Primary Immunodeficiency Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: IM0301

The Blueprint Genetics Primary Immunodeficiency Panel is a 228 gene test for genetic diagnostics of patients with clinical suspicion of autoinflammatory disorders, combined immunodeficiencies, complement deficiencies, congenital defects of phagocytes, defects in innate immunity, diseases of immune dysregulation or immunodeficiencies with antibody defects.

Primary immunodeficiencies (PIDs) are a very heterogenous group of diseases. This Panel covers comprehensively genes associated with PIDs inherited either in autosomal recessive, autosomal dominant or X-linked manner. In addition to familial diseases, some specific types of PIDs are often caused by de novo mutations. This comprehensive Panel includes Complement System Disorder Panel, Severe Combined Immunodeficiency Panel, Dyskeratosis Congenita Panel, Autoinflammatory Syndrome Panel, Congenital Neutropenia Panel and Chronic Granulomatous Disease Panel and has differential diagnostics power to any phenotypes detectable by these Panels.

About Primary Immunodeficiency

Primary immunodeficiencies (PIDs) are a genetically very heterogenous group of diseases. The International Union of Immunological Societies Expert Committee categorize PIDs into nine different catogories: 1) combined immunodeficiencies, 2) combined immunodeficiencies with associated or syndromic features, 3) predominantly antibody deficiencies, 4) diseases of immune dysregulation, 5) congenital defects of phagocyte number, function, or both, 6) defects in innate immunity, 7) autoinflammatory disorders, 8) complement deficiencies and 9) phenocopies of PIDs. Despite of a heterogenous genetic basis, the core symptoms are often very similar complicating the definite diagnosis and many PIDs may be included in more than one category. Treatment choice without specific information on the causative gene and mutation may therefore be complicated. Also, type and site of and specific organisms causing the infections may help to classify the disease. In addition to immune-related symptoms, many PIDs have nonimmune manifestations. The prevalence of individual PIDs have a wide range, but combined prevalence of all primary immunodeficiencies is reported to be as high as 5-8:10 000. Some recently found PIDs are extremely rare.


Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more.

Genes in the Primary Immunodeficiency Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ACP5Spondyloenchondrodysplasia with immune dysregulationAR1024
ACTB*Baraitser-Winter syndromeAD2726
ADASevere combined immunodeficiency due to adenosine deaminase deficiencyAR3588
ADARDyschromatosis symmetrica hereditaria, Aicardi-Goutières syndromeAD/AR16202
ADIPOQComplement systemAD/AR122
ADIPOR1*Complement systemAD/AR4
ADIPOR2Complement systemAD/AR2
AICDAImmunodeficiency with hyper-IgMAR1248
AIREAutoimmune polyendocrinopathy syndromeAD/AR30122
AK2Reticular dysgenesisAR1417
AP3B1Hermansky-Pudlak syndromeAR1423
ARMC4*Ciliary dyskinesiaAR1215
ATMBreast cancer, Ataxia-TelangiectasiaAD/AR455853
BLMBloom syndromeAR5392
BTKHypogammaglobulinemia, Agammaglobulinemia and isolated hormone deficiency, AgammaglobulinemiaXL70886
C1QAC1q deficiencyAR18
C1QBC1q deficiencyAR17
C1QBPPrimary immunodeficiencyAD/AR
C1QCC1q deficiencyAR37
C1SComplement component C1s deficiencyAR48
C2*Complement component 2 deficiencyAR47
C3Hemolytic uremic syndrome, atypical, Complement component 3 deficiencyAD/AR486
C3AR1Complement systemAD/AR13
C4A*Blood group, Chido/Rodgers systemBG18
C4B*Complement component 4B deficiencyAR9
C4BPAComplement systemAD/AR5
C4BPBComplement systemAD/AR
C5Eculizumab, poor response to, Complement component 5 deficiencyAD/AR520
C5AR1Complement systemAD/AR
C5AR2Complement systemAD/AR4
C6Complement component 6 deficiencyAR610
C7Complement component 7 deficiencyAR1130
C8AComplement component 8 deficiencyAR24
C8BComplement component 8 deficiencyAR77
C9Complement component 9 deficiencyAR67
CARD11B-cell expansion with NFKB and T-cell anergy, ImmunodeficiencyAD/AR68
CASP8Caspase 8 defiencyAR26
CASP10Autoimmune lymphoproliferative syndromeAD66
CCDC39Ciliary dyskinesiaAR1338
CCDC40Ciliary dyskinesiaAR1531
CCDC65Ciliary dyskinesiaAR21
CCDC103Ciliary dyskinesiaAR24
CCDC114Ciliary dyskinesiaAR57
CCNOCiliary dyskinesiaAR79
CD8ACD8 deficiencyAR11
CD19Immunodeficiency, common variableAR69
CD27Lymphoproliferative syndromeAR26
CD40Immunodeficiency with Hyper-IgMAR413
CD40LGImmunodeficiency, with hyper-IgMXL21227
CD46*Hemolytic uremic syndrome, atypicalAD/AR262
CD55Blood group, Cromer systemBG1
CD59CD59 deficiencyAR36
CD93Complement systemAD/AR
CECR1Polyarteritis nodosa, ADA2 deficiencyAR1131
CFBComplement factor B deficiency, Hemolytic uremic syndrome, atypicalAD/AR224
CFDComplement factor D deficiencyAR23
CFH*Hemolytic uremic syndrome, atypical, Complement factor H deficiencyAD/AR15260
CFHR1*Hemolytic uremic syndrome, atypicalAD/AR/Digenic29
CFHR3*Hemolytic uremic syndrome, atypicalAD/AR/Digenic14
CFIHemolytic uremic syndrome, atypical, Complement factor I deficiencyAD/AR6118
CFPProperdin deficiencyXL516
CIITABare lymphocyte syndromeAR617
CLUComplement systemAD/AR20
COLEC113MC syndromeAR66
CR1*Blood group, Knops systemBG129
CR2Common variable immunodeficiencyAR27
CRPComplement systemAD/AR
CSF2RA*Surfactant metabolism dysfunction, pulmonaryXL214
CTC1Cerebroretinal microangiopathy with calcifications and cystsAR1329
CTSCPeriodontitis, juvenile, Haim-Munk syndrome, Papillon-Lefevre syndromeAR1591
CYBAChronic granulomatous diseaseAR1167
CYBBChronic granulomatous disease, ImmunodeficiencyXL44734
DCLRE1C*Omenn syndrome, Severe combined immunodeficiency with sensitivity to ionizing radiationAR1676
DDX58Singleton-Merten syndromeAD27
DGKENephrotic syndromeAR1021
DKC1Hoyeraal-Hreidarsson syndrome, Dyskeratosis congenitaXL4569
DNAAF1Ciliary dyskinesiaAR828
DNAAF2Ciliary dyskinesiaAR43
DNAAF3Primary ciliary dyskinesiaAD/AR33
DNAAF5Ciliary dyskinesiaAR22
DNAH5Ciliary dyskinesiaAR36135
DNAH11*Ciliary dyskinesiaAR2590
DNAI1Ciliary dyskinesiaAR1028
DNAI2Ciliary dyskinesiaAR76
DNAL1Ciliary dyskinesiaAR31
DNMT3BImmunodeficiency-centromeric instability-facial anomalies syndromeAR1246
DOCK8Hyper-IgE recurrent infection syndromeAR28135
DRC1Primary ciliary dyskinesiaAD/AR32
DYX1C1Ciliary dyskinesiaAR617
FASAutoimmune lymphoproliferative syndromeAD/AR22136
FCN1Complement systemAD/AR4
FCN2Complement systemAD/AR7
FCN3Immunodeficiency due to Ficolin 3 deficiencyAR1
FERMT3Leukocyte adhesion deficiencyAR813
FOXP3Immunodysregulation, polyendocrinopathy, and enteropathyXL1883
G6PC3Neutropenia, severe congenital, Dursun syndromeAR1237
G6PDGlucose-6-phosphate dehydrogenase deficiencyXL36214
GATA2Myelodysplastic syndrome, Chronic neutropenia associated with monocytopenia, evolving to myelodysplasia and acute myeloid leukemia, Acute myeloid leukemia, Emberger syndrome, ImmunodeficiencyAD1976
HAX1Neutropenia, severe congenitalAR819
HYDIN*Primary ciliary dyskinesiaAD/AR313
IFIH1Singleton-Merten syndromeAD1017
IKBKG*Incontinentia pigmenti, Ectodermal, dysplasia, anhidrotic, lymphedema and immunodeficiency, Immunodeficiency, Invasive pneumococcal disease, recurrent, isolated, Osteopetrosis with ectodermal dysplasia and immune defect (OLEDAID)XL30141
IL1RNOsteomyelitis, sterile multifocal, with periostitis and pustulosisAR516
IL2RAInterleukin 2 receptor, alpha, deficiencyAR513
IL2RGCombined immunodeficiencyXL27215
IL7*Interleukin 7 deficiency, Generalized verrucosis, HPV susceptibilityAD/AR
IL7RSevere combined immunodeficiency, , T-cell negative, B-cell positive, NK cell positiveAR1542
IL10RAInflammatory bowel diseaseAR527
IL10RBInflammatory bowel diseaseAR214
IL36RNPustular psoriasis, generalizedAR819
ISG15Immunodeficiency, with basal ganglia calcificationAR33
ITGB2Leukocyte adhesion deficiencyAR27114
ITKLymphoproliferative syndromeAR310
JAGN1Neutropenia, severe congenitalAR88
JAK3Severe combined immunodeficiency, , T cell-negative, B cell-positive, natural killer cell-negativeAR1356
LIG4Severe combined immunodeficiency with sensitivity to ionizing radiation, LIG4 syndromeAR836
LPIN2Majeed syndromeAR810
LRBACommon variable immunodeficiencyAR1045
LRRC6Ciliary dyskinesiaAR814
LYSTChediak-Higashi syndromeAR4578
MAGT1Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasiaXL410
MASP13MC syndromeAR714
MASP2MASP2 deficiencyAR18
MAT2A*Complement systemAD/AR2
MEFVFamilial Mediterranean feverAD/AR24177
MRE11AAtaxia-telangiectasia-like disorder-1AD2538
MVKMevalonic aciduria, Hyper-IgD syndromeAR27168
NBNBreast cancer, Nijmegen breakage syndromeAD/AR5762
NCF1*Chronic granulomatous diseaseAR1536
NCF2Chronic granulomatous diseaseAR1066
NCF4Granulomatous diseaseAR34
NFKB1Common variable immunodeficiencyAD312
NFKB2Common variable immunodeficiencyAD57
NFKBIAEctodermal dysplasia, anhidrotic, with T-cell immunodeficiencyAD414
NHEJ1Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiationAR813
NHP2Dyskeratosis congenitaAR33
NLRP3Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndromeAD15125
NLRP12Familial cold autoinflammatory syndromeAD39
NME8Ciliary dyskinesiaAR16
NOD2Blau syndrome, Sarcoidosis, early-onsetAD/AR1093
NOP10Dyskeratosis congenitaAR11
NRASNoonan syndromeAD178
OFD1Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndromeXL129148
PIGA*Multiple congenital anomalies-hypotonia-seizures syndromeXL1914
PLCG2Familial cold autoinflammatory syndrome 3 (PLAID), Autoinflammation, antibody deficiency, and immune dysregulation syndrome (APLAID)AD48
PMS2*Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR151266
PNPPurine nucleoside phosphorylase deficiencyAR1034
PRF1Lymphoma, non-Hodgkin, Aplastic anemia, adult-onset, Hemophagocytic lymphohistiocytosisAR15165
PSMB8Nakajo-Nishimura syndrome, Chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature syndrome, Autoinflammation, lipodystrophy, and dermatosis syndrome, Joint contractures, muscular atrophy, microcytic anemia, and panniculitis-induced lipodystrophy syndromeAR410
PSTPIP1Pyogenic sterile arthritis, pyoderma gangrenosum, and acneAD525
PTPRCSevere combined immunodeficiency, , T-cell negative, B-cell positive, NK cell positiveAR48
PTX3Complement systemAD/AR
RAB27AGriscelli syndrome, Elejalde syndromeAR1045
RAG1Omenn syndrome, Alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus infection, and autoimmunity, T cell-negative, B cell-negative, natural killer cell-positive severe combined immunodeficiency, Combined cellular and humoral immune defects with granulomasAR35168
RAG2Omenn syndrome, Combined cellular and humoral immune defects with granulomasAR1866
RFX5Bare lymphocyte syndromeAR56
RFXANKMHC class II deficiencyAR612
RFXAPBare lymphocyte syndromeAR57
RHOHT-cell immunodeficiency with epidermodysplasia verruciformisAD/AR1
RMRPCartilage-hair hypoplasia, Metaphyseal dysplasia without hypotrichosis, Anauxetic dysplasiaAR24119
RNASEH2AAicardi-Goutières syndromeAR1221
RNASEH2BAicardi-Goutières syndromeAR539
RNASEH2CAicardi-Goutières syndromeAR414
RPGRRetinitis pigmentosaXL41184
RSPH1Ciliary dyskinesiaAR910
RSPH4ACiliary dyskinesiaAR721
RSPH9Ciliary dyskinesiaAR211
RTEL1Pulmonary fibrosis and/or bone marrow failure, Dyskeratosis congenitaAD/AR2726
SAMHD1Aicardi-Goutières syndromeAR2248
SBDS*Aplastic anemia, Shwachman-Diamond syndrome, Severe spondylometaphyseal dysplasiaAD/AR1288
SH2D1ALymphoproliferative syndromeXL14120
SLC37A4Glycogen storage diseaseAR25107
SMARCAL1Schimke immunoosseous dysplasiaAR970
SP110Hepatic venoocclusive disease with immunodeficiencyAR710
SPAG1Primary ciliary dyskinesiaAD/AR710
SPINK5Netherton syndromeAR884
STAT3Hyper-IgE recurrent infection syndrome, Autoimmune disease, multisystem, infantile onsetAD27133
STAT4Behçet disease, Juvenile rheumatoid factor-negative polyarthritis, Oligoarticular juvenile arthritis, Pediatric systemic lupus erythematosusAD/AR3
STAT5B*Growth hormone insensitivity with immunodeficiencyAR511
STIM1Stormorken syndrome, ImmunodeficiencyAD/AR1019
STK4T-cell immunodeficiency syndrome, recurrent infections, autoimmunity,AR36
STXBP2Hemophagocytic lymphohistiocytosis, familialAR860
TAP1Bare lymphocyte syndromeAR28
TAP2Bare lymphocyte syndromeAR213
TAPBPBare lymphocyte syndromeAR13
TBX1Conotruncal anomaly face syndromeAD759
TCIRG1Osteopetrosis, severe neonatal or infantile forms (OPTB1)AR9127
TERCAplastic anemia, Pulmonary fibrosis and/or bone marrow failure, telomere-related, Dyskeratosis congenitaAD3660
TERTAplastic anemia, Pulmonary fibrosis and/or bone marrow failure, telomere-related, Dyskeratosis congenitaAD/AR39133
THBDThrombophilia due to thrombomodulin defect, Hemolytic uremic syndrome, atypicalAD527
TINF2Revesz syndrome, Dyskeratosis congenitaAD2033
TMEM173STING-associated vasculopathy, infantile-onsent (SAVI)AD37
TNFRSF1APeriodic fever (TNF receptor-associated periodic syndrome)AD18101
TNFRSF13BCommon variable immunodeficiency, Immunoglobulin A deficiencyAD/AR546
TRACT-cell receptor-alpha/beta deficiencyAR11
TREX1Vasculopathy, retinal, with cerebral leukodystrophy, Chilblain lupus, Aicardi-Goutières syndromeAD/AR2465
USB1Poikiloderma with neutropeniaAR421
VSIG4Complement systemXL1
VTNComplement systemAD/AR
WASNeutropenia, severe congenital, Thrombocytopenia, Wiskott-Aldrich syndromeXL32429
WRAP53Dyskeratosis congenitaAR56
XIAP*Lymphoproliferative syndromeXL478
ZAP70Selective T-cell defectAR1020
ZMYND10Ciliary dyskinesiaAR616
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (; HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, The list of associated (gene specific) phenotypes are generated from CDG ( or Orphanet ( databases.

Blueprint Genetics offers a comprehensive Primary Immunodeficiency Panel that covers classical genes associated with autoinflammatory disorders, combined immunodeficiencies, complement deficiencies, congenital defects of phagocytes, defects in innate immunity, diseases of immune dysregulation and immunodeficiencies with antibody defects. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (, the NHLBI GO Exome Sequencing Project (ESP;, the Exome Aggregation Consortium (ExAC;, ClinVar database of genotype-phenotype associations ( and the Human Gene Mutation Database ( The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (, Polyphen (, and Mutation Taster (

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes


ICD codes

Commonly used ICD-10 codes when ordering the Primary Immunodeficiency Panel

D80.9Immunodeficiencies with antibody defects
D84.1Complement deficiencies
D81Combined immunodeficiencies

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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