GeneBe

PKM

pyruvate kinase M1/2

Basic information

Region (hg38): 15:72199029-72231819

Previous symbols: [ "PKM2" ]

Links

ENSG00000067225 ∙ NCBI:5315 ∙ OMIM:179050 ∙ HGNC:9021 ∙ Uniprot:P14618 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PKM gene.

  • not_specified (43 variants)
  • not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKM gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002654.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
3
clinvar
 8
missense
40
clinvar
 40
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 40 5 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PKMprotein_codingprotein_codingENST00000319622 1032795
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.8550.1451257330151257480.0000596
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.092213270.6750.00002103484
Missense in Polyphen3383.9120.393271005
Synonymous-0.6061241161.070.000006891082
Loss of Function3.78423.90.1670.00000154257

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.00009930.0000992
East Asian0.0001630.000163
Finnish0.000.00
European (Non-Finnish)0.00007920.0000791
Middle Eastern0.0001630.000163
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio between the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival. {ECO:0000269|PubMed:17308100, ECO:0000269|PubMed:18191611, ECO:0000269|PubMed:21620138}.;
Pathway
Pyruvate metabolism - Homo sapiens (human);Glycolysis / Gluconeogenesis - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Type II diabetes mellitus - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Abacavir Pathway, Pharmacokinetics/Pharmacodynamics;Warburg Effect;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Photodynamic therapy-induced HIF-1 survival signaling;Amino Acid metabolism;Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;Neutrophil degranulation;Metabolism of carbohydrates;Citrate cycle;Folate metabolism;Alanine Aspartate Asparagine metabolism;Glycolysis Gluconeogenesis;Glycolysis and Gluconeogenesis;TCR;Purine metabolism;Innate Immune System;Immune System;Metabolism;Pyrimidine metabolism;Glycolysis;Purine nucleotides nucleosides metabolism;EGFR1;Pyruvate metabolism;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Glucose metabolism;HIF-1-alpha transcription factor network (Consensus)

Recessive Scores

pRec
0.181

Intolerance Scores

loftool
rvis_EVS
-0.42
rvis_percentile_EVS
25.56

Haploinsufficiency Scores

pHI
0.777
hipred
Y
hipred_score
0.825
ghis
0.588

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pkm
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; neoplasm;

Gene ontology

Biological process
response to hypoxia;liver development;glycolytic process;response to nutrient;response to gravity;programmed cell death;response to muscle inactivity;animal organ regeneration;cellular response to insulin stimulus;neutrophil degranulation;skeletal muscle tissue regeneration;protein homotetramerization;canonical glycolysis;positive regulation of sprouting angiogenesis
Cellular component
extracellular region;nucleus;cytoplasm;mitochondrion;cytosol;cilium;vesicle;secretory granule lumen;myelin sheath;collagen-containing extracellular matrix;extracellular exosome;pyruvate kinase complex;extracellular vesicle;ficolin-1-rich granule lumen
Molecular function
magnesium ion binding;RNA binding;pyruvate kinase activity;protein binding;ATP binding;kinase activity;MHC class II protein complex binding;potassium ion binding;identical protein binding;ADP binding;cadherin binding;thyroid hormone binding