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Condition report · Hematological

Sickle Cell Disease

Whole genome sequencing characterizes the complete HBB genotype, including compound heterozygous combinations, severity-modifying loci, and co-inherited alpha-thalassemia variants that standard carrier screens systematically miss.

A condition report looks for rare variants known to cause the conditions it covers.

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About this condition

An inherited red blood cell disorder caused by variants in the HBB gene. Red cells take a rigid sickle shape, which causes anaemia, painful crises, infections and organ damage. Carriers (sickle cell trait) usually have no symptoms.

Sickle cell disease (SCD) is an autosomal recessive hemoglobinopathy caused by a glutamic acid-to-valine substitution at codon 6 of the beta-globin gene (HBB p.Glu7Val; rs334). This single nucleotide variant causes hemoglobin S (HbS) to polymerize under deoxygenated conditions, distorting erythrocytes into a rigid sickle shape. These deformed cells obstruct small blood vessels, triggering vaso-occlusive crises, hemolytic anemia, and progressive organ damage across nearly every system, including the spleen, kidneys, lungs, brain, and skeleton. Sickle cell disease affects approximately 300,000 newborns annually worldwide, with the highest prevalence in sub-Saharan Africa, India, and the Middle East, though it occurs across all populations.

The genotypic architecture of SCD is more complex than the classic HbSS picture. HbSC disease (HBB Glu7Val/Glu6Lys) and HbS-beta-thalassemia (HbS/beta⁰ or HbS/beta⁺) produce distinct clinical phenotypes with different severity profiles and management implications. Severity is further modulated by fetal hemoglobin (HbF) levels (influenced by variants in BCL11A, HBS1L-MYB, and the HBB locus itself) and by co-inherited alpha-thalassemia (HBA1/HBA2 deletions), which reduces HbS polymerization and is associated with milder disease. Standard two-allele carrier testing identifies the core Glu7Val variant but is not designed to report the full genotypic complexity that determines an individual's disease trajectory.

Carrier status identification before or during pregnancy is the primary use case for genetic testing in families without a prior affected member. Cascade testing in known carrier families and confirmatory genotyping for newborn screening positives are standard clinical indications. For affected patients, complete genotyping, including HbF modifier loci and co-inherited alpha-thalassemia, is increasingly recognized as relevant to predicting hydroxyurea response and informing bone marrow transplantation eligibility criteria.

HbSS, HbSC, HbS-beta⁰ thalassemia, and HbS-beta⁺ thalassemia each carry distinct clinical prognoses. HBB genotype alone does not predict severity; modifier loci and co-inherited variants are part of the complete picture.

The 5 conditions we analyse

Sickle Cell Disease

Autosomal recessive

A haemoglobinopathy caused by haemoglobin S, alone or with another HBB variant, leading to haemolytic anaemia and vaso-occlusive crises.

What a diagnosis changes

Hydroxyurea (HbF induction), voxelotor, crizanlizumab, L-glutamine; curative hematopoietic stem cell transplantation and gene therapy (exagamglogene autotemcel)

Genes analysed

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/Hb-C disease without crisis; sickling disorder due to Haemoglobin S; sickling disorder due to Hemoglobin S

Includes 4 related subtypes ↓
  • sickle cell disease due to hemoglobin S and a non-S/non-C hemoglobin variant
  • sickle cell S-Lepore disease
  • sickle cell S-O Arab disease
  • sickle cell-hemoglobin c disease syndrome
MONDO:0011382OMIM 603903Orphanet 232MedGen 287

Sickle Cell-Beta-Thalassaemia

Autosomal recessive

A form of sickle cell disease in which one copy of HBB carries the sickle variant and the other a beta-thalassaemia variant; severity ranges from mild to as severe as sickle cell anaemia.

What a diagnosis changes

Care needs are similar to other forms of sickle cell disease, including infection prevention and monitoring for complications.

Also known as

Haemoglobin sickle-beta thalassemia; Hb S beta-thalassemia; HbS - beta-thalassemia; HbS-beta-thalassemia syndrome; Hemoglobin sickle-beta thalassemia; S-Beta thalassemia; sickle beta thalassemia; sickle cell - beta-thalassemia disease; sickle cell-Beta thalassemia

Includes 2 related subtypes ↓
  • sickle cell-beta plus-thalassemia
  • sickle cell-beta zero-thalassemia
MONDO:0016668Orphanet 251359MedGen 452211

Sickle Cell-Haemoglobin D Disease

Autosomal recessive

A form of sickle cell disease caused by one sickle variant and one haemoglobin D variant in HBB.

What a diagnosis changes

Care needs are similar to other forms of sickle cell disease, including infection prevention and monitoring for complications.

Also known as

HbSD disease; sickle cell - hemoglobin D disease

MONDO:0016670Orphanet 251370MedGen 452366

Sickle Cell-Haemoglobin E Disease

Autosomal recessive

A form of sickle cell disease caused by one sickle variant and one haemoglobin E variant in HBB, usually milder than sickle cell anaemia.

What a diagnosis changes

Care needs are similar to other forms of sickle cell disease, including infection prevention and monitoring for complications.

Also known as

HbSE disease

MONDO:0016671Orphanet 251375MedGen 1669602

Sickle Cell-Hereditary Persistence of Fetal Haemoglobin

Autosomal recessive

Inheritance of the sickle variant together with a change that keeps fetal haemoglobin production high into adulthood, which usually protects against sickling, so symptoms are typically mild or absent.

What a diagnosis changes

Knowing about it explains blood test findings and is relevant to family planning.

Also known as

HPFH-sickle cell disease syndrome

MONDO:0016672Orphanet 251380MedGen 1679967

Why whole genome sequencing

Standard carrier testing finds the Glu7Val variant. It does not characterize the full genotype, modifier loci, or co-inherited variants that determine clinical course.

The compound heterozygous picture matters as much as carrier status

A person who inherits one HbS allele and one beta-thalassemia allele has sickle cell disease, not simply sickle cell trait. Standard two-variant carrier tests are designed to report the rs334 Glu7Val substitution but are not optimized to simultaneously characterize beta-thalassemia alleles across the full HBB gene. Whole genome sequencing reads the complete HBB coding and regulatory sequence, identifying any co-inherited beta-thalassemia variant alongside the Glu7Val allele, determining whether a carrier couple's risk is for HbSS, HbSC, HbS-beta thalassemia, or HbS trait.

HbF modifier loci and alpha-thalassemia co-inheritance are invisible to standard panels

Fetal hemoglobin level is the strongest known modifier of sickle cell disease severity. High HbF suppresses HbS polymerization, reducing vaso-occlusive events and end-organ damage. HbF levels are regulated by common variants in BCL11A (rs1427407), HBS1L-MYB intergenic region (rs28384513), and the HBB locus Xmn1 site. Co-inherited alpha-thalassemia (HBA1/HBA2 gene deletions) further modulates disease severity. None of these modifier loci are included in standard two-allele carrier screens or hemoglobinopathy panels. Whole genome sequencing captures all of them simultaneously with the primary HBB genotype.

Other hematological conditions

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