Sickle cell disease

disease
On this page

Also known as Haemoglobin S diseaseHaemoglobin S disease without crisisHb-S/Hb-C diseaseHbS diseaseHemoglobin S diseaseHPA 1 recognition polymorphism, beta-globin-relatedHPA1sickle cell anemiasickle-cell/Hb-C disease without crisissickling disorder due to Haemoglobin Ssickling disorder due to Hemoglobin S

Summary

Sickle cell disease (MONDO:0011382) is a disease caused by HBB (GenCC Strong), with 6 cohort genes (5 GWAS associations across 4 studies) and 932 clinical trials. Top therapeutic interventions include alemtuzumab, voxelotor, and hydroxyurea.

At a glance

  • Prevalence: 1-5 / 10 000 (Europe) [Orphanet-validated]
  • Causal gene: HBB (GenCC Strong)
  • Cohort genes: 6
  • GWAS associations: 5
  • ClinVar variants: 123
  • Phenotypes (HPO): 37
  • Clinical trials: 932

Clinical features

Epidemiology

Prevalence records

12 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Point prevalence1-5 / 10 00010EuropeValidated
Annual incidence1-5 / 10 00021.6262BrazilValidated
Point prevalence1-5 / 10 00030United StatesValidated
Prevalence at birth1-5 / 10 00042FranceValidated
Prevalence at birth1-5 / 10 00025GermanyValidated
Prevalence at birth1-5 / 10 00047.5BelgiumValidated
Prevalence at birth1-5 / 10 00032.8United StatesValidated
Prevalence at birth1-5 / 10 00041.7United KingdomNot yet validated
Prevalence at birth>1 / 1000344.8GuadeloupeNot yet validated
Prevalence at birth>1 / 1000248.75MartiniqueNot yet validated
Prevalence at birth>1 / 1000467.3GuyanaNot yet validated
Prevalence at birth1-5 / 10 00020.15ReunionNot yet validated

Signs & symptoms

Clinical features (HPO)

37 HPO clinical features (Orphanet curated; top 37 by frequency):

HPO IDTermFrequency
HP:0004870Chronic hemolytic anemiaObligate (100%)
HP:0001878Hemolytic anemiaVery frequent (80-99%)
HP:0002719Recurrent infectionsVery frequent (80-99%)
HP:0012531PainVery frequent (80-99%)
HP:0000488RetinopathyFrequent (30-79%)
HP:0000939OsteoporosisFrequent (30-79%)
HP:0000952JaundiceFrequent (30-79%)
HP:0001743Abnormality of the spleenFrequent (30-79%)
HP:0001891Iron deficiency anemiaFrequent (30-79%)
HP:0001894ThrombocytosisFrequent (30-79%)
HP:0001923ReticulocytosisFrequent (30-79%)
HP:0001974LeukocytosisFrequent (30-79%)
HP:0002754OsteomyelitisFrequent (30-79%)
HP:0010885Avascular necrosisFrequent (30-79%)
HP:0011981Pigment gallstonesFrequent (30-79%)
HP:0012622Chronic kidney diseaseFrequent (30-79%)
HP:0100749Chest painFrequent (30-79%)
HP:0000707Abnormality of the nervous systemOccasional (5-29%)
HP:0001081CholelithiasisOccasional (5-29%)
HP:0001406Intrahepatic cholestasisOccasional (5-29%)
HP:0002092Pulmonary arterial hypertensionOccasional (5-29%)
HP:0002140Ischemic strokeOccasional (5-29%)
HP:0002597Abnormality of the vasculatureOccasional (5-29%)
HP:0003259Elevated circulating creatinine concentrationOccasional (5-29%)
HP:0008282Unconjugated hyperbilirubinemiaOccasional (5-29%)
HP:0011886HyphemaOccasional (5-29%)
HP:0011904Persistence of hemoglobin FOccasional (5-29%)
HP:0012418HypoxemiaOccasional (5-29%)
HP:0025326Retinal arterial occlusionOccasional (5-29%)
HP:0025435Increased circulating lactate dehydrogenase concentrationOccasional (5-29%)
HP:0031090Finger dactylitisOccasional (5-29%)
HP:0034336Splenic infarctionOccasional (5-29%)
HP:0200023PriapismOccasional (5-29%)
HP:0200042Skin ulcerOccasional (5-29%)
HP:0001931Hypochromic anemiaVery rare (<1-4%)
HP:0001935Microcytic anemiaVery rare (<1-4%)
HP:0005518Increased mean corpuscular volumeVery rare (<1-4%)

Identifiers

Disease identifiers

FieldValue
Canonical namesickle cell disease
Mondo IDMONDO:0011382
MeSHD000755
OMIM603903
Orphanet232
DOIDDOID:0081445, DOID:10923
ICD-10-CMD57.2
NCITC34383
UMLSC0002895
MedGen287
GARD0008614
MedDRA10040641
NORD1714
Is cancer (heuristic)no

Also known as: Haemoglobin S disease · Haemoglobin S disease without crisis · Hb-S/Hb-C disease · HbS disease · Hemoglobin S disease · HPA 1 recognition polymorphism, beta-globin-related · HPA1 · sickle cell anemia · Sickle Cell Disease · sickle cell disease · sickle-cell/Hb-C disease without crisis · sickling disorder due to Haemoglobin S · sickling disorder due to Hemoglobin S

Data availability: 123 ClinVar variants · 5 GWAS associations (4 studies) · 3 GenCC gene-disease records · 85 cell lines.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal recessive diseasesickle cell disease

Related subtypes (218): immunodeficiency-centromeric instability-facial anomalies syndrome, hypercalcemia, infantile, Ochoa syndrome, autosomal recessive Ehlers-Danlos syndrome, vascular type, hydrolethalus syndrome, 3-M syndrome, isolated hyperchlorhidrosis, dacryocystitis-osteopoikilosis syndrome, Hutchinson-Gilford progeria syndrome, achalasia microcephaly syndrome, acrorenal syndrome, autosomal recessive, beta-ketothiolase deficiency, autosomal recessive Alport syndrome, Alstrom syndrome, microphthalmia with limb anomalies, camptodactyly-arthropathy-coxa vara-pericarditis syndrome, Behr syndrome, bifid nose, autosomal recessive, Bloom syndrome, Bowen-Conradi syndrome, camptodactyly with fibrous tissue hyperplasia and skeletal dysplasia, heart defects-limb shortening syndrome, autosomal recessive palmoplantar keratoderma and congenital alopecia, COFS syndrome, craniometaphyseal dysplasia, autosomal recessive, Fraser syndrome, cystic fibrosis, polycystic lipomembranous osteodysplasia with sclerosing leukoencephaly, persistent hyperplastic primary vitreous, autosomal recessive, Donnai-Barrow syndrome, Schöpf-Schulz-Passarge syndrome, cleft lip/palate-ectodermal dysplasia syndrome, Ellis-van Creveld syndrome, Wolcott-Rallison syndrome, autosomal recessive faciodigitogenital syndrome, acromesomelic dysplasia 2B, brittle cornea syndrome, triple-A syndrome, autosomal recessive humeroradial synostosis, multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome, hydrocephalus, nonsyndromic, autosomal recessive 1, autosomal recessive hydrocephalus due to congenital stenosis of aqueduct of Sylvius, hypertelorism, microtia, facial clefting syndrome, hypoparathyroidism-retardation-dysmorphism syndrome, Vici syndrome, Johanson-Blizzard syndrome, autosomal recessive Kenny-Caffey syndrome, Papillon-Lefevre disease, Haim-Munk syndrome, Laurence-Moon syndrome, Donohue syndrome, lipase deficiency, combined, autosomal recessive familial Mediterranean fever, thiamine-responsive megaloblastic anemia syndrome, cartilage-hair hypoplasia, Nijmegen breakage syndrome, pseudo-TORCH syndrome, Galloway-Mowat syndrome, mulibrey nanism, myotonia congenita, autosomal recessive, Schwartz-Jampel syndrome, proteosome-associated autoinflammatory syndrome, Netherton syndrome, Niemann-Pick disease type A, oculodentodigital dysplasia, autosomal recessive, odonto-onycho-dermal dysplasia, autosomal recessive omodysplasia, osteoporosis-pseudoglioma syndrome, Shwachman-Diamond syndrome, phenylketonuria, Bjornstad syndrome, Laron syndrome, autosomal recessive polycystic kidney disease, autosomal recessive inherited pseudoxanthoma elasticum, autosomal recessive multiple pterygium syndrome, rapadilino syndrome, short-rib thoracic dysplasia 9 with or without polydactyly, autosomal recessive Robinow syndrome, Sjogren-Larsson syndrome, scapuloperoneal spinal muscular atrophy, autosomal recessive, spondyloepiphyseal dysplasia tarda, autosomal recessive, inherited threoninemia, Pendred syndrome, autosomal recessive spondylocostal dysostosis, Werner syndrome, ABCD syndrome, Naxos disease, autosomal recessive amelia, human HOXA1 syndromes, autosomal recessive proximal renal tubular acidosis, hyper-IgM syndrome type 2, temtamy preaxial brachydactyly syndrome, TH-deficient dopa-responsive dystonia, craniosynostosis syndrome, autosomal recessive, Niemann-Pick disease type B, skin fragility-woolly hair-palmoplantar keratoderma syndrome, CoQ-responsive OXPHOS deficiency, familial adenomatous polyposis 2, Pierson syndrome, palmoplantar keratoderma-XX sex reversal-predisposition to squamous cell carcinoma syndrome, cardiomyopathy-hypotonia-lactic acidosis syndrome, PHARC syndrome, Kahrizi syndrome, cutis laxa with severe pulmonary, gastrointestinal and urinary anomalies, congenital prothrombin deficiency, immunodeficiency 31B, dyskeratosis congenita, autosomal recessive 2, dyskeratosis congenita, autosomal recessive 3, Nestor-Guillermo progeria syndrome, leukoencephalopathy with calcifications and cysts, mitochondrial pyruvate carrier deficiency, branched-chain keto acid dehydrogenase kinase deficiency, dyskeratosis congenita, autosomal recessive 5, hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome, alacrima, achalasia, and intellectual disability syndrome, hyperlipoproteinemia, type 1D, microcephaly and chorioretinopathy 2, congenital stationary night blindness 1G, combined oxidative phosphorylation deficiency 29, hypermanganesemia with dystonia 2, growth retardation, intellectual developmental disorder, hypotonia, and hepatopathy, gnb5-related intellectual disability-cardiac arrhythmia syndrome, autosomal recessive spastic paraplegia type 78, autosomal recessive limb-girdle muscular dystrophy, Bardet-Biedl syndrome, autosomal recessive cerebellar ataxia, neuronopathy, distal hereditary motor, autosomal recessive, UV-sensitive syndrome, Ehlers-Danlos syndrome, kyphoscoliotic type 1, Cockayne syndrome, hyperphenylalaninemia due to tetrahydrobiopterin deficiency, leukoencephalopathy-palmoplantar keratoderma syndrome, autosomal recessive hypohidrotic ectodermal dysplasia, Warburg micro syndrome, autosomal recessive primary microcephaly, autosomal recessive progressive external ophthalmoplegia, Meier-Gorlin syndrome, autosomal recessive sideroblastic anemia, autosomal recessive intermediate Charcot-Marie-Tooth disease, Perrault syndrome, autosomal recessive hypophosphatemic rickets, de Barsy syndrome, leukocyte adhesion deficiency, Senior-Loken syndrome, autosomal recessive spastic ataxia, childhood-onset autosomal recessive myopathy with external ophthalmoplegia, autosomal recessive cerebral atrophy, GM3 synthase deficiency, autosomal recessive distal renal tubular acidosis, pigmentation defects-palmoplantar keratoderma-skin carcinoma syndrome, autosomal recessive brachyolmia, Aicardi-Goutieres syndrome, homocystinuria without methylmalonic aciduria, Niemann-Pick disease type C, nephronophthisis, autosomal recessive osteopetrosis, peroxisome biogenesis disorder, congenital non-bullous ichthyosiform erythroderma, Seckel syndrome, Usher syndrome, autosomal recessive cutis laxa type 1, autosomal recessive cutis laxa type 2, hearing loss, autosomal recessive, microcephaly, growth restriction, and increased sister chromatid exchange 2, encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, 1, congenital vertebral-cardiac-renal anomalies syndrome, hair defect with photosensitivity and intellectual disability syndrome, autosomal recessive severe congenital neutropenia, severe combined immunodeficiency due to CARMIL2 deficiency, extraoral halitosis due to methanethiol oxidase deficiency, neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities, mitochondrial complex 2 deficiency, nuclear type 3, mitochondrial complex 2 deficiency, nuclear type 4, mismatch repair cancer syndrome, spondyloepimetaphyseal dysplasia with joint laxity, type 3, Kilquist syndrome, Duane anomaly-myopathy-scoliosis syndrome, autosomal recessive axonal charcot-marie-tooth disease due to copper metabolism defect, immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections-lymphopenia syndrome, optic atrophy-ataxia-peripheral neuropathy-global developmental delay syndrome, congenital myopathy with reduced type 2 muscle fibers, NAD(P)HX dehydratase deficiency, autosomal recessive ocular albinism, ichthyosis linearis circumflexa, eosinophil peroxidase deficiency, hyperphenylalaninemia due to DNAJC12 deficiency, autosomal recessive epidermolytic ichthyosis, Ehlers-Danlos syndrome, classic-like, 2, joint laxity, short stature, and myopia, HELIX syndrome, auditory neuropathy-optic atrophy syndrome, glycosylphosphatidylinositol biosynthesis defect 15, neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures, SCN4A-related myopathy, autosomal recessive, Uner Tan Syndrome, nephropathic cystinosis, Imerslund-Grasbeck syndrome type 1, Imerslund-Grasbeck syndrome type 2, permanent neonatal diabetes mellitus 1, growth hormone insensitivity with immune dysregulation 1, autosomal recessive, Rajab interstitial lung disease with brain calcifications 1, Roberts-SC phocomelia syndrome, neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities, RPE65-related recessive retinopathy, GUCY2D-related recessive retinopathy, autosomal recessive titinopathy, intellectual disability, autosomal recessive, ALPL-related autosomal recessive hypophosphatasia, spastic paraplegia 18b, autosomal recessive, CEP164-related ciliopathy, RP1-related recessive retinopathy, pseudohypoaldosteronism, type IB2, autosomal recessive, pseudohypoaldosteronism, type IB3, autosomal recessive, spastic paraplegia 30B, autosomal recessive, cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1, brain small vessel disease 2B, autosomal recessive, IMPG1-related recessive retinopathy, PROM1-related recessive retinopathy

Subtypes (2): sickle cell-hemoglobin c disease syndrome, sickle cell disease due to hemoglobin S and a non-S/non-C hemoglobin variant

Genetics & variants

GWAS landscape

5 GWAS associations across 4 studies. Top hits map to 6 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs734045493e-61HBG2, HBE1?21.96
rs24452841e-29OR51L1 - OR51P1PG0.82
rs79484713e-10HBG2, OR51B5, HBE1, OR51I2A0.26
rs72035602e-09NPRL3C0.44
rs7664329e-07BCL11A?0.22

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90481652Verma A20241,396120,613Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST000513Sebastiani P20091770Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study.
GCST90837517Koyama S202500Genetics and context for precision health in Greater Boston.
GCST001862Milton JN201300Genetic determinants of haemolysis in sickle cell anaemia.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic5

MAF distribution

BucketVariants
common (>=0.05)5
low_freq (0.01-0.05)0
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
intron_variant4
intergenic_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs73404549115299424C>T0.05intron_variantHBG2, HBE13e-61Tier 4: intronic/intergenic
rs2445284115008473C>A,T0.05intergenic_variantOR51L1 - OR51P1P1e-29Tier 4: intronic/intergenic
rs7948471115450516G>A0.21intron_variantHBG2, OR51B5, HBE1, OR51I23e-10Tier 4: intronic/intergenic
rs720356016134391T>G0.07intron_variantNPRL32e-09Tier 4: intronic/intergenic
rs766432260492835C>A,G,T0.05intron_variantBCL11A9e-07Tier 4: intronic/intergenic

ClinVar germline variants

123 retrieved; paginated sample, class counts are floors:

43 pathogenic, 24 uncertain significance, 24 pathogenic/likely pathogenic, 23 conflicting classifications of pathogenicity, 5 likely pathogenic, 2 benign/likely benign, 1 benign, 1 likely benign

ClinVarVariant (HGVS)GeneClassificationReview
15126NM_000518.4(HBB):c.19G>A (p.Glu7Lys)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15152NM_000518.4(HBB):c.364G>C (p.Glu122Gln)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15161NM_000518.5(HBB):c.79G>A (p.Glu27Lys)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15234NM_000518.4(HBB):c.92G>C (p.Arg31Thr)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15239NM_000518.5(HBB):c.82G>T (p.Ala28Ser)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15292NM_000518.4(HBB):c.364G>A (p.Glu122Lys)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15300NM_000518.5(HBB):c.61G>A (p.Val21Met)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15333NM_000518.5(HBB):c.20A>T (p.Glu7Val)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15352NM_000518.4(HBB):c.332T>C (p.Leu111Pro)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15401NM_000518.5(HBB):c.52A>T (p.Lys18Ter)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15402NM_000518.5(HBB):c.118C>T (p.Gln40Ter)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15404NM_000518.5(HBB):c.364G>T (p.Glu122Ter)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15407NM_000518.5(HBB):c.184A>T (p.Lys62Ter)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15408NM_000518.5(HBB):c.108C>A (p.Tyr36Ter)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15413NM_000518.5(HBB):c.25_26del (p.Lys9fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15414NM_000518.5(HBB):c.51del (p.Lys18fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15415NM_000518.5(HBB):c.135del (p.Phe46fs)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15417NM_000518.5(HBB):c.126_129del (p.Phe42fs)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15418NM_000518.5(HBB):c.20del (p.Glu7fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15419NM_000518.5(HBB):c.217dup (p.Ser73fs)HBBPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15422NM_000518.5(HBB):c.17_18del (p.Pro6fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15426NM_000518.5(HBB):c.45dup (p.Trp16fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15431NM_000518.5(HBB):c.112del (p.Trp38fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15432NM_000518.5(HBB):c.85dup (p.Leu29fs)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15434NM_000518.5(HBB):c.2T>G (p.Met1Arg)HBBPathogeniccriteria provided, multiple submitters, no conflicts
15436NM_000518.5(HBB):c.92+1G>AHBBPathogeniccriteria provided, multiple submitters, no conflicts
15438NM_000518.5(HBB):c.315+1G>AHBBPathogeniccriteria provided, multiple submitters, no conflicts
15446NM_000518.5(HBB):c.93-1G>AHBBPathogeniccriteria provided, multiple submitters, no conflicts
15447NM_000518.5(HBB):c.92+5G>CHBBPathogeniccriteria provided, multiple submitters, no conflicts
15448NM_000518.5(HBB):c.92+5G>THBBPathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 33 · Orphanet: 32 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 1

Dual-evidence genes (GWAS + Mendelian — highest-confidence targets)

GeneHGNCEvidence routes
BCL11ABCL11AGWAS, Orphanet

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
HBBStrongAutosomal recessivesickle cell disease33

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
HBBOrphanet:2132Hemoglobin C disease
HBBOrphanet:2133Hemoglobin E disease
HBBOrphanet:231214Beta-thalassemia major
HBBOrphanet:231222Beta-thalassemia intermedia
HBBOrphanet:231226Unstable beta globin chain variant disease
HBBOrphanet:231237Delta-beta-thalassemia
HBBOrphanet:231242Hemoglobin C-beta-thalassemia syndrome
HBBOrphanet:231249Hemoglobin E-beta-thalassemia syndrome
HBBOrphanet:232Sickle cell anemia
HBBOrphanet:247511Autosomal dominant secondary polycythemia
HBBOrphanet:251365Sickle cell S-C disease
HBBOrphanet:251370Sickle cell S-D Punjab disease
HBBOrphanet:251375Sickle cell S-E disease
HBBOrphanet:251380Hereditary persistence of fetal hemoglobin-sickle cell disease syndrome
HBBOrphanet:330041Hemoglobin M disease
HBBOrphanet:46532Hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome
HBBOrphanet:695140Sickle cell-beta zero-thalassemia
HBBOrphanet:695147Sickle cell-beta plus-thalassemia
HBBOrphanet:699822Sickle cell S-Lepore disease
HBBOrphanet:700090Sickle cell S-O Arab disease
HBBOrphanet:700107Sickle cell S-other specified hemoglobin variant
HBBOrphanet:700111Homozygous hemoglobin O Arab disease
HBBOrphanet:715125Hemoglobin E-beta-thalassemia intermedia
HBBOrphanet:715128Hemoglobin E-beta-thalassemia major
HBBOrphanet:715135Hemoglobin Lepore-beta-thalassemia intermedia
HBBOrphanet:715140Hemoglobin Lepore-beta-thalassemia major
HBBOrphanet:715143Heterozygous beta-thalassemia intermedia with supernumerary alpha-globin gene
HBBOrphanet:715157Low oxygen affinity beta chain hemoglobin disease
HBBOrphanet:90039Hemoglobin D disease
BCL11AOrphanet:251380Hereditary persistence of fetal hemoglobin-sickle cell disease syndrome
BCL11AOrphanet:619233Hereditary persistence of fetal hemoglobin-intellectual disability syndrome
NPRL3Orphanet:98820Familial focal epilepsy with variable foci

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only5
multi_evidence1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
HBBHGNC:4827ENSG00000244734P68871Hemoglobin subunit betagencc,clinvar
BCL11AHGNC:13221ENSG00000119866Q9H165BCL11 transcription factor Agwas
NPRL3HGNC:14124ENSG00000103148Q12980GATOR1 complex protein NPRL3gwas
OR51L1HGNC:14759ENSG00000176798Q8NGJ5Olfactory receptor 51L1gwas
OR51I1HGNC:15200ENSG00000167359Q9H343Olfactory receptor 51I1gwas
OR51I2HGNC:15201ENSG00000187918Q9H344Olfactory receptor 51I2gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
HBBHemoglobin subunit betaInvolved in oxygen transport from the lung to the various peripheral tissues.
BCL11ABCL11 transcription factor ATranscription factor.
NPRL3GATOR1 complex protein NPRL3As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the mTORC1 pathway.
OR51L1Olfactory receptor 51L1Odorant receptor.
OR51I1Olfactory receptor 51I1Odorant receptor.
OR51I2Olfactory receptor 51I2Odorant receptor.

Protein-family classification

Druggable: 3 · Difficult: 1 · Unknown: 2 · Druggable fraction: 0.5

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
GPCR312.0×0.004
Transcription factor11.4×0.809
Other/Unknown20.6×0.936

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
HBBOther/UnknownnoGlobin, Hemoglobin_b, Globin-like_sf
BCL11ATranscription factornoZnf_C2H2_type, Znf_C2H2_sf, Dev/Hematopoietic_TF
NPRL3Other/UnknownnoNpr3, HTH_NPRL3
OR51L1GPCRyesGPCR_Rhodpsn, Olfact_rcpt, GPCR_Rhodpsn_7TM
OR51I1GPCRyesGPCR_Rhodpsn, Olfact_rcpt, GPCR_Rhodpsn_7TM
OR51I2GPCRyesGPCR_Rhodpsn, Olfact_rcpt, GPCR_Rhodpsn_7TM

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

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

Top tissues across cohort

TissueCohort genes
monocyte1
trabecular bone tissue1
vena cava1
cortical plate1
ganglionic eminence1
primary visual cortex1
blood1
hindlimb stylopod muscle1
right uterine tube1
colonic epithelium1
sural nerve1
ventricular zone1
nasal cavity epithelium1
oocyte1
skeletal muscle tissue of rectus abdominis1
ileal mucosa1
pancreatic ductal cell1
tibialis anterior1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
HBB284broadmarkermonocyte, trabecular bone tissue, vena cava
BCL11A247ubiquitousmarkercortical plate, ganglionic eminence, primary visual cortex
NPRL3276ubiquitousmarkerblood, hindlimb stylopod muscle, right uterine tube
OR51L12markercolonic epithelium, sural nerve, ventricular zone
OR51I13yesskeletal muscle tissue of rectus abdominis, nasal cavity epithelium, oocyte
OR51I24markertibialis anterior, ileal mucosa, pancreatic ductal cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
BCL11A2,389
NPRL31,511
HBB454
OR51I1230
OR51I2202
OR51L1193

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
HBBP68871350
BCL11AQ9H16517
NPRL3Q1298010

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
OR51I2Q9H34490.87
OR51L1Q8NGJ589.38
OR51I1Q9H34388.80

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 20. Enrichment computed across 6 evidence-associated genes (6 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 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Heme assimilation1634.4×0.016HBB
Expression and translocation of olfactory receptors314.1×0.016OR51L1, OR51I1, OR51I2
Erythrocytes take up oxygen and release carbon dioxide1211.5×0.023HBB
ALK mutants bind TKIs1158.6×0.023BCL11A
Erythrocytes take up carbon dioxide and release oxygen1146.4×0.023HBB
Scavenging of heme from plasma1146.4×0.023HBB
Formation of the embryonic stem cell BAF (esBAF) complex1100.2×0.028BCL11A
Chaperone Mediated Autophagy182.8×0.029HBB
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)176.1×0.029BCL11A
Late endosomal microautophagy154.4×0.037HBB
Signaling by ALK in cancer145.3×0.040BCL11A
Heme signaling135.9×0.046HBB
Amino acids regulate mTORC1133.4×0.046NPRL3
Cytoprotection by HMOX1130.7×0.046HBB
Signaling by ALK fusions and activated point mutants125.0×0.051BCL11A
Olfactory Signaling Pathway124.1×0.051OR51L1
Factors involved in megakaryocyte development and platelet production111.1×0.102HBB
Diseases of signal transduction by growth factor receptors and second messengers19.5×0.112BCL11A
Neutrophil degranulation13.9×0.246HBB
Disease12.2×0.380BCL11A

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
cellular response to lipid3247.8×6e-06OR51L1, OR51I1, OR51I2
negative regulation of neuron remodeling12808.7×0.005BCL11A
negative regulation of branching morphogenesis of a nerve12808.7×0.005BCL11A
sensory perception of smell252.0×0.006OR51I1, OR51I2
negative regulation of protein homooligomerization1936.2×0.008BCL11A
negative regulation of dendrite extension1702.2×0.009BCL11A
nitric oxide transport1561.7×0.010HBB
negative regulation of dendrite development1351.1×0.012BCL11A
positive regulation of collateral sprouting1312.1×0.012BCL11A
cellular oxidant detoxification1312.1×0.012HBB
renal absorption1280.9×0.012HBB
cellular response to L-glutamate1280.9×0.012BCL11A
negative regulation of collateral sprouting1255.3×0.012BCL11A
carbon dioxide transport1216.1×0.013HBB
oxygen transport1175.5×0.015HBB
regulation of dendrite development1165.2×0.015BCL11A
aorta morphogenesis1147.8×0.015NPRL3
cardiac muscle tissue development1147.8×0.015NPRL3
negative regulation of axon extension1122.1×0.017BCL11A
hydrogen peroxide catabolic process1112.3×0.017HBB
blood vessel diameter maintenance1104.0×0.018HBB
erythrocyte development187.8×0.020HBB
ventricular septum development182.6×0.020NPRL3
response to hydrogen peroxide178.0×0.020HBB
positive regulation of nitric oxide biosynthetic process175.9×0.020HBB
platelet aggregation156.2×0.025HBB
protein sumoylation154.0×0.025BCL11A
negative regulation of TORC1 signaling154.0×0.025NPRL3
cellular response to amino acid starvation153.0×0.025NPRL3
roof of mouth development141.3×0.031NPRL3

Therapeutics

Drugs indicated for this disease

7 approved, 23 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
CrizanlizumabApproved (phase 4)
DeferiproneApproved (phase 4)
Exagamglogene AutotemcelApproved (phase 4)
GlutamineApproved (phase 4)
HydroxyureaApproved (phase 4)
Lovotibeglogene AutotemcelApproved (phase 4)
VoxelotorApproved (phase 4)
AcetylcysteinePhase 3 (in late-stage trials)
AlemtuzumabPhase 3 (in late-stage trials)
ApixabanPhase 3 (in late-stage trials)
ArgininePhase 3 (in late-stage trials)
Arginine HydrochloridePhase 3 (in late-stage trials)
DeferasiroxPhase 3 (in late-stage trials)
DexamethasonePhase 3 (in late-stage trials)
FludarabinePhase 3 (in late-stage trials)
HydromorphonePhase 3 (in late-stage trials)
KetaminePhase 3 (in late-stage trials)
Magnesium Sulfate AnhydrousPhase 3 (in late-stage trials)
MelphalanPhase 3 (in late-stage trials)
MethylphenidatePhase 3 (in late-stage trials)
MorphinePhase 3 (in late-stage trials)
OxygenPhase 3 (in late-stage trials)
PoloxamerPhase 3 (in late-stage trials)
PrasugrelPhase 3 (in late-stage trials)
RivipanselPhase 3 (in late-stage trials)
SenicapocPhase 3 (in late-stage trials)
Sodium ChloridePhase 3 (in late-stage trials)
TicagrelorPhase 3 (in late-stage trials)
VepoloxamerPhase 3 (in late-stage trials)
Zinc IonPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Acetylcholine, Atorvastatin, Azathioprine, Buprenorphine, Busulfan, Canakinumab, Cannabinol, Chloroquine, Crovalimab, Dalteparin Sodium, Daratumumab, Decitabine, Deferoxamine, Defibrotide, Dipyridamole, Doconexent, Dronabinol, Ergocalciferol, Famotidine, Filgrastim, Fludarabine Phosphate, Folic Acid, Gabapentin, Levetiracetam, Losartan, Magnesium, Methotrexate, Mitapivat, Mometasone, Mometasone Furoate, Montelukast, Mycophenolate Mofetil, Niacin, Nitric Oxide, Nitrous Oxide, OMEGA-3 FATTY ACIDS, Pectin, Phenytoin, Plerixafor, Propranolol, Regadenoson Anhydrous, Rifaximin, Riociguat, Rituximab, Rivaroxaban, Simvastatin, Sirolimus, Tacrolimus Anhydrous, Thiotepa, Tilarginine, Vorinostat, Zinc Sulfate.

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 5

Druggability breadth: 2 of 6 evidence-associated genes (33%) 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
HBBCANDESARTAN CILEXETIL

Top cohort targets by molecule count

SymbolMoleculesMax phase
HBB234
BCL11A00
NPRL300
OR51L100
OR51I100
OR51I200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
CANDESARTAN CILEXETIL4HBB
MECHLORETHAMINE HYDROCHLORIDE4HBB
PHENAZOPYRIDINE HYDROCHLORIDE4HBB
MERCAPTOPURINE ANHYDROUS4HBB
AZACITIDINE4HBB
AZATHIOPRINE4HBB
TOPOTECAN HYDROCHLORIDE4HBB
ACYCLOVIR4HBB
FLUOROURACIL4HBB
RAUWOLFIA SERPENTINA4HBB
HYDROQUINONE4HBB
MENADIONE4HBB
THIOTEPA4HBB
THIOGUANINE4HBB
RESERPINE4HBB
CURCUMIN3HBB
HYDROXYCAMPTOTHECIN3HBB
MOLIBRESIB2HBB
FISETIN2HBB
TEROXIRONE2HBB
5-FLUOROURIDINE2HBB
ELLAGIC ACID2HBB
BAICALEIN2HBB

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
HBB68Binding:50, Functional:18

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

23 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)
CANDESARTAN CILEXETIL4HBB
MECHLORETHAMINE HYDROCHLORIDE4HBB
PHENAZOPYRIDINE HYDROCHLORIDE4HBB
MERCAPTOPURINE ANHYDROUS4HBB
AZACITIDINE4HBB
AZATHIOPRINE4HBB
TOPOTECAN HYDROCHLORIDE4HBB
ACYCLOVIR4HBB
FLUOROURACIL4HBB
RAUWOLFIA SERPENTINA4HBB
HYDROQUINONE4HBB
MENADIONE4HBB
THIOTEPA4HBB
THIOGUANINE4HBB
RESERPINE4HBB
CURCUMIN3HBB
HYDROXYCAMPTOTHECIN3HBB
MOLIBRESIB2HBB
FISETIN2HBB
TEROXIRONE2HBB
5-FLUOROURIDINE2HBB
ELLAGIC ACID2HBB
BAICALEIN2HBB

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1HBB
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug3OR51L1, OR51I1, OR51I2
EDifficult family or no structure, no drug2BCL11A, NPRL3

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
BCL11A0
NPRL30
OR51L10
OR51I10
OR51I20

Clinical trials & evidence

Clinical trials

Clinical trials: 932.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified486
PHASE2165
PHASE185
PHASE373
PHASE1/PHASE265
PHASE430
PHASE2/PHASE314
EARLY_PHASE114

Top trials by phase / activity

NCTPhaseStatusTitle
NCT04657822PHASE4RECRUITINGRollover Study for Patients With Sickle Cell Disease Who Have Completed a Prior Novartis-Sponsored Crizanlizumab Study
NCT05730205PHASE4RECRUITINGEffects of the Contraceptive Implant in Women With Sickle Cell Disease
NCT06526117PHASE4RECRUITINGStroke Prevention in Nigeria 2 Trial
NCT06579703PHASE4NOT_YET_RECRUITINGKetorolac for Acute Vaso-Occlusive Crisis in Pediatric Sickle Cell Disease
NCT06665997PHASE4RECRUITINGClinical and Biomarker Effects of Depot Medroxyprogesterone Acetate in Females With Sickle Cell Disease
NCT06979492PHASE4RECRUITINGProphylactic Transfusion In Pregnant in Women With Sickle Cell Disease
NCT07177300PHASE4RECRUITINGEffectiveness of Nontraditional Hydroxyurea Algorithms: Novel and Clinical Evaluations (ENHANCE)
NCT07488520PHASE4NOT_YET_RECRUITINGIntegrating Point of Care Testing (POCT) For Newborn Screening and Early Care for Sickle Cell Disease in Yopougon, Côte d’Ivoire
NCT00252122PHASE4TERMINATEDPilot Study on the Effects of Intravenous Ketamine on Acute Pain Crisis in Patients With Sickle Cell Disease
NCT00513864PHASE4WITHDRAWNAssessment of Opioid Analgesia in Sickle Cell
NCT00749515PHASE4COMPLETEDPilot Study for Patients With Poor Response to Deferasirox
NCT00880373PHASE4TERMINATEDIbuprofen and Opioid (Morphine or Diamorphine) for Acute Pain in Sickle Cell Disease - Sickle With Ibuprofen & Morphine
NCT00937144PHASE4WITHDRAWNEndothelial Function in Patients With Sickle Cell Anemia Before and After Sildenafil
NCT02041299PHASE4TERMINATEDEfficacy and Safety of Ferriprox® in Patients With Sickle Cell Disease or Other Anemias
NCT02149537PHASE4COMPLETEDRisk Clinical Stratification of Sickle Cell Disease in Nigeria, Assessment of Efficacy/Safety of Hydroxyurea Treatment
NCT02222246PHASE4COMPLETEDComparing Acute Pain Management Protocols for Patients With Sickle Cell Disease
NCT02443545PHASE4TERMINATEDLong-term Safety and Efficacy of Ferriprox® in Iron Overloaded Patients With Sickle Cell Disease or Other Anemias
NCT02522104PHASE4COMPLETEDEvaluation of the Impact of Renal Function on the Pharmacokinetics of SIKLOS ® (DARH)
NCT02594462PHASE4COMPLETEDContraception in Women With Sickle Cell Disease
NCT02731157PHASE4COMPLETEDRejuvesol® Washed RBC in Sickle Cell Patients Requiring Frequent Transfusions
NCT03682211PHASE4COMPLETEDIntranasal Fentanyl Versus Intravenous Morphine in the Treatment of Severe Painful Sickle Cell Crises in Children
NCT03903133PHASE4COMPLETEDEndothelial Monocyte-activating Polypeptide-II in Egyptian Sickle Patients
NCT04400487PHASE4COMPLETEDActigraphy Improvement With Voxelotor (ActIVe) Study
NCT04581356PHASE4COMPLETEDVoxelotor Sickle Cell Exercise Study
NCT04662931PHASE4COMPLETEDAn Indian Multi-centric Phase IV Study to Assess the Safety of Crizanlizumab in Sickle Cell Disease Patients
NCT04684381PHASE4COMPLETEDPharmacokinetics and Safety of Endari (L-glutamine) in Sickle Cell Disease Patients
NCT05081349PHASE4COMPLETEDHydoxycarbamide and L-Carnitine Therapy in Sickle Cell Anemia
NCT05228821PHASE4WITHDRAWNVoxelotor Brain Oxygenation and Neurocognitive Study
NCT05371184PHASE4COMPLETEDGlutamine Role in Preventing Vaso-occlusive Crisis Among SCD Patients
NCT05848531PHASE4UNKNOWNClonidine With Morphine in Patient Controlled Analgesia Pump in Vaso-Occlusive Crisis in Sickle Cell Disease Patient
NCT03814746PHASE3ACTIVE_NOT_RECRUITINGStudy of Two Doses of Crizanlizumab Versus Placebo in Adolescent and Adult Sickle Cell Disease Patients
NCT04084080PHASE3ACTIVE_NOT_RECRUITINGSickle Cell Disease and CardiovAscular Risk - Red Cell Exchange Trial (SCD-CARRE)
NCT04208529PHASE3ENROLLING_BY_INVITATIONA Long-term Follow-up Study in Participants Who Received CTX001
NCT04293185PHASE3ACTIVE_NOT_RECRUITINGA Study Evaluating Gene Therapy With BB305 Lentiviral Vector in Sickle Cell Disease
NCT04624659PHASE3ACTIVE_NOT_RECRUITINGA Study of Etavopivat in Adults and Adolescents With Sickle Cell Disease (HIBISCUS)
NCT05031780PHASE2/PHASE3ACTIVE_NOT_RECRUITINGA Study Evaluating the Efficacy and Safety of Mitapivat (AG-348) in Participants With Sickle Cell Disease (RISE UP)
NCT05285917PHASE3RECRUITINGPromoting Utilization and Safety of Hydroxyurea Using Precision in Africa
NCT05329649PHASE3ACTIVE_NOT_RECRUITINGEvaluation of Safety and Efficacy of CTX001 in Pediatric Participants With Severe Sickle Cell Disease (SCD)
NCT05392894PHASE3RECRUITINGRElated Haplo-DonoR Haematopoietic stEm Cell Transplantation for Adults With Severe Sickle Cell Disease
NCT05431088PHASE2/PHASE3RECRUITINGA Phase 2/3 Study in Adult and Adolescent Participants With SCD

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
ALEMTUZUMAB422
VOXELOTOR419
HYDROXYUREA417
CRIZANLIZUMAB412
PLERIXAFOR411
KETAMINE47
DEFERASIROX46
GLUTAMINE46
MORPHINE46
DEFEROXAMINE45
EXAGAMGLOGENE AUTOTEMCEL44
MITAPIVAT44
NITRIC OXIDE44
NITROUS ACID44
ACETYLCHOLINE43
DEFERIPRONE43
DEXTROMETHORPHAN43
PENTOSTATIN43
REGADENOSON43
ZINC SULFATE43
CLOTRIMAZOLE42
CODEINE42
CROVALIMAB42
DRONABINOL42
FLUDARABINE PHOSPHATE42
2-MERCAPTOETHANESULFONIC ACID41
ABCIXIMAB41
ACETYLCYSTEINE41
ALEFACEPT41
AMBRISENTAN41