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 B-positive SCID associated genes

Gene
(OMIM)
Locus Causative variants frequency 1 Disease  
CD3D 
186790
11q23.3 1.5%-3% Immunodeficiency 19 (615617)
CD3E 
186830
11q23.3 1.5%-3% Immunodeficiency 18 (615615)
CD247
186780
1q24.2 1.5%-3% Immunodeficiency 25 (610163)
FOXN1
600838
17q11.2Rare T-cell immunodeficiency, congenital alopecia, and nail dystrophy 
IL2RG
308380
Xq13.1 40% Combined immunodeficiency, X-linked, moderate (312863); Severe combined immunodeficiency, X-linked (300400)
IL7R
146661
5p13.2 10% Severe combined immunodeficiency, T-cell negative, B-cell/natural killer cell-positive 
JAK3
600173
19p13.11 Rare SCID, autosomal recessive, T-negative/B-positive type (600802)
ORAI1 
610277
12q24.31 Rare Immunodeficiency 9 (612782); Myopathy, tubular aggregate, 2 (615883)
PNP
164050
14q11.2 4% Immunodeficiency due to purine nucleoside phosphorylase deficiency (613179)
PTPRC
151460
11q13.2 Rare Severe combined immunodeficiency, T cell-negative, B-cell/natural killer-cell positive (608971); Hepatitic C virus, susceptibility to (609532)
RMRP
157660
9p13.3 ~90% in CHH Anauxetic dysplasia 1 (607095); Cartilage-hair hypoplasia        250250 Metaphyseal dysplasia without hypotrichosis (250460)
STAT5B
604260
17q21.2 Rare Growth hormone insensitivity with immunodeficiency (245590); Leukemia, acute promyelocytic, somatic (102578)
STIM1
605921
11p15.4 Rare Immunodeficiency 10 (612783), Myopathy, tubular aggregate, 1 (160565); Stormorken syndrome (185070)
TBX1
602054
22q11.21 Rare Conotruncal anomaly face syndrome (217095); DiGeorge syndrome (1884009; Tetralogy of Fallot (187500); Velocardiofacial syndrome  (192430)
ZAP70
176947
2q11.2 Rare Autoimmune disease, multisystem, infantile-onset, 2 (617006); Immunodeficiency 48 (269840)

CENTOGENE offers full gene 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.