the phosphoglycerate kinase 1 gene, and is expressed specifically in the testis. Initially assumed to be a pseudogene, the encoded protein is actually a functional phosphoglycerate kinase that catalyzes the reversible conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate, during the Embden-Meyerhof-Parnas pathway of glycolysis, in the later stages of spermatogenesis.[provided by RefSeq, May 2010]
Orthologs: all
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Genomic context

Location:: 6p12.3

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (49785660..49787285, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (49627627..49629252, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (49753373..49754998, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Germ Cell-Specific Markers ZPBP2 and PGK2 in Testicular Biopsies Can Predict the Presence as well as the Quality of Sperm in Non-obstructive Azoospermia Patients.
Title: The Germ Cell-Specific Markers ZPBP2 and PGK2 in Testicular Biopsies Can Predict the Presence as well as the Quality of Sperm in Non-obstructive Azoospermia Patients.
Study of (Co-IP) and reverse co-immunoprecipitation (Co-IP) of CBP86-IV (TSCBP86-IV or CABYR) in human sperm cell lysate identified phosphoglycerate kinase 2 (PGK2) as interacting partner of CABYR. Protein interactions were further confirmed by yeast two-hybrid system.
Title: Testis-specific calcium-binding protein CBP86-IV (CABYR) binds with phosphoglycerate kinase 2 in vitro and in vivo experiment.
Data from studies in transgenic mice suggest that Pgk2 core promoter elements are required to direct demethylation of DNA and reconfiguration of nucleosomes in testis during sexual maturation and spermatogenesis.
Title: Sequence-specific promoter elements regulate temporal-specific changes in chromatin required for testis-specific activation of the Pgk2 gene.

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of phosphoglycerate kinase 2 (PGK2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Pgk1 (e-PCR), detects polymorphism
- UniSTS:531394

STS-X05246 (e-PCR)
- UniSTS:66262

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ADP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphoglycerate kinase activity	EXP Inferred from Experiment more info	PubMed
enables phosphoglycerate kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphoglycerate kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables phosphoglycerate kinase activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in canonical glycolysis	TAS Traceable Author Statement more info
involved_in flagellated sperm motility	IEA Inferred from Electronic Annotation more info
involved_in gluconeogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in gluconeogenesis	TAS Traceable Author Statement more info
involved_in glycolytic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycolytic process	NAS Non-traceable Author Statement more info	PubMed
involved_in phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphorylation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
is_active_in sperm fibrous sheath	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: phosphoglycerate kinase 2

Names: epididymis secretory protein Li 272; phosphoglycerate kinase autosomal pseudogene; phosphoglycerate kinase, testis specific; testicular tissue protein Li 139

NP_620061.2

EC 2.7.2.3

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.