1. B-positive SCID panel

B-positive SCID panel

January 18, 2018

Disease synonyms

Severe combined immunodeficiency, SCID, X-Linked Severe Combined Immunodeficiency, SCIDX1, X-Linked SCID, X-SCID, B cell-positive SCID


Inheritance pattern

X-linked recessive, autosomal recessive


Clinical features

Severe combined immunodeficiency (SCID) is a group of rare monogenic primary immunodeficiency disorders characterized by a block in T lymphocyte differentiation 1.

Clinical presentation is fairly uniform and is characterized by early onset of infections, mainly of the respiratory tract and gut. Patients will typically present in infancy with severe, persistent infections of bacterial, viral, fungal and/or protozoal origin 1, 2. In addition, these individuals have poor wound healing and failure to thrive. The most frequent infections observed in SCID patients include oral candidiasis, persistent diarrhea with growth impairment and/or interstitial pneumonitis. The persistence and recurrence of infections in SCID patients rapidly leads to growth impairment and malnutrition.

SCIDs are classified according to immunological phenotype into SCID with absence of T cells but presence of B cells (B-positive SCID) or SCID with absence of both (B-negative SCID) 3. About 20% of patients with SCID have a phenotype characterized by an absence of mature T and B lymphocytes, while functional natural killer cells are detectable. Usually the thymus is hypoplastic and the condition can be cured by allogeneic bone marrow transplantation 3.

B-positive SCID can result from pathogenic variants in multiple genes which encode components of the immune system 1, 3, 4. SCID is almost universally fatal in the first two years of life unless reconstitution of the immune system is achieved through bone marrow transplants or gene therapy. Newborn screening for SCID has demonstrated that the incidence of SCID in the United States is 1 per 58,000 live births and has led to life-saving treatment of affected children 2.

Clinical features of SCID include the following 1, 2:

  • Recurrent or persistent severe infections
  • Failure to thrive
  • Marked lymphocytopenia and/or T cell lymphopenia
  • Severe defect in T cell proliferation
  • Marked decrease in thymic function
  • B cells are generally present, but dysfunctional.

The most common form of B-positive SCID is X-linked, caused by pathogenic variants in the IL2RG gene which accounts for 50-60% of all cases 1, 4, 5. The incidence of X-SCID is unknown; it is estimated to be at least 1:50,000-100,000 births 1, 2, with males showing a higher prevalence, and with regional differences and higher incidences among populations with a higher consanguinity rate.

More than 200 disease causing variants have been described throughout the IL2RG gene with exons 3-5 being hotspots 6. Missense mutations are found most frequently (40%), followed by nonsense (24%), splice site alterations (19%), and small insertions/deletions (17%) with each mutation type being fully penetrant for the disease. Maternal mosaicism for IL2RG mutations exists in ~13% cases of X-SCID 6, 7. Together with somatic reversion that has been reported in subsets of immune precursor cells, this results in variable clinical phenotypes.

Pathogenic variants in the IL2RG, and IL7R genes account for ~75% of all cases of SCID 1, 4. The IL7R gene encodes a component of the Interleukin 7 receptor that which binds the cytokine, IL7. 

Homozygous mutations in the FOXN1 gene are cause a form subtype of SCID associated with congenital alopecia 1, 4. Only 3 mutations have been reported as disease-causing to date: c.958C>T (p.R320W), c.763C>T (p.R255*), and small deletion c.562delA 9.

Pathogenic variants in JAK3 are cause severe immunodeficiency which has a clinical phenotype identical to X-linked SCID1, 4. More than 40 pathogenic variants have been far so far reported, the majority of which are missense and splicing variants 10.

Primary immunodeficiency-9 is caused by homozygous or compound heterozygous pathogenic variants in the ORAI1 gene, which encodes a subunit of the plasma membrane calcium channel.  Missense variants and  small insertions have been reported in this gene.

Another form of SCID, associated with purine nucleoside phosphorylase deficiency, is caused by pathogenic variants in the PNP gene 1, 4. More than 30 variants, the majority of which are missense, have been reported so far as causing disease 11.

Pathogenic variants in the PTPRC gene (CD45) cause a loss of lymphocyte function and result in the SCID phenotype. To date, only loss of function variants have been identified in this gene as disease causing: nonsense c.1624A>T p.K542*, splicing c.1450+1G>A, small deletion at position 1090, and gross deletion of 3´ end of the gene1, 4.

Pathogenic variants found in RMRP are mostly regulatory variants, affecting the expressional pattern of the RMPR gene1, 4.

Pathogenic variants in the STAT5B gene cause immunodeficiency with growth hormone insensitivity, a form of genetic dwarfism1, 4. Frameshift variants, nonsense variants, and small deletions were reported in the STAT5B gene as causing disease 1, 4

Genetic testing for SCID and a newborn screening test could identify children with SCID, as well as those with other serious immune deficiencies, many of which would not be apparent until the child had already developed an infection. These simple tests could be life-saving and they would allow treatment of SCID and improvement of health status of these affected infants.

Immune reconstitution by bone marrow transplantation or gene replacement therapy is required for survival of the patients, thus an early diagnosis enables early immune reconstitution and prevents severe complications.

Infections are treated with specific antibiotic, antifungal, and antiviral agents and administration of intravenous immunoglobulin (IVIg); prophylaxis is provided for pneumocystis jiroveci infection. Immune reconstitution by bone marrow transplantation or gene replacement therapy is required for survival; thus an early diagnosis enables early immune reconstitution and prevents severe complications.

Table 1. Overview of genes included in B-positive SCID

Gene OMIM (Gene) Associated diseases (OMIM) Inheritance CentoMD® exclusive variant numbers (++)
CD247 186780 ?Immunodeficiency 25 AR 0
CD3D 186790 Immunodeficiency 19 AR 0
CD3E 186830 Immunodeficiency 18; Immunodeficiency 18, SCID variant AR 1
FOXN1 600838 T-cell immunodeficiency, congenital alopecia, and nail dystrophy AR 2
IL2RG 308380 Severe combined immunodeficiency, X-linked; Combined immunodeficiency, X-linked, moderate XL R 2
IL7R 146661 Severe combined immunodeficiency, T-cell negative, B-cell/natural killer cell-positive type AR 1
JAK3 600173 SCID, autosomal recessive, T-negative/B-positive type AR 4
ORAI1 610277 Immunodeficiency 9; Myopathy, tubular aggregate, 2 AD, AR 1
PNP 164050 Immunodeficiency due to purine nucleoside phosphorylase deficiency AR 0
PTPRC 151460 Severe combined immunodeficiency, T cell-negative, B-cell/natural killer-cell positive; Hepatitis C virus, susceptibility to AR 0
RMRP 157660 Cartilage-hair hypoplasia; Metaphyseal dysplasia without hypotrichosis; Anauxetic dysplasia 1 AR 5
STAT5B 604260 Leukemia, acute promyelocytic, somatic; Growth hormone insensitivity with immunodeficiency 0
STIM1 605921 Myopathy, tubular aggregate, 1; Stormorken syndrome; Immunodeficiency 10 AD, AR 1
TBX1 602054 Tetralogy of Fallot; DiGeorge syndrome; Velocardiofacial syndrome; Conotruncal anomaly face syndrome AD 9
ZAP70 176947 Immunodeficiency 48; Autoimmune disease, multisystem, infantile-onset, 2 AR 0

CENTOGENE offers sequencing and deletion/duplication analysis of genes in the B-positive SCID panel (CD3D, CD3E, CD247, FOXN1, IL2RG, IL7R, JAK3, ORAI1, PNP, PTPRC, RMRP, STAT5B, STIM1, TBX1, ZAP70). 


Differential diagnosis

The differential diagnosis of B-positive SCID includes the following diseases - depending on the major presenting symptoms:

  • Agammaglobulinemia
  • Lymphoproliferative disorders
  • Wiskott-Aldrich syndrome
  • Hyperimmunoglobulinemia E syndrome
  • Lymphohistiocytosis (hemophagocytic lymphohistiocytosis)

Diagnostic strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free Whole Genome Sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage. 

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for B- positive SCID using NGS Panel Genomic targeted towards this specific phenotype:

Step 1:       Whole genome sequencing from a single filter card. The sequencing covers the entire gene (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the B-positive SCID panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2:       If no clinically relevant variant is identified after analysis of the B- positive SCID panel, we further recommend continuing the bioinformatics analysis of the data using whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.   


Referral reasons

The following individuals are candidates for B-positive SCID gene testing:

  • Individuals with a family history of B- positive SCID and presentation of the most common symptoms, including visual and hearing abnormalities
  • Individuals without a positive family history, but with symptoms resembling B- positive SCID
  • Individuals with a negative but suspected family history, in order to perform proper genetic counseling (prenatal analyses are recommended in families with affected individuals).

Test utility

Sequencing, deletion/duplication of B-positive SCID related genes should be performed in all individuals suspected of having this condition. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of clinically relevant variants, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of B- positive SCID, identify at-risk family members, provide information about reproductive risks as well as preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.


More information on CENTOGENE´s B-positive SCID panel can be found in our genetic test catalogue.