PMC Primary Immunodeficiency Panel

Associated Conditions
- activated PI3K-delta syndrome
- agammaglobulinemia and hypogammaglobulinemia
- Asphyxiating thoracic dysplasia (ATD; Jeune)
- autoimmune lymphoproliferative syndrome
- chronic granulomatous disease
- chronic mucocutaneous candidiasis
- combined immunodeficiency
- combined immunodeficiency with syndromic features
- complement deficiencies
- congenital neutropenia
- Cranioectodermal dysplasia (Levin-Sensenbrenner)
- Culler-Jones syndrome
- dyskeratosis congenita
- Ellis-van Creveld syndrome
- epidermodysplasia verruciformis
- familial cold autoinflammatory syndromes
- familial hemophagocytic lymphohistiocytosis and related disorders
- familial Mediterranean fever
- Hermansky-Pudlak syndrome
- herpes simplex encephalitis
- hyper IgE syndrome, including Netherton syndrome
- hyper IgM syndrome
- immunodeficiency- centromeric instability- facial anomalies syndrome
- Jeune asphyxiating thoracic dystrophy
- Joubert syndrome
- leukocyte adhesion deficiency
- major histocompatibility complex class I and II deficiencies
- Mendelian susceptibility to mycobacterial infections
- monogenic autoimmunity
- monogenic autoinflammatory syndromes
- monogenic common variable immune deficiency
- monogenic congenital diarrhea
- monogenic inflammatory bowel disease
- Nephronophthisis
- Orofaciodigital syndrome (Mohr-Majewski syndrome)
- periodic fever syndromes
- pulmonary alveolar proteinosis
- Retinitis pigmentosa
- Senior-Loken syndrome
- Sensenbrenner syndrome
- severe combined immunodeficiency
- Short -rib thoracic dysplasia with or without polydactyly
- Short-rib thoracic dysplasia
- SRPS type 2 (Majewski)
- Weyers acrodental dysostosis
- Weyers acrofacial dysostosis
- WHIM syndrome

Methodology

Targeted Exome/ Slice Exome (Next Generation Sequencing including Copy Number Variation)

Coverage

120x

Ordering information

Turnaround Time: 10 business days

Preferred Speciment: Saliva Kits (available upon request)

Alternate Specimens: Nail clippings or 3-mL whole blood in purple top EDTA tube

Request a specimen collection kit

Limitations

All sequencing technologies have limitations. A negative result from this analysis does not rule out a possible genetic diagnosis as some variants may not be detected by this test. This test is not designed to detect low level mosaicism, structural rearrangements, indels >40bp, deep intronic variants of unknown clinical significance, or large cytogenetic CNVs. Certain inherent qualities of the human genome, for example repetitive regions/homopolymers, GC rich, pseudogenes, and rare polymorphisms, pose significant technical challenges such as sequence misalignment that may potentially impact the accuracy of the results. False negative results may also occur in the setting of allogeneic bone marrow, stem cell transplantation, active or chronic hematologic conditions, recent blood transfusions, suboptimal DNA quality or PCR trace contamination. Other potential sources of error include sample mix-ups and clerical issues.

References
- 1. Richards S et al. Genetics in medicine. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. 2015 May;17(5):405-24 (PMID: 25741868)
- 2. GnomAD (gnomAD)
- 3. CSPEC (ClinGen variant classification rules registry) Criteria Specification Registry
- 4. Normal copy number variation in healthy individuals database of genomic variants: http://dgv.tcag.ca/dgv/app/home
- 5. Riggs, E.R., Andersen, E.F., Cherry, A.M. et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 22, 245–257 (2020). https://doi.org/10.1038/s41436-019-0686-8
- 6. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan 1;42(1):D980-5. doi: 10.1093/nar/gkt1113. PubMed PMID: 24234437.
- 7. Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), Copyright® 1966-2012. World Wide Web URL: http://omim.org.
- 8. http://tinyurl.com/ACMGv4 (ACMG/ Clingen draft Interpretation SOP); clingen_variant-curation_sopv1.pdf

Tagged Genes

Primary panel:

504 genes selected

ACD ACP5 ACTB ADA ADA2 ADAM17 ADAR ADGRE2 AICDA AIRE AK2 ALG6 ALPI ALPK1 AMN ANGPT1 ANKZF1 AP3B1 AP3D1 ARHGEF1 ARMC4 ARPC1B ASAH1 ATM ATP6AP1 B2M BACH2 BCL10 BCL11B BLM BLNK BLOC1S3 BLOC1S6 BTK C11ORF70 C17ORF62 C1QA C1QB C1QC C1S C2 C21ORF59 C3 C5 C6 C7 C8A C8B C9 CARD11 CARD14 CARD8 CARD9 CARMIL2 CASP10 CASP8 CBL CCBE1 CCDC103 CCDC114 CCDC151 CCDC39 CCDC40 CCDC65 CCNO CD19 CD247 CD27 CD3D CD3E CD3G CD4 CD40 CD40LG CD46 CD55 CD59 CD70 CD79A CD79B CD81 CD8A CDC42 CDCA7 CDK9 CEBPE CECR1 CENPF CFAP57 CFB CFD CFH CFI CFP CFTR CHD7 CIB1 CIITA CLCN7 CLPB COG6 COL7A1 COLEC11 COPA CORO1A CR2 CSF2RA CSF2RB CSF3R CTC1 CTLA4 CTPS1 CTSC CXCR2 CXCR4 CYBA CYBB CYP27A1 DBR1 DCLRE1C DDX58 DEF6 DGAT1 DGKE DIAPH1 DKC1 DNAAF1 DNAAF2 DNAAF3 DNAAF5 DNAH1 DNAH11 DNAH5 DNAH8 DNAH9 DNAI1 DNAI2 DNAJB13 DNAJC21 DNAL1 DNASE1L3 DNASE2 DNMT3B DOCK2 DOCK8 DRC1 DSG1 DTNBP1 DUOX2 DYX1C1 EFL1 EIF2AK3 ELANE EPG5 ERBIN ERCC2 ERCC3 ERCC6L2 EXTL3 FADD FANCA FANCB FANCE FANCF FANCI FANCL FAS FASLG FAT4 FCGR3A FCHO1 FERMT1 FERMT3 FNIP1 FOXI3 FOXN1 FOXP3 FPR1 G6PC G6PC3 G6PD GAS2L2 GAS8 GATA1 GATA2 GFI1 GINS1 GTF2E2 GTF2H5 GUCY2C HAVCR2 HAX1 HELLS HMOX1 HPS1 HPS3 HPS4 HPS5 HPS6 HTRA2 HYDIN HYOU1 ICOS ICOSLG IFIH1 IFNAR1 IFNAR2 IFNGR1 IFNGR2 IGLL1 IKBKB IKZF1 IL10 IL10RA IL10RB IL12B IL12RB1 IL12RB2 IL17F IL17RA IL17RC IL18BP IL1RN IL21 IL21R IL23R IL2RA IL2RB IL2RG IL36RN IL6R IL6ST IL7 IL7R INVS IRAK4 IRF2BP2 IRF4 IRF7 IRF8 IRF9 ISG15 ITCH ITGAM ITGB2 ITK JAGN1 JAK1 JAK3 KAT6A KDM6A KMT2A KMT2D KRAS LAMTOR2 LAT LCK LCT LIG1 LIG4 LIPA LPIN2 LRBA LRRC56 LRRC6 LRRC8A LYN LYST MAD2L2 MAGT1 MALT1 MAP3K14 MASP1 MCIDAS MCM4 MEFV MKL1 MOGS MPLKIP MRE11A MS4A1 MSN MTHFD1 MVK MYD88 MYO5A MYO5B MYSM1 NBAS NBN NCF1 NCF2 NCF4 NCKAP1L NCSTN NEUROG3 NFAT5 NFE2L2 NFKB1 NFKB2 NFKBIA NHEJ1 NHP2 NLRC4 NLRP1 NLRP12 NLRP3 NME8 NOD2 NOP10 NRAS NSMCE3 OAS1 OBFC1 OFD1 ORAI1 OSTM1 OTULIN PARN PAX1 PEPD PGM3 PIGA PIH1D3 PIK3CD PIK3R1 PLCG2 PLVAP PMM2 PMS2 PNLIP PNP POLA1 POLD1 POLD2 POLE POLE2 POLR3A POLR3F POMP PRF1 PRG4 PRKCD PRKDC PSENEN PSMA3 PSMB4 PSMB8 PSMG2 PSTPIP1 PTPRC RAB27A RAC2 RAG1 RAG2 RANBP2 RASGRP1 RBCK1 RECQL4 REL RELA RELB RFWD3 RFX5 RFXANK RFXAP RHOH RIPK1 RLTPR RMRP RNASEH2A RNASEH2B RNASEH2C RNF113A RNF168 RNF31 RNU4ATAC RORC RPGR RPSA RSPH1 RSPH3 RSPH4A RSPH9 RTEL1 SAMD9 SAMD9L SAMHD1 SAR1B SBDS SCO2 SEC61A1 SEMA3E SERPING1 SGPL1 SH2D1A SH3BP2 SH3KBP1 SI SIAE SKIV2L SLC10A2 SLC26A3 SLC29A3 SLC35C1 SLC37A4 SLC39A7 SLC46A1 SLC51B SLC5A1 SLC7A7 SLC9A3 SLX4 SMARCAL1 SMARCD2 SNX10 SP110 SPAG1 SPINK5 SPINT2 SPPL2A SRP54 SRP72 STAT1 STAT2 STAT3 STAT4 STAT5B STIM1 STK36 STK4 STN1 STX11 STX3 STXBP2 TAOK2 TAP1 TAP2 TAPBP TAZ TBX1 TCF3 TCIRG1 TCN2 TERC TERT TFRC TGFB1 TGFBR1 TGFBR2 THBD TICAM1 TIMM50 TINF2 TLR3 TLR7 TMC6 TMC8 TMEM173 TMPRSS15 TNFAIP3 TNFRSF11A TNFRSF13B TNFRSF13C TNFRSF1A TNFRSF4 TNFRSF6B TNFRSF9 TNFSF11 TNFSF12 TONSL TOP2B TP63 TPP2 TRAF3 TRAF3IP2 TREX1 TRNT1 TTC25 TTC37 TTC7A TYK2 UBA1 UNC119 UNC13D UNC45A UNC93B1 UNG USB1 USP18 VAV1 VPS13B VPS45 WAS WDR1 WIPF1 WNT2B WRAP53 XIAP ZAP70 ZBTB24 ZCCHC8 ZMYND10 ZNF341

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Test Description

Associated Conditions

Methodology

Coverage

Ordering information

Limitations

References

Tagged Genes