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ZAP70-Related Severe Combined Immunodeficiency

Synonym: Zeta-Associated Protein 70 Deficiency

, MD and , MD.

Author Information
, MD
Division of Allergy and Immunology
Children’s Hospital of Pittsburgh
Pittsburgh, Pennsylvania
, MD
Division of Allergy and Immunology
Children’s Hospital of Pittsburgh
Pittsburgh, Pennsylvania

Initial Posting: ; Last Update: September 25, 2014.


Clinical characteristics.

ZAP70-related severe combined immunodeficiency (ZAP70-related SCID) is a cell-mediated immunodeficiency caused by abnormal T-cell receptor (TCR) signaling. Affected children usually present in the first year of life with recurrent bacterial, viral, and opportunistic infections; diarrhea; and failure to thrive. Severe lower-respiratory infections and oral candidiasis are common. Affected children usually do not survive past their second year without hematopoietic stem cell transplantation (HSCT).


The diagnosis is established by lymphocyte counts (particularly of CD3, CD4, and CD8 T cells), lymphocyte function testing, ZAP-70 protein expression, and ZAP70 molecular genetic testing.


Treatment of manifestations: Short-term treatment includes immediate intravenous immunoglobulin (IVIG) and antibacterial, antifungal, and anti-protozoal prophylaxis to control and reduce the occurrence of infections.

Prevention of primary manifestations: Allogeneic HSCT to reconstitute the immune system, preferably within the first three months of life.

Prevention of secondary complications: Use of irradiated, cytomegalic virus (CMV), Epstein-Barr virus (EBV)-negative blood products; deferment of immunizations until immune reconstitution; consideration for formula feeds in place of breast feeding until CMV status of mother known.

Surveillance: Following a successful HSCT, monitoring of the following every six to 12 months: immune status, liver and renal function, complete blood count, growth, and psychomotor development.

Agents/circumstances to avoid: Non-irradiated blood products; live viral and live bacterial vaccinations.

Evaluation of relatives at risk: Because the outcome in children with SCID is significantly improved by HSCT in the first three months of life, consider early testing to establish the genetic status of at-risk sibs.

Genetic counseling.

ZAP70-related SCID is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being a carrier, and a 25% chance of being unaffected and not a carrier. Carrier testing for at-risk family members and prenatal diagnosis for pregnancies at increased risk are possible if the pathogenic allelic variants in the family are known.


Suggestive Findings

Diagnosis of ZAP70-related severe combined immunodeficiency (ZAP70-related SCID) should be suspected in individuals with the following findings:

  • Recurrent viral, bacterial, and opportunistic infections
  • Failure to thrive
  • Presentation in the first year of life
  • Specific results of lymphocyte subset analysis of CD3, CD4, and CD8 T cells, lymphocyte function testing, and ZAP-70 protein expression (as detailed below)

Lymphocyte counts and lymphocyte cell surface expression. In ZAP70-related SCID, total lymphocyte counts can range from normal to high.

  • T cell counts
    • CD8+ cells are absent or cell counts are very low. Note: T cells expressing CD8+ make up 0%-2% of the child’s total T-cell count in individuals with ZAP70 related SCID [Arpaia et al 1994, Noraz et al 2000].
    • CD4+ cell counts are normal or elevated. Note: CD4+ cells account for 60%-80% of mononuclear cells in the lymphocyte count of individuals with ZAP70-related SCID.
    • CD3+ cell counts are normal. Note: Most CD3+ cells are composed of CD4+ cells in ZAP70-related SCID.
  • B cell counts and NK cell counts. Normal

Lymphocyte function. T-cell responses to stimuli that act through the T-cell receptor (TCR) are absent or severely diminished:

  • Absence of proliferation of CD4+ cells in response to mitogens (e.g., PHA)
  • Absence of proliferation of CD4+ cells in response to antigens (e.g., ConA)

Note: T-cell responses to phorbol myristic acetate and ionomycin stimulation (which bypasses the TCR) are normal [Elder et al 1994, Elder 1997].

ZAP-70 protein expression. Immunocytochemistry testing of CD4+ T cells reveals absence of ZAP-70 protein in most cases.

Immunoglobulin concentrations and function

  • Immunoglobulin levels vary by individual. A majority of affected individuals have severe hypogammaglobulinemia, but hypergammaglobulinemia and normal immunoglobulin levels have been seen [Turul et al 2009].
  • Although functional antibody responses to immunization are present in a few persons [Turul et al 2009], this finding does not indicate that all specific antigenic responses are intact.

Newborn screening. The use of routine newborn screening for T SCID by measuring T-cell receptor excision circle (TREC) levels continues to increase. Despite normal quantitative levels of CD4 cells in individuals with ZAP70-related SCID, TREC levels in already known cases of ZAP70-related SCID were found to be very low compared to age-matched controls [Roifman et al 2012], suggesting that detection of ZAP70-related SCID may be possible through newborn screening methods utilizing TREC quantitation. This highlights the need to consider this diagnosis in an abnormal TREC screening assay.

Establishing the Diagnosis

The diagnosis of ZAP70-related SCID is established by detection of biallelic pathogenic variants in ZAP70, the only gene known to be associated with ZAP70-related severe combined immunodeficiency (see Table 1).

One approach for molecular diagnosis of a proband suspected of having this condition is sequence analysis of ZAP70.

An alternative approach is use of a multi-gene panel that includes ZAP70 and other genes of interest (see Differential Diagnosis). Note: The genes included and the methods used in multi-gene panels vary by laboratory and over time.

Table 1.

Summary of Molecular Genetic Testing Used in ZAP70-Related Severe Combined Immunodeficiency

Gene 1Test MethodProportion of Probands with a Pathogenic Variant Detectable by This Method
ZAP70Sequence analysis 215/15 3
Deletion/duplication analysis 4None reported

See Table A. Genes and Databases for chromosome locus and protein. See Molecular Genetics for information on allelic variants.


Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Pathogenic variants may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.


See Table 2 in Karaca et al [2013] for a comprehensive list of pathogenic variants and phenotypes identified.


Testing that identifies exon or whole-gene deletions/duplications not detectable by sequence analysis of the coding and flanking intronic regions of genomic DNA. Included in the variety of methods that may be used are: quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA) that includes this gene/chromosome segment.

Clinical Characteristics

Clinical Description

Individuals with ZAP70-related SCID usually present in the first year of life with recurrent bacterial, viral, and opportunistic infections, diarrhea, and failure to thrive. Severe lower-respiratory infections are typically seen, most notably Pneumocystis jiroveci infections and viral infections. Oral candidiasis is common.

Whereas the above presentation is characteristic of ZAP70-related SCID, there are exceptions:

  • Reports of milder phenotypes in sibs of children who had died from ZAP70-related SCID include a child age five months with recurrent lower-respiratory disease but no severe infections [Turul et al 2009] and a child with persistent dermatitis resistant to therapy [Katamura et al 1999].
  • Picard et al [2009] described a child age nine years with a ZAP70 hypomorphic intronic pathogenic variant and an attenuated clinical and immunologic phenotype (see Genotype-Phenotype Correlations).
  • Newell et al [2011] reported a child age 11 months with ZAP70-related SCID who presented with lymphoma.
  • Santos et al [2010] reported ZAP70 deficiency in cousins (ages 5 and 6 months) presenting as axillary lymphadenitis following BCG vaccine.

Other presenting findings [Elder et al 1995, Parry et al 1996, Turul et al 2009]:

  • Subcutaneous nodules
  • Lymphadenopathy
  • Exfoliative dermatitis
  • Thrombocytopenia
  • Chronic gastroenteritis
  • Ulcerative colitis

The long-term prognosis of untreated ZAP70-related SCID is death from infection. Affected children have a declining quality of life and usually do not survive past their second year without hematopoietic stem cell transplantation (HSCT). A long-term study found that following HSCT, three-year survival rates were 77% and 54% for HLA-identical and HLA-mismatched transplants, respectively [Antoine et al 2003, Müller & Friedrich 2005]. Note: Survival rates given are for cohorts that comprise various forms of SCID, including ZAP70-related SCID; statistical outcomes specifically for ZAP70-related SCID are unknown.

Children with preexisting viral infections are at increased risk of developing graft-versus-host disease (GVHD) following HSCT, leading to a poor prognosis [Dvorak & Cowan 2008].

Genotype-Phenotype Correlations

A possible genotype-phenotype correlation is illustrated in a child with a hypomorphic intronic pathogenic variant (c.837+121G>A in intron 7) who had had chronic eczema from age two months and recurrent infections from age two years. Other findings in this child:

  • Low levels of alternative splicing resulting in 20% expression of ZAP-70 protein in T cells and partial T-cell activation
  • Low overall T-lymphocyte count
  • Low CD8+ cell count typical of ZAP70-related SCID
  • Low CD4+ cell counts atypical for ZAP70-related SCID

Each infection was treated individually until age six years, when the frequency of infection declined following introduction of cotrimoxazole and IVIG prophylaxis. Of note, an older sib with a history of multiple infections had died at age one year [Picard et al 2009].


The prevalence of ZAP70-related SCID is unknown but much lower than that of all forms of SCID, which is estimated at 1:50,000.

ZAP70-related SCID was first described in 1994. About 20 cases have been described in the literature [Fischer et al 2010].

Most cases of ZAP70-related SCID have occurred in genetically isolated Mennonite communities and/or in offspring of consanguineous relationships. One new pathogenic variant was described in a Turkish family [Karaca et al 2013], and Zap-70 deficiency was reported in two brothers with consanguineous parents of Turkish origin [Hönig et al 2012].

Differential Diagnosis

Human immunodeficiency virus infection. Infants positive for human immunodeficiency virus (HIV+) may present with recurring infections and failure to thrive similar to SCID. Individuals with HIV have CD4+ lymphopenia, in contrast to the CD8+ lymphopenia in ZAP70-related SCID. In a neonate, the definitive diagnosis of HIV should be made by detection of cell-associated human immunodeficiency proviral DNA by polymerase chain reaction (PCR) amplification. See Table 2 for additional considerations.

Table 2.

Combined Immunodeficiencies in the Differential Diagnosis of ZAP70-Related SCID

Disease NameGene InvolvedMode of InheritanceLymphocyte Phenotype
ZAP70-related SCIDZAP70AR+++CD4+/CD8-
Familial CD8 deficiencyCD8AAR+++CD4+/CD8
CD25 deficiencyIL2RAAR+++CD4/CD8+
MHC II deficiency (BLS)See Major histocompatibility complex (below)AR+++CD4/CD8+

MHC II = major histocompatibility complex class II

BLS = bare lymphocyte syndrome

Familial CD8 deficiency (OMIM 608957) may have a presentation similar to ZAP70-related SCID; the diagnosis can be confirmed with CD8A molecular genetic testing. The two individuals reported with this disease had recurring infections from early childhood and lived past their twenties [de la Calle-Martin et al 2001, Mancebo et al 2008].

CD25 deficiency (OMIM 606367) also presents with recurring infections early in life with low to normal T-cell counts. However, the T cells are CD4/CD8+. The diagnosis can be confirmed with molecular genetic testing of IL2RA (CD25), which encodes the interleukin-2 receptor alpha chain.

Major histocompatibility complex (MHC) class II deficiency (also known as bare lymphocyte syndrome) (OMIM 209920) may have normal or elevated T-cell counts; however, the T cells are CD4/CD8+. As in other forms of SCID, pathologic findings manifest within the first year of life. Major histocompatibility complex II expression is decreased. Molecular genetic testing may reveal pathogenic variants in RFX5, RFXAP, MHC2TA, or RFXANK, the four genes in which pathogenic variant is known to cause this disorder.

Table 3 differentiates several forms of severe combined immunodeficiency. Since SCID presents as a phenotypically heterogeneous class of diseases, it is useful to recognize forms of SCID that present with low to normal T-cell counts. Lymphocyte subset testing and molecular genetic testing can implicate or rule out these other forms of SCID.

Table 3.

T-Cell-Negative Forms of SCID in the Differential Diagnosis of ZAP70-Related SCID

Disease NameGene(s) InvolvedMode of InheritanceDefectLymphocyte Phenotype
ZAP70-related SCIDZAP70ARDecreased protein expression+++
JAK3-related SCIDJAK3AR+
CD45 deficiencyCD45AR+
ADA deficiencyADAARDecreased protein production
RAG1/2 deficiencyRAG1, RAG2AR+
X-linked SCIDIL2RGXLRDysfunctional receptor+

Omenn syndrome (OMIM 603554). Two children with ZAP70-related SCID presented with an Omenn syndrome-like phenotype that included lymphadenopathy, hepatosplenomegaly, and eosinophilia. Lymphocyte subset tests consistent with ZAP70-related SCID in both cases eliminated Omenn syndrome as a possible diagnosis.


Evaluations Following Initial Diagnosis

To establish the extent of disease and needs in an individual diagnosed with ZAP70-related severe combined immunodeficiency (SCID), the following evaluations are recommended:

  • Evaluation for common and opportunistic viral, bacterial, and fungal disease-causing agents
  • Assessment of growth
  • Complete metabolic panel (liver and renal function) and CBC with differential and platelet count
  • Medical genetics consultation
  • Immunology consultation, if not performed already

Treatment of Manifestations

Treatment relies on prompt reconstitution of the individual’s immune system (see Prevention of Primary Manifestations).

Short-term treatment includes immediate intravenous immunoglobulin (IVIG) and antibacterial, antifungal, and anti-protozoal prophylaxis to control and reduce the occurrence of infections.

Prevention of Primary Manifestations

The standard of therapy to cure SCID is allogeneic hematopoietic stem cell transplantation (HSCT). The outcome of HSCT in children with SCID is significantly improved by performing HSCT in the first three months of life [Buckley 2004]. Several children with ZAP70-related SCID have been transplanted [Arpaia et al 1994, Elder et al 1994, Noraz et al 2000, Elder et al 2001].

  • Outcomes are the best with HLA-matched, related donors.
  • If a related, HLA-matched donor is not available, alternatives include:
    • Matched unrelated donor
    • Umbilical cord blood donor
    • Haploidentical parental bone marrow or mobilized peripheral blood stem cells that have been T cell depleted
  • In contrast to individuals with other forms of SCID, individuals with ZAP70-related SCID are typically treated with a chemotherapeutic conditioning regimen prior to HSCT.
    • Hönig et al [2012] described the successful use of lymphocyte transfusion from a previously transplanted HLA identical sib without the use of conditioning for reconstituting the immune system in an individual with ZAP70-SCID.
    • Kim et al [2013] described use of a myeloablative protocol including conditioning with success. Two years post-transplant the patient is doing well.
  • Cellular reconstitution following HSCT takes three to four months and restoration of humoral immunity can take one to two years or more.
  • Complications from HSCT include graft-versus-host disease, failure to reconstitute the humoral immune compartment, graft failure over time, and post-transplant lymphoproliferative disease [Skoda-Smith et al 2001].
  • Affected individuals with poor humoral reconstitution are maintained on long-term immunoglobulin replacement.

Individuals with mild initial findings are maintained on immunoglobulin replacement and prophylactic antimicrobial therapy. They need to be monitored for worsening of immune function manifest by increased susceptibility to severe or opportunistic infections (see also Surveillance). If clinical status worsens, curative HSCT should be considered.

Prevention of Secondary Complications

The following are appropriate:

  • Use of irradiated, CMV-negative blood products
    Note: While not routinely screened for, the use of blood products from a known Epstein-Barr virus (EBV)-negative source should be considered as EBV-related lymphoma has been described in ZAP70-SCID [Newell et al 2011].
  • Delay of immunizations until immune reconstitution
  • Consideration for formula feeds in place of breast feeding until CMV status of mother known


Following a successful HSCT, the following should be monitored every six to 12 months:

  • Immune status
  • Liver and renal function
  • Complete blood count
  • Growth
  • Psychomotor development

Individuals with milder findings need to be monitored for worsening of immune function with at least semiannual assessment of clinical status and functional lymphocyte responsiveness.

Agents/Circumstances to Avoid

Individuals with ZAP70-related SCID should never receive the following:

  • Non-irradiated blood products
  • Live virus vaccinations
  • Mycobacterium bovis (BCG) vaccine against tuberculosis, Salmonella typhi (Ty21a) vaccine against typhoid fever, and Vibrio cholerae (CVD 103-HgR) vaccine against cholera, which may be part of the routine vaccination schedule in countries where these diseases are endemic

Evaluation of Relatives at Risk

Because the outcome of HSCT in children with SCID is significantly improved by performing HSCT in the first three months of life, early testing of at-risk sibs should be considered.

  • If the ZAP70 pathogenic variants in the family are known, molecular genetic testing can be used to clarify the genetic status of at-risk sibs.
  • If the pathogenic variants in the family are not known, CBC, quantitative immunoglobulins, and lymphocyte subsets and proliferation can be used to clarify the genetic status (immunologic status) of at-risk sibs.

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Pregnancy Management

Appropriately screened blood products should be available, if needed, during the course of the pregnancy or delivery.

Therapies Under Investigation

Gene therapy. While gene therapy has been used for other forms of SCID (notably ADA deficiency and X-linked SCID), it has not been performed in ZAP70-related SCID. Experimental studies utilizing gene therapy for this disease have been conducted on murine models [Adjali et al 2005, Irla et al 2008] as well as human cells in vitro [Steinberg et al 2000, Kofler et al 2004].

Adverse oncogenic reactions have been documented in some individuals with X-linked SCID transduced with retroviral vector [Buckley 2003, Fischer et al 2005]. Nonviral transfer methods (e.g., electro-gene transfer) have been used to correct ZAP-70 deficiency in a murine model [Irla et al 2008].

Search for access to information on clinical studies for a wide range of diseases and conditions.

Genetic Counseling

Genetic counseling is the process of providing individuals and families with information on the nature, inheritance, and implications of genetic disorders to help them make informed medical and personal decisions. The following section deals with genetic risk assessment and the use of family history and genetic testing to clarify genetic status for family members. This section is not meant to address all personal, cultural, or ethical issues that individuals may face or to substitute for consultation with a genetics professional. —ED.

Mode of Inheritance

ZAP70-related severe combined immunodeficiency is inherited in an autosomal recessive manner.

Risk to Family Members

Parents of a proband

  • Each parent is a carrier for a pathogenic variant in ZAP70.
  • Parents do not usually have SCID-like symptoms. Turul et al [2009] analyzed the ZAP70 expression in the parents of probands and demonstrated that parents who did not appear to have clinical symptoms had intermediate expression levels compared to healthy controls. Further studies suggested a Zap 70 protein level threshold effect which may explain why parents with decreased ZAP70 expression may have no clinical features [Cauwe et al 2014].

Sibs of a proband

  • At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being a carrier, and a 25% chance of being unaffected and not a carrier.
  • Once an at-risk sib is known to be unaffected, the risk of his/her being a carrier is 2/3.
  • Even if the sibs of a proband are asymptomatic, molecular genetic testing to determine their genetic status should be considered for the purpose of early diagnosis and treatment of those who have inherited both pathogenic variants (see Evaluation of Relatives at Risk).

Offspring of a proband

  • The offspring of an individual with ZAP70-related severe combined immunodeficiency will inherit one pathogenic variant from the proband.
  • The genetic status of the offspring will depend on the genetic status of the reproductive partner of the proband.
    • If the reproductive partner is not affected and not a carrier, all offspring will be carriers.
    • If the reproductive partner is a carrier of a ZAP70 pathogenic variant, each child will have a 50% chance of being affected and a 50% chance of being a carrier.
    • If the reproductive partner is also affected, all offspring will be affected.
  • Most individuals with ZAP70-related SCID are from genetically isolated Mennonite communities and/or have consanguineous parents.

Other family members. A detailed family history that includes the ancestry and culture of the proband’s family may reveal consanguinity and geographic and genetic isolation – risk factors that increase the likelihood of autosomal recessive diseases in a family. Some of the grandparents of the proband are carriers for ZAP70 pathogenic variants; therefore, sibs of the proband’s parents and their offspring are at risk of being carriers.

Carrier Detection

Carrier testing for at-risk family members is possible once the ZAP70 pathogenic variants have been identified in the family.

Related Genetic Counseling Issues

See Management, Evaluation of Relatives at Risk for information on evaluating at-risk relatives for the purpose of early diagnosis and treatment.

Family planning

  • The optimal time for determination of genetic risk, clarification of carrier status, and discussion of the availability of prenatal testing is before pregnancy.
  • It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to young adults who are affected, are carriers, or are at risk of being carriers.

DNA banking is the storage of DNA (typically extracted from white blood cells) for possible future use. Because it is likely that testing methodology and our understanding of genes, allelic variants, and diseases will improve in the future, consideration should be given to banking DNA of affected individuals.

Prenatal Testing and Preimplantation Genetic Diagnosis

Once the ZAP70 pathogenic variants have been identified in an affected family member, prenatal testing and preimplantation genetic diagnosis for a pregnancy at increased risk for ZAP70-related severe combined immunodeficiency are possible options.

An affected fetus does not require any specific management prior to delivery. Following delivery, early evaluation for potential HSCT should be performed because of the known benefit of early HSCT (see Evaluation of Relatives at Risk).


GeneReviews staff has selected the following disease-specific and/or umbrella support organizations and/or registries for the benefit of individuals with this disorder and their families. GeneReviews is not responsible for the information provided by other organizations. For information on selection criteria, click here.

  • Immune Deficiency Foundation (IDF)
    40 West Chesapeake Avenue
    Suite 308
    Towson MD 21204
    Phone: 800-296-4433 (toll-free)
  • International Patient Organisation for Primary Immunodeficiencies (IPOPI)
    Main Road
    Downderry Cornwall PL11 3LE
    United Kingdom
    Phone: +44 01503 250 668
    Fax: +44 01503 250 668
  • Jeffrey Modell Foundation/National Primary Immunodeficiency Resource Center
    747 Third Avenue
    New York NY 10017
    Phone: 866-463-6474 (toll-free); 212-819-0200
    Fax: 212-764-4180
  • Canadian Immunodeficiencies Patient Organization (CIPO)
    362 Concession Road 12
    RR #2
    Hastings Ontario K0L 1Y0
    Phone: 877-262-2476 (toll-free)
    Fax: 866-942-7651 (toll-free)
  • National Human Genome Research Institute (NHGRI)
  • NCBI Genes and Disease
  • European Society for Immunodeficiencies (ESID) Registry
    Dr. Gerhard Kindle
    University Medical Center Freiburg Centre of Chronic Immunodeficiency
    Engesserstr. 4
    79106 Freiburg
    Phone: 49-761-270-34450
  • Primary Immunodeficiency Diseases Registry at USIDNET
    40 West Chesapeake Avenue
    Suite 308
    Towson MD 21204-4803
    Phone: 866-939-7568
    Fax: 410-321-0293
  • RDCRN Patient Contact Registry: Primary Immune Deficiency Treatment Consortium

Molecular Genetics

Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.

Table A.

ZAP70-Related Severe Combined Immunodeficiency: Genes and Databases

Data are compiled from the following standard references: gene from HGNC; chromosome locus, locus name, critical region, complementation group from OMIM; protein from UniProt. For a description of databases (Locus Specific, HGMD) to which links are provided, click here.

Table B.

OMIM Entries for ZAP70-Related Severe Combined Immunodeficiency (View All in OMIM)


Gene structure. ZAP70 spans 26.3 kb of genomic DNA. The gene consists of 14 exons comprising 2450 bp. For a detailed summary of gene and protein information, see Table A.

Pathogenic allelic variants. ZAP70 pathogenic variants reside mostly in the kinase domain, although pathogenic variants that result in loss of transcription or are located in the N-terminal SH2 domain and result in rapid degradation of ZAP-70 protein have been reported [Matsuda et al 1999, Au-Yeung et al 2009]. More than a dozen pathogenic variants consisting of single nucleotide variants, splice defects, and intragenic deletions have been reported. A pathogenic variant in the arginine residue (p.Arg465Cys) of the DLAARN motif of the kinase domain has been described (see Abnormal gene product). Selected pathogenic variants can be viewed in Table 4 and Table A. Details on other pathogenic variants may also be found in Karaca et al [2013].

Table 4.

Selected ZAP70 Pathogenic Variants

DNA Nucleotide Change
(Alias 1)
Protein Amino Acid ChangeReference Sequences
See Abnormal gene product

Note on variant classification: Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.

Note on nomenclature: GeneReviews follows the standard naming conventions of the Human Genome Variation Society (www​ See Quick Reference for an explanation of nomenclature.


Variant designation that does not conform to current naming conventions

Normal gene product. ZAP70 codes for an enzyme in the Syk-protein tyrosine kinase family that plays a role in T-cell development and activation. This enzyme is phosphorylated at tyrosine residues upon T-cell receptor (TCR) stimulation and functions in the initial step of TCR-mediated signal transduction with Src family kinases. ZAP-70 comprises 619 amino acids and contains two SH2 domains and one kinase domain. The pathogenic variants that lead to ZAP70-related SCID occur in or close to the region coding the kinase domain.

Abnormal gene product. Most noted pathogenic variants affect the kinase domain of ZAP70 and cause a lack of protein expression. The p.Arg465Cys alteration in the highly conserved DLAARN motif of the kinase domain compromises ZAP-70 protein stability and eliminates the protein’s catalytic function [Elder et al 2001]. Both the p.Pro80Gln and p.Met572Leu altered proteins undergo temperature-sensitive degradation [Matsuda et al 1999]. Picard et al [2009] described a hypomorphic pathogenic variant in ZAP70 intron 7 (c.837+121G>A) that creates a new in-frame splice product with a new stop codon within intron 7. In addition to the truncated product, the pathogenic variant allowed residual expression of the wild type protein (20% expression level in the patient’s T cells), resulting in an attenuated clinical and immunologic phenotype (see Genotype-Phenotype Correlations) [Picard et al 2009].


Literature Cited

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Suggested Reading

  1. Pessach IM, Notarangelo LD. Gene therapy for primary immunodeficiencies: looking ahead, toward gene correction. J Allergy Clin Immunol. 2011;127:1344–50. [PMC free article: PMC3105180] [PubMed: 21440291]

Chapter Notes

Author History

Tara Capece, MPH; University of Pittsburgh (2009-2012)
Marc Ikeda, MD; Children’s Hospital of Pittsburgh (2012-2014)
Allyson Larkin, MD (2012-present)
David Nash, MD; Children’s Hospital of Pittsburgh (2009-2012)
Stacy Lyn Rosenberg, MD (2014-present)

Revision History

  • 25 September 2014 (me) Comprehensive update posted live
  • 6 September 2012 (cd) Revision: prenatal diagnosis available clinically
  • 1 March 2012 (me) Comprehensive update posted live
  • 20 October 2009 (me) Review posted live
  • 1 June 2009 (tc) Original submission
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