Alpha thalassemia spectrum

disease
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Also known as A-thalassemiaalpha thalassaemiaalpha-thalassemiaalpha-thalassemia traitthalassemia, alpha-thalassemias, alpha-

Summary

Alpha thalassemia spectrum (MONDO:0011399) is a disease caused by variants in HBA1 and HBA2, with 5 cohort genes and 9 clinical trials. The dominant Reactome pathway is Heme assimilation (3 cohort genes).

At a glance

  • Prevalence: Unknown (Europe) [Orphanet-validated]
  • Causal genes: HBA1 (GenCC Definitive), HBA2 (GenCC Strong)
  • Cohort genes: 5
  • ClinVar variants: 445
  • Phenotypes (HPO): 23
  • Clinical trials: 9

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-5 / 10 00010.3United StatesValidated

Signs & symptoms

Clinical features (HPO)

23 HPO clinical features (Orphanet curated; top 23 by frequency):

HPO IDTermFrequency
HP:0001935Microcytic anemiaVery frequent (80-99%)
HP:0011902Abnormal hemoglobinVery frequent (80-99%)
HP:0001433HepatosplenomegalyFrequent (30-79%)
HP:0001635Congestive heart failureFrequent (30-79%)
HP:0001698Pericardial effusionFrequent (30-79%)
HP:0001923ReticulocytosisFrequent (30-79%)
HP:0001978Extramedullary hematopoiesisFrequent (30-79%)
HP:0002202Pleural effusionFrequent (30-79%)
HP:0007430Generalized edemaFrequent (30-79%)
HP:0001081CholelithiasisOccasional (5-29%)
HP:0001744SplenomegalyOccasional (5-29%)
HP:0001789Hydrops fetalisOccasional (5-29%)
HP:0001878Hemolytic anemiaOccasional (5-29%)
HP:0001903AnemiaOccasional (5-29%)
HP:0001971HypersplenismOccasional (5-29%)
HP:0002863MyelodysplasiaOccasional (5-29%)
HP:0004823AnisopoikilocytosisOccasional (5-29%)
HP:0005507Hemoglobin BartsOccasional (5-29%)
HP:0010620Malar prominenceOccasional (5-29%)
HP:0010978Abnormality of immune system physiologyOccasional (5-29%)
HP:0100543Cognitive impairmentOccasional (5-29%)
HP:0430028Hyperplasia of the maxillaOccasional (5-29%)
HP:0000952JaundiceOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namealpha thalassemia spectrum
Mondo IDMONDO:0011399
MeSHD017085
OMIM604131
Orphanet846
DOIDDOID:1099
ICD-10-CMD56.0
ICD-11531667506
NCITC34368
SNOMED CT68913001
UMLSC0002312
MedGen1434
GARD0000621
MedDRA10043390
Is cancer (heuristic)no

Also known as: A-thalassemia · alpha thalassaemia · alpha thalassemia spectrum · alpha-thalassemia · alpha-thalassemia trait · thalassemia, alpha- · thalassemias, alpha-

Data availability: 445 ClinVar variants · 5 GenCC gene-disease records · 26 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 diseaseinherited hemoglobinopathythalassemiaalpha thalassemia spectrum

Related subtypes (1): beta thalassemia

Subtypes (2): digenic alpha thalassemia spectrum, monogenic alpha thalassemia spectrum

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

445 retrieved; paginated sample, class counts are floors:

173 likely pathogenic, 84 uncertain significance, 83 pathogenic, 53 pathogenic/likely pathogenic, 20 conflicting classifications of pathogenicity, 12 likely benign, 10 benign, 6 benign/likely benign, 3 not provided, 1 uncertain significance; other

ClinVarVariant (HGVS)GeneClassificationReview
375745NM_000517.4:c.[339C>G;340_351delCTCCCCGCCGAG]Pathogenicno assertion criteria provided
375750NM_000517.4:c.[-2_-3delAC;-alpha3.7]Pathogenicno assertion criteria provided
4820116NC_000016.9:g.208984_(235732_238422)delPathogeniccriteria provided, single submitter
487442NC_000016.10:g.(?151209)(182142_?)delHBA-LCRPathogenicno assertion criteria provided
869337NC_000016.10:g.151479_182582delHBA-LCRPathogenicno assertion criteria provided
1048833NM_000558.5(HBA1):c.95+2_95+6delHBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1331033NM_000558.5(HBA1):c.328del (p.Leu110fs)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15624NM_000517.4(HBA2):c.427T>C (p.Ter143Gln)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
15849NM_000558.3(HBA1):c.179G>A (p.Gly60Asp)HBA1Pathogeniccriteria provided, multiple submitters, no conflicts
15879NM_000558.5(HBA1):c.283_300+3dupHBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2428550NM_000558.5(HBA1):c.62_63insT (p.Ala22fs)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2428673NM_000558.5(HBA1):c.1A>G (p.Met1Val)HBA1Pathogeniccriteria provided, multiple submitters, no conflicts
2580349GRCh37/hg19 16p13.3(chr16:215947-231157)x1HBA1Pathogeniccriteria provided, single submitter
2681961NM_000558.5(HBA1):c.95+1G>AHBA1Pathogeniccriteria provided, multiple submitters, no conflicts
2920892NM_000558.5(HBA1):c.96-2A>GHBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3075902NM_000558.5(HBA1):c.44G>A (p.Trp15Ter)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3220863Single alleleHBA1Pathogeniccriteria provided, single submitter
3579876NM_000558.5(HBA1):c.2T>C (p.Met1Thr)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3579878NM_000558.5(HBA1):c.95+2T>CHBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
375753NC_000016.10:g.172005_177200delHBA1Pathogenicno assertion criteria provided
38635NM_005332.2(HBZ):c.330_*22601delHBA1Pathogenicno assertion criteria provided
38636NG_000006.1(HBA1):g.34247_38050delHBA1Pathogenicno assertion criteria provided
3893661NC_000016.10:g.173384_177187dupHBA1Pathogenicno assertion criteria provided
3903433NC_000016.10:g.175997_178388delHBA1Pathogenicno assertion criteria provided
439103NM_000558.5(HBA1):c.43T>C (p.Trp15Arg)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
4533035NM_000558.5(HBA1):c.349G>T (p.Glu117Ter)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
4814422NM_000558.5(HBA1):c.95+1G>CHBA1Pathogeniccriteria provided, single submitter
487448NC_000016.10:g.(?169780)(182142_?)delHBA1Pathogenicno assertion criteria provided
618153NM_000558.5(HBA1):c.187del (p.Val63fs)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
619842NM_000558.5(HBA1):c.237del (p.Asn79fs)HBA1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 24 · Orphanet: 45 · 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
HBA1DefinitiveSemidominantalpha thalassemia spectrum13
HBA2StrongAutosomal recessivealpha thalassemia spectrum11

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
HBA1Orphanet:163596Hemoglobin Bart’s fetalis syndrome
HBA1Orphanet:247511Autosomal dominant secondary polycythemia
HBA1Orphanet:330041Hemoglobin M disease
HBA1Orphanet:707789Unstable alpha globin chain variant disease
HBA1Orphanet:715143Heterozygous beta-thalassemia intermedia with supernumerary alpha-globin gene
HBA1Orphanet:93616Hemoglobin H disease
HBA1Orphanet:98791Alpha-thalassemia-intellectual disability syndrome linked to chromosome 16
HBA2Orphanet:163596Hemoglobin Bart’s fetalis syndrome
HBA2Orphanet:247511Autosomal dominant secondary polycythemia
HBA2Orphanet:330041Hemoglobin M disease
HBA2Orphanet:707789Unstable alpha globin chain variant disease
HBA2Orphanet:715143Heterozygous beta-thalassemia intermedia with supernumerary alpha-globin gene
HBA2Orphanet:715154Low oxygen affinity alpha chain hemoglobin disease
HBA2Orphanet:93616Hemoglobin H disease
HBA2Orphanet:98791Alpha-thalassemia-intellectual disability syndrome linked to chromosome 16
NPRL3Orphanet:98820Familial focal epilepsy with variable foci
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

Cohort genes → proteins

5 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
HBA1HGNC:4823ENSG00000206172P69905Hemoglobin subunit alphagencc,clinvar
HBA2HGNC:4824ENSG00000188536P69905Hemoglobin subunit alphagencc,clinvar
NPRL3HGNC:14124ENSG00000103148Q12980GATOR1 complex protein NPRL3clinvar
HBMHGNC:4826ENSG00000206177Q6B0K9Hemoglobin subunit muclinvar
HBBHGNC:4827ENSG00000244734P68871Hemoglobin subunit betaclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
HBA1Hemoglobin subunit alphaInvolved in oxygen transport from the lung to the various peripheral tissues.
HBA2Hemoglobin subunit alphaInvolved in oxygen transport from the lung to the various peripheral tissues.
NPRL3GATOR1 complex protein NPRL3As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the mTORC1 pathway.
HBBHemoglobin subunit betaInvolved in oxygen transport from the lung to the various peripheral tissues.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 5 · Druggable fraction: 0.0

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
Other/Unknown51.8×0.054

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
HBA1Other/UnknownnoGlobin, Hemoglobin_a-typ, Hemoglobin_pi
HBA2Other/UnknownnoGlobin, Hemoglobin_a-typ, Hemoglobin_pi
NPRL3Other/UnknownnoNpr3, HTH_NPRL3
HBMOther/UnknownnoGlobin, Hemoglobin_a-typ, Globin-like_sf
HBBOther/UnknownnoGlobin, Hemoglobin_b, Globin-like_sf

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)0
moderate (6-20)0
broad (>20)5
unknown0

Top tissues across cohort

TissueCohort genes
blood4
monocyte3
bone marrow2
trabecular bone tissue2
bone element1
hindlimb stylopod muscle1
right uterine tube1
vena cava1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
HBA1133tissue_specificmarkermonocyte, blood, bone marrow
HBA2143tissue_specificmarkermonocyte, blood, bone element
NPRL3276ubiquitousmarkerblood, hindlimb stylopod muscle, right uterine tube
HBM139tissue_specificmarkertrabecular bone tissue, bone marrow, blood
HBB284broadmarkermonocyte, trabecular bone tissue, vena cava

Protein interactions among cohort

Intra-cohort edges: 4.

Hub genes (top 10 by interactor count)

SymbolInteractor count
NPRL31,511
HBM553
HBB454
HBA1434
HBA2434

Intra-cohort edges

ABSources
HBA1HBA2biogrid_interaction, intact
HBA1HBBintact
HBA2HBBintact
HBBHBMbiogrid_interaction, intact

Structural data

PDB: 5 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
HBA1P69905356
HBA2P69905356
HBBP68871350
NPRL3Q1298010
HBMQ6B0K91

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 11. Enrichment computed across 5 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Heme assimilation32855.0×2e-10HBA1, HBA2, HBB
Erythrocytes take up oxygen and release carbon dioxide3951.7×7e-09HBA1, HBA2, HBB
Erythrocytes take up carbon dioxide and release oxygen3658.9×1e-08HBA1, HBA2, HBB
Scavenging of heme from plasma3658.9×1e-08HBA1, HBA2, HBB
Heme signaling3161.6×8e-07HBA1, HBA2, HBB
Cytoprotection by HMOX13138.2×1e-06HBA1, HBA2, HBB
Chaperone Mediated Autophagy1124.1×0.013HBB
Late endosomal microautophagy181.6×0.017HBB
Amino acids regulate mTORC1150.1×0.024NPRL3
Factors involved in megakaryocyte development and platelet production116.6×0.065HBB
Neutrophil degranulation15.8×0.162HBB

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
oxygen transport4842.6×5e-11HBA1, HBA2, HBM, HBB
erythrocyte development4421.3×5e-10HBA1, HBA2, HBM, HBB
nitric oxide transport32022.2×8e-10HBA1, HBA2, HBB
cellular oxidant detoxification31123.5×5e-09HBA1, HBA2, HBB
carbon dioxide transport3777.8×1e-08HBA1, HBA2, HBB
hydrogen peroxide catabolic process3404.4×1e-07HBA1, HBA2, HBB
response to hydrogen peroxide3280.9×3e-07HBA1, HBA2, HBB
inflammatory response322.6×4e-04HBA1, HBA2, HBB
renal absorption1337.0×0.007HBB
aorta morphogenesis1177.4×0.010NPRL3
cardiac muscle tissue development1177.4×0.010NPRL3
blood vessel diameter maintenance1124.8×0.013HBB
ventricular septum development199.1×0.015NPRL3
positive regulation of nitric oxide biosynthetic process191.1×0.016HBB
platelet aggregation167.4×0.018HBB
negative regulation of TORC1 signaling164.8×0.018NPRL3
cellular response to amino acid starvation163.6×0.018NPRL3
roof of mouth development149.6×0.022NPRL3
regulation of blood pressure144.4×0.024HBB
positive regulation of autophagy141.6×0.024NPRL3

Therapeutics

Drugs indicated for this disease

0 approved, 1 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
MitapivatPhase 3 (in late-stage trials)

Drug target analysis

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

Druggability breadth: 3 of 5 evidence-associated genes (60%) 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
HBA100
HBA200
NPRL300
HBM00

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
HBA159Binding:46, Functional:13
HBA259Binding:46, Functional:13

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; 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 drug0
EDifficult family or no structure, no drug4HBA1, HBA2, NPRL3, HBM

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
HBA159HBB
HBA259HBB
NPRL30
HBM0

Clinical trials & evidence

Clinical trials

Clinical trials: 9.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified7
PHASE1/PHASE21
PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT01419704PHASE1/PHASE2WITHDRAWNPhase I/II Pilot Study of Mixed Chimerism to Treat Hemoglobinopathies
NCT02986698PHASE1TERMINATEDIn Utero Hematopoietic Stem Cell Transplantation for Alpha-thalassemia Major (ATM)
NCT02692872Not specifiedACTIVE_NOT_RECRUITINGScreening for Alpha Thalassemia in Healthy Volunteers
NCT04872179Not specifiedRECRUITINGInternational Registry of Patients With Alpha Thalassemia
NCT06539169Not specifiedRECRUITINGFLOWER: Following Longitudinal Outcomes With Epidemiology for Rare Diseases
NCT06591936Not specifiedRECRUITINGGenetic Profile of Alpha Thalassemia Children at Sohag University Hospital .
NCT00159029Not specifiedCOMPLETEDGenetics of Alpha Thalassemia in Israeli Ethnic Groups
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening
NCT06831799Not specifiedCOMPLETEDERN-EuroBloodNet Registry on Patients With Rare Red Blood Cell Defects and COVID-19