Pyruvate kinase deficiency of red cells

disease
On this page

Also known as anemia, congenital, nonspherocytic hemolytic, 2, pyruvate kinase deficienthemolytic anaemia due to pyruvate Kinase deficiencyhemolytic anaemia due to red cell pyruvate kinase deficiencyhemolytic anemia due to pyruvate Kinase deficiencyhemolytic anemia due to red cell pyruvate kinase deficiencyPK deficiencyPyruvate Kinase Deficiencypyruvate kinase deficiency of erythrocytepyruvate kinase deficiency of erythrocytes

Summary

Pyruvate kinase deficiency of red cells (MONDO:0009950) is a disease caused by PKLR (GenCC Definitive), with 3 cohort genes and 14 clinical trials. Top therapeutic interventions include mitapivat and ascorbic acid.

At a glance

  • Prevalence: 1-9 / 100 000 (Europe) [Orphanet-validated]
  • Causal gene: PKLR (GenCC Definitive)
  • Cohort genes: 3
  • ClinVar variants: 143
  • Phenotypes (HPO): 15
  • Clinical trials: 14

Clinical features

Epidemiology

Prevalence records

3 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Point prevalence1-9 / 100 0005EuropeValidated
Point prevalence1-9 / 100 0005.1Specific populationValidated
Point prevalence1-9 / 1 000 0000.96Specific populationValidated

Signs & symptoms

Clinical features (HPO)

15 HPO clinical features (Orphanet curated; top 15 by frequency):

HPO IDTermFrequency
HP:0001744SplenomegalyVery frequent (80-99%)
HP:0001903AnemiaVery frequent (80-99%)
HP:0001923ReticulocytosisVery frequent (80-99%)
HP:0004870Chronic hemolytic anemiaVery frequent (80-99%)
HP:0008282Unconjugated hyperbilirubinemiaVery frequent (80-99%)
HP:0025109Reduced red cell pyruvate kinase levelVery frequent (80-99%)
HP:0001789Hydrops fetalisFrequent (30-79%)
HP:0003281Increased circulating ferritin concentrationFrequent (30-79%)
HP:0003452Increased serum ironFrequent (30-79%)
HP:0004804Congenital hemolytic anemiaFrequent (30-79%)
HP:0006579Prolonged neonatal jaundiceFrequent (30-79%)
HP:0001877Abnormal erythrocyte morphologyOccasional (5-29%)
HP:0004447PoikilocytosisOccasional (5-29%)
HP:0011273AnisocytosisOccasional (5-29%)
HP:0012463Elevated transferrin saturationOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namepyruvate kinase deficiency of red cells
Mondo IDMONDO:0009950
MeSHC564858
OMIM266200
Orphanet766
DOIDDOID:0111077
NCITC99037
SNOMED CT124331002
UMLSC0340968
MedGen473069
GARD0007514
NORD1642
Is cancer (heuristic)no

Also known as: anemia, congenital, nonspherocytic hemolytic, 2, pyruvate kinase deficient · hemolytic anaemia due to pyruvate Kinase deficiency · hemolytic anaemia due to red cell pyruvate kinase deficiency · hemolytic anemia due to pyruvate Kinase deficiency · hemolytic anemia due to red cell pyruvate kinase deficiency · PK deficiency · Pyruvate Kinase Deficiency · pyruvate kinase deficiency · pyruvate kinase deficiency of erythrocyte · pyruvate kinase deficiency of erythrocytes · pyruvate kinase deficiency of red cells

Data availability: 143 ClinVar variants · 5 GenCC gene-disease records · 2 cell lines.

Disease family

Classification path: disease › human disease › disease by body system or component › hematologic disorderanemiacongenital anemiacongenital nonspherocytic hemolytic anemiapyruvate kinase deficiency of red cells

Related subtypes (9): anemia, nonspherocytic hemolytic, gamma-glutamylcysteine synthetase deficiency, glutathione synthetase deficiency without 5-oxoprolinuria, non-spherocytic hemolytic anemia due to hexokinase deficiency, hemolytic anemia due to pyrimidine 5’ nucleotidase deficiency, hemolytic anemia due to adenylate kinase deficiency, hemolytic anemia due to glucophosphate isomerase deficiency, hemolytic anemia due to glutathione reductase deficiency, hemolytic anemia due to erythrocyte adenosine deaminase overproduction

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

143 retrieved; paginated sample, class counts are floors:

59 uncertain significance, 29 conflicting classifications of pathogenicity, 21 likely pathogenic, 17 pathogenic, 10 pathogenic/likely pathogenic, 4 benign, 3 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1163643NM_000298.6(PKLR):c.993C>A (p.Asp331Glu)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1163645NM_000298.6(PKLR):c.826del (p.Val276fs)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
1163647NM_000298.6(PKLR):c.307del (p.Arg103fs)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1187215NM_000298.6(PKLR):c.1178A>G (p.Asn393Ser)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1505PKLR, 1-BP DELPKLRPathogenicno assertion criteria provided
1507NM_000298.6(PKLR):c.1151C>T (p.Thr384Met)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1509NM_000298.6(PKLR):c.1261C>A (p.Gln421Lys)PKLRPathogenicno assertion criteria provided
1510NM_000298.6(PKLR):c.1436G>A (p.Arg479His)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
1511NM_000298.6(PKLR):c.1529G>A (p.Arg510Gln)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
1513NM_000298.6(PKLR):c.1456C>T (p.Arg486Trp)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1514NM_000298.6(PKLR):c.389C>A (p.Ser130Tyr)PKLRPathogenicno assertion criteria provided
1515NC_000001.11:g.155301478C>GPKLRPathogenicno assertion criteria provided
1516NM_000298.6(PKLR):c.1318G>T (p.Glu440Ter)PKLRPathogeniccriteria provided, single submitter
1517NM_000298.6(PKLR):c.1269G>A (p.Ala423=)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1687397NM_000298.6(PKLR):c.1015del (p.Asp339fs)PKLRPathogeniccriteria provided, single submitter
1705384NM_000298.6(PKLR):c.808C>T (p.Arg270Ter)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
2202852NM_000298.6(PKLR):c.1462C>T (p.Arg488Ter)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
2437867NM_000298.6(PKLR):c.1022G>C (p.Gly341Ala)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
280113NM_000298.6(PKLR):c.721G>T (p.Glu241Ter)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
292815NM_000298.6(PKLR):c.391_393del (p.Ile131del)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2956937NM_000298.6(PKLR):c.694+2T>GPKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3235888NM_000298.6(PKLR):c.695-1G>APKLRPathogeniccriteria provided, single submitter
3341365NM_000298.6(PKLR):c.603G>A (p.Trp201Ter)PKLRPathogeniccriteria provided, single submitter
3376903NM_000298.6(PKLR):c.1618+1delPKLRPathogeniccriteria provided, single submitter
3775965NM_000298.6(PKLR):c.403del (p.Arg135fs)PKLRPathogeniccriteria provided, single submitter
522658NM_000298.6(PKLR):c.331G>A (p.Gly111Arg)PKLRPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
983093NM_000298.6(PKLR):c.1594C>T (p.Arg532Trp)PKLRPathogeniccriteria provided, multiple submitters, no conflicts
1299505NM_000298.6(PKLR):c.224T>C (p.Leu75Pro)PKLRLikely pathogeniccriteria provided, single submitter
1380720NM_000298.6(PKLR):c.1595G>C (p.Arg532Pro)PKLRLikely pathogeniccriteria provided, multiple submitters, no conflicts
2431446NM_000298.6(PKLR):c.1511G>T (p.Arg504Leu)PKLRLikely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 5 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
PKLRDefinitiveAutosomal recessivepyruvate kinase deficiency of red cells6

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
PKLROrphanet:766Hemolytic anemia due to red cell pyruvate kinase deficiency
NTRK1Orphanet:146Differentiated thyroid carcinoma
NTRK1Orphanet:642Hereditary sensory and autonomic neuropathy type 4
NTRK1Orphanet:64752Hereditary sensory and autonomic neuropathy type 5
NTRK1Orphanet:99361Isolated familial medullary thyroid carcinoma

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
PKLRHGNC:9020ENSG00000143627P30613Pyruvate kinase PKLRgencc,clinvar
HCN3HGNC:19183ENSG00000143630Q9P1Z3Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3clinvar
NTRK1HGNC:8031ENSG00000198400P04629High affinity nerve growth factor receptorclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
PKLRPyruvate kinase PKLRPyruvate kinase that catalyzes the conversion of phosphoenolpyruvate to pyruvate with the synthesis of ATP, and which plays a key role in glycolysis.
HCN3Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3Hyperpolarization-activated ion channel that are permeable to sodium and potassium ions, with an about 3:1 preference for potassium ions.
NTRK1High affinity nerve growth factor receptorReceptor tyrosine kinase involved in the development and the maturation of the central and peripheral nervous systems through regulation of proliferation, differentiation and survival of sympathetic and nervous neurons.

Protein-family classification

Druggable: 3 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Kinase218.5×0.008
Ion channel137.2×0.027

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
PKLRKinaseyes2.7.1.40Pyr_Knase, Pyrv_Knase-like_insert_dom_sf, Pyrv_Knase_brl
HCN3Ion channelyescNMP-bd_dom, K_chnl_volt-dep_EAG/ELK/ERG, Ion_trans_dom
NTRK1Kinaseyes2.7.10.1Cys-rich_flank_reg_C, Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom

Expression context

Cohort genes with no expression data: 0.

3 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)3
unknown0

Top tissues across cohort

TissueCohort genes
duodenum1
liver1
right lobe of liver1
cerebellum1
cortical plate1
right hemisphere of cerebellum1
apex of heart1
dorsal root ganglion1
male germ line stem cell (sensu Vertebrata) in testis1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
PKLR69tissue_specificmarkerliver, right lobe of liver, duodenum
HCN3132ubiquitousmarkercortical plate, right hemisphere of cerebellum, cerebellum
NTRK1160broadmarkerdorsal root ganglion, apex of heart, male germ line stem cell (sensu Vertebrata) in testis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
NTRK19,181
HCN3899
PKLR94

Structural data

PDB: 3 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
NTRK1P0462965
PKLRP3061358
HCN3Q9P1Z33

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 16. Enrichment computed across 3 evidence-associated genes (3 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
TRKA activation by NGF11903.3×0.004NTRK1
PLC-gamma1 signalling11268.9×0.004NTRK1
Signalling to STAT311268.9×0.004NTRK1
HCN channels1951.7×0.004HCN3
NGF-independant TRKA activation1761.3×0.004NTRK1
Signalling to p38 via RIT and RIN1761.3×0.004NTRK1
ARMS-mediated activation1543.8×0.004NTRK1
ChREBP activates metabolic gene expression1423.0×0.004PKLR
PI3K/AKT activation1423.0×0.004NTRK1
Frs2-mediated activation1317.2×0.005NTRK1
Retrograde neurotrophin signalling1271.9×0.005NTRK1
Signalling to RAS1223.9×0.006NTRK1
Regulation of gene expression in beta cells1173.0×0.007PKLR
Pyruvate metabolism1135.9×0.008PKLR
Glycolysis195.2×0.011PKLR
SARS-CoV-1-host interactions158.6×0.017PKLR

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
programmed cell death involved in cell development12808.7×0.010NTRK1
olfactory nerve development11872.4×0.010NTRK1
behavioral response to formalin induced pain11872.4×0.010NTRK1
response to hydrostatic pressure11404.3×0.010NTRK1
mechanoreceptor differentiation11123.5×0.010NTRK1
regulation of SA node cell action potential1936.2×0.010HCN3
pyruvate biosynthetic process1702.2×0.010PKLR
cellular response to nicotine1702.2×0.010NTRK1
regulation of membrane depolarization1624.1×0.010HCN3
peptidyl-tyrosine autophosphorylation1624.1×0.010NTRK1
axonogenesis involved in innervation1561.7×0.010NTRK1
response to metal ion1510.7×0.010PKLR
nerve growth factor signaling pathway1432.1×0.010NTRK1
cellular response to epinephrine stimulus1432.1×0.010PKLR
positive regulation of programmed cell death1374.5×0.010NTRK1
detection of mechanical stimulus involved in sensory perception of pain1374.5×0.010NTRK1
Sertoli cell development1374.5×0.010NTRK1
neurotrophin TRK receptor signaling pathway1351.1×0.010NTRK1
response to ATP1330.4×0.010PKLR
sympathetic nervous system development1312.1×0.010NTRK1
positive regulation of Ras protein signal transduction1295.6×0.010NTRK1
detection of temperature stimulus involved in sensory perception of pain1280.9×0.010NTRK1
response to electrical stimulus1216.1×0.012NTRK1
positive regulation of synaptic transmission, glutamatergic1208.1×0.012NTRK1
sodium ion import across plasma membrane1208.1×0.012HCN3
response to axon injury1170.2×0.014NTRK1
response to cAMP1170.2×0.014PKLR
cellular response to nerve growth factor stimulus1156.0×0.014NTRK1
peptidyl-tyrosine phosphorylation1140.4×0.015NTRK1
glycolytic process1127.7×0.016PKLR

Therapeutics

Drug target analysis

Approved (phase 4): 2 · Phase ≥3: 2 · Phased (≥1): 2 · Undrugged: 1

Druggability breadth: 3 of 3 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
PKLRMITAPIVAT
NTRK1PONATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
NTRK1664
PKLR34
HCN300

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
MITAPIVAT4PKLR
PONATINIB4NTRK1
FEDRATINIB4NTRK1
AXITINIB4NTRK1
SORAFENIB4NTRK1
RUXOLITINIB4NTRK1
ENTRECTINIB4NTRK1
CABOZANTINIB4NTRK1
CERITINIB4NTRK1
BOSUTINIB4NTRK1
LORLATINIB4NTRK1
ABEMACICLIB4NTRK1
LAROTRECTINIB4NTRK1
LAROTRECTINIB SULFATE4NTRK1
REPOTRECTINIB4NTRK1
NINTEDANIB4NTRK1
SUNITINIB4NTRK1
QUIZARTINIB4NTRK1
CRIZOTINIB4NTRK1
MIDOSTAURIN4NTRK1
AMITRIPTYLINE4NTRK1
SURAMIN3PKLR
CRENOLANIB3NTRK1
LINIFANIB3NTRK1
DEFACTINIB3NTRK1
ENTOSPLETINIB3NTRK1
SITRAVATINIB3NTRK1
ALISERTIB3NTRK1
DOVITINIB3NTRK1
LESTAURTINIB3NTRK1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
NTRK11,194Binding:1182, ADMET:7, Functional:5
PKLR82Binding:69, Functional:12, ADMET:1
HCN33Binding:1, ADMET:1, Functional:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PKLR2.7.1.40pyruvate kinase
NTRK12.7.10.1receptor protein-tyrosine kinase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
NTRK11,194

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

29 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
PONATINIB4NTRK1
FEDRATINIB4NTRK1
AXITINIB4NTRK1
SORAFENIB4NTRK1
RUXOLITINIB4NTRK1
ENTRECTINIB4NTRK1
CABOZANTINIB4NTRK1
CERITINIB4NTRK1
BOSUTINIB4NTRK1
LORLATINIB4NTRK1
ABEMACICLIB4NTRK1
LAROTRECTINIB4NTRK1
LAROTRECTINIB SULFATE4NTRK1
REPOTRECTINIB4NTRK1
NINTEDANIB4NTRK1
SUNITINIB4NTRK1
QUIZARTINIB4NTRK1
CRIZOTINIB4NTRK1
MIDOSTAURIN4NTRK1
AMITRIPTYLINE4NTRK1
SURAMIN3PKLR
CRENOLANIB3NTRK1
LINIFANIB3NTRK1
DEFACTINIB3NTRK1
ENTOSPLETINIB3NTRK1
SITRAVATINIB3NTRK1
ALISERTIB3NTRK1
DOVITINIB3NTRK1
LESTAURTINIB3NTRK1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)2PKLR, NTRK1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1HCN3
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug0

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
HCN33

Clinical trials & evidence

Clinical trials

Clinical trials: 14.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified6
PHASE33
PHASE22
PHASE12
PHASE41

Top trials by phase / activity

NCTPhaseStatusTitle
NCT05777993PHASE4ENROLLING_BY_INVITATIONA Study to Provide Continued Access to Mitapivat for Participants Who Previously Completed an Agios-Sponsored Mitapivat Study
NCT03548220PHASE3COMPLETEDA Study to Evaluate Efficacy and Safety of AG-348 in Not Regularly Transfused Adult Participants With Pyruvate Kinase Deficiency (PKD)
NCT03559699PHASE3COMPLETEDA Study Evaluating the Efficacy and Safety of AG-348 in Regularly Transfused Adult Participants With Pyruvate Kinase Deficiency (PKD)
NCT03853798PHASE3COMPLETEDExtension Study of AG-348 in Adult Participants With Pyruvate Kinase Deficiency Previously Enrolled in AG-348-006 or AG348-C-007
NCT02476916PHASE2COMPLETEDA Study of AG-348 in Adult Participants With Pyruvate Kinase (PK) Deficiency
NCT06422351PHASE2SUSPENDEDClinical Trial to Evaluate the Efficacy of Gene Therapy for Pyruvate Kinase Deficiency
NCT07612345PHASE1NOT_YET_RECRUITINGHigh-Dose Vitamin C in G6PDA and Pyruvate Kinase Deficiency: A Safety Study
NCT04105166PHASE1COMPLETEDGene Therapy for Pyruvate Kinase Deficiency (PKD)
NCT03481738Not specifiedACTIVE_NOT_RECRUITINGPyruvate Kinase Deficiency Global Longitudinal Registry
NCT02053480Not specifiedCOMPLETEDPyruvate Kinase Deficiency Natural History Study
NCT03866590Not specifiedCOMPLETEDPyruvate Kinase Deficiency Epidemiological Study (PIECE)
NCT04902833Not specifiedCOMPLETEDAcquired Pyruvate Kinase Deficiency In Clonal Myeloid Neoplasms
NCT04964323Not specifiedTERMINATEDPyruvate Kinase (PK) Deficiency Global Longitudinal Registry: Patient-Reported Outcomes (PRO)
NCT04995315Not specifiedCOMPLETEDPyruvate Kinase Deficiency Global Longitudinal Registry Substudy of Protocol AG348-C-008

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
MITAPIVAT45
ASCORBIC ACID41