Documenti di Didattica
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Patien
tientt N
Name
ame DOB Se
Sexx MRN Invitae #
Simón Leiva 01.22.2009 Male 22.928.780-k RQ422787
Clinical T
Team
eam Report D
Daate Sampl
Samplee Sampl
Samplee C
Coll
ollection
ection D
Daate Sampl
Samplee A
Acccession D
Daate
Genometrics Chile 07.24.2018 Type 07.12.2018 07.16.2018
Alfonso Moraga Saliva
Test P
Perf
erformed
ormed Reason ffor
or T
Testing
esting
Sequence analysis and deletion/duplication testing of the 207 genes listed in the Diagnostic test for a personal history of disease
results section below.
• Invitae Primary Immunodeficiency Panel
Summary
Variants of Uncertain Significance identified in CIITA, CR2, PSTPIP1 and RMRP.
Clinical S
Summary
ummary
• A Variant of Uncertain Significance, c.3175G>A (p.Val1059Met), was identified in CIITA.
• The CIITA gene is associated with autosomal recessive major histocompatibility complex class II (MHCII)
deficiency, also known as bare lymphocyte syndrome (BLS), type II (MedGen UID: 444051).
• The clinical significance of this variant is uncertain at this time, although because MHCII deficiency is
autosomal recessive, any single variant is likely insufficient as an explanation for disease. Until this
uncertainty can be resolved, caution should be exercised before using this result to inform clinical
management decisions.
• This variant is not eligible for complimentary family studies as part of our VUS Resolution Program
because the results are unlikely to assist Invitae in reclassifying this particular variant. However, if desired,
testing for this variant in other family members can be ordered at a reduced cost through the Family
Variant Testing Program. Details on our VUS Resolution and Family Variant Testing Programs can be
found at www.invitae.com.
• A Variant of Uncertain Significance, c.2685G>T (p.Trp895Cys), was identified in CR2.
• The CR2 gene currently has no well-established disease association; however, there is preliminary
evidence supporting a correlation with autosomal recessive hypogammaglobulinemia due to CD21
deficiency (PMID: 22035880).
• The clinical significance of this variant is uncertain at this time. Until this uncertainty can be resolved,
caution should be exercised before using this result to inform clinical management decisions.
• This variant is not eligible for complimentary family studies as part of our VUS Resolution Program
because the results are unlikely to assist Invitae in reclassifying this particular variant. However, if desired,
testing for this variant in other family members can be ordered at a reduced cost through the Family
Variant Testing Program. Details on our VUS Resolution and Family Variant Testing Programs can be
found at www.invitae.com.
• A Variant of Uncertain Significance, c.1213C>T (p.Arg405Cys), was identified in PSTPIP1.
• The PSTPIP1 gene is associated with autosomal dominant pyogenic sterile arthritis, pyoderma
gangrenosum, and acne (PAPA) syndrome (MedGen UID: 346801).
• The clinical significance of this variant is uncertain at this time. Until this uncertainty can be resolved,
caution should be exercised before using this result to inform clinical management decisions.
• This variant is not eligible for complimentary family studies as part of our VUS Resolution Program
because the results are unlikely to assist Invitae in reclassifying this particular variant. However, if desired,
testing for this variant in other family members can be ordered at a reduced cost through the Family
Labor
Laboraatory DDir
irect
ector
or Swaroop Aradhya, Ph.D., FACMG 1/6
Invitae 1400 16th Street, San Francisco, CA 94103
E: clientservices@invitae.com P: 415.374.7782 or 800.436.3037
Name DOB
Simón Leiva 01.22.2009
Variant Testing Program. Details on our VUS Resolution and Family Variant Testing Programs can be
found at www.invitae.com.
• A Variant of Uncertain Significance, n.45C>T (RNA change), was identified in RMRP.
• The RMRP gene is associated with autosomal recessive cartilage-hair hypoplasia-anauxetic dysplasia
spectrum disorders (MedGen UID: 375972).
• The clinical significance of this variant is uncertain at this time, although because RMRP-related
conditions are autosomal recessive, any single variant is likely insufficient as an explanation for disease.
Until this uncertainty can be resolved, caution should be exercised before using this result to inform
clinical management decisions.
• This variant is not eligible for complimentary family studies as part of our VUS Resolution Program
because the results are unlikely to assist Invitae in reclassifying this particular variant. However, if desired,
testing for this variant in other family members can be ordered at a reduced cost through the Family
Variant Testing Program. Details on our VUS Resolution and Family Variant Testing Programs can be
found at www.invitae.com.
• These results should be interpreted within the context of additional laboratory results, family history, and clinical
findings. Genetic counseling is recommended to discuss the implications of this result. For access to a network of
genetic providers, please contact Invitae at clientservices@invitae.com, or visit www.nsgc.org or tagc.med.sc.edu/
professional_organizations.asp.
Compl
omplet
etee R
Resul
esults
ts
Gene Varian
ariantt Zy gosity Varian
ariantt Classifica
Classification
tion
The following genes were evaluated for sequence changes and exonic deletions/duplications:
ACD, ACP5, ACTB, ADA, ADA2, ADAM17, ADAR, AICDA, AIRE, AK2, AP3B1, ATM, B2M, BCL10, BLNK, BLOC1S6, BTK, CARD11,
CARD14, CARD9, CASP10, CASP8, CD247, CD27, CD3D, CD3E, CD3G, CD40LG, CD79A, CD79B, CD8A, CEBPE, CHD7, CIITA,
CLPB, COPA, CORO1A, CR2, CSF3R, CTC1, CTLA4, CTPS1, CTSC, CXCR4, CYBA, CYBB, DCLRE1B, DCLRE1C, DKC1, DNMT3B,
DOCK2, DOCK8, ELANE, EPG5, FADD, FAS, FASLG, FERMT3, FOXN1, FOXP3, FPR1, G6PC3, GATA2, GFI1, HAX1, ICOS, IFIH1,
IFNGR1, IFNGR2, IGLL1, IKBKB, IL10, IL10RA, IL10RB, IL12B, IL12RB1, IL17F, IL17RA, IL17RC, IL1RN, IL21, IL21R, IL2RA, IL2RG,
IL36RN, IL7R, IRAK4, IRF7, IRF8, ISG15, ITCH, ITGB2, ITK, JAGN1, JAK3, LAMTOR2, LCK, LIG4, LPIN2, LRBA, LYST, MAGT1, MALT1,
MAP3K14, MEFV, MOGS, MVK, MYD88, NBN, NCF2, NCF4, NFAT5, NFKB2, NFKBIA, NHEJ1, NHP2, NLRC4, NLRP12, NLRP3,
NOD2, NOP10, ORAI1, PARN, PGM3, PIK3CD, PIK3R1, PLCG2, PMS2, PNP, POLE, PRF1, PRKCD, PRKDC, PSMB8, PSTPIP1,
PTPRC, RAB27A, RAC2, RAG1, RAG2, RBCK1, RFX5, RFXANK, RFXAP, RHOH, RMRP, RNASEH2A, RNASEH2B, RNASEH2C, RORC,
RTEL1, SAMHD1, SEMA3E, SH2D1A, SH3BP2, SLC29A3, SLC35C1, SLC37A4, SLC7A7, SMARCAL1, SP110, SPINK5, STAT1, STAT2,
STAT3, STAT5B, STIM1, STK4, STX11, STXBP2, TAP1, TAP2, TAPBP, TAZ, TBK1, TCN2, TERC, TERT, TICAM1, TINF2, TLR3, TMC6,
TMC8, TMEM173, TNFRSF13B, TNFRSF13C, TNFRSF1A, TNFRSF4, TNFSF12, TPP2, TRAF3, TRAF3IP2, TREX1, TRNT1, TTC7A,
TYK2, UNC13D, UNC93B1, UNG, VPS13B, VPS45, WAS, WIPF1, XIAP, ZAP70, ZBTB24
The following genes were evaluated for sequence changes only:
CSF2RA
Results are negative unless otherwise indicated
Benign, Likely Benign, and silent and intronic variants with no evidence towards pathogenicity are not included in this report but are available upon request.
Labor
Laboraatory DDir
irect
ector
or Swaroop Aradhya, Ph.D., FACMG 2/6
Invitae 1400 16th Street, San Francisco, CA 94103
E: clientservices@invitae.com P: 415.374.7782 or 800.436.3037
Name DOB
Simón Leiva 01.22.2009
Varian
ariantt D
Details
etails
CIITA, Exon 17, c.3175G>A (p.Val1059Met), heterozygous, Uncertain Significance
• This sequence change replaces valine with methionine at codon 1059 of the CIITA protein (p.Val1059Met). The
valine residue is weakly conserved and there is a small physicochemical difference between valine and
methionine.
• This variant is present in population databases (rs200742204, ExAC 0.05%).
• This variant has not been reported in the literature in individuals with CIITA-related disease.
• Algorithms developed to predict the effect of missense changes on protein structure and function output the
following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is
found in multiple mammalian species, suggesting that this missense change does not adversely affect protein
function. These predictions have not been confirmed by published functional studies and their clinical
significance is uncertain.
• In summary, the available evidence is currently insufficient to determine the role of this variant in disease.
Therefore, it has been classified as a Variant of Uncertain Significance.
CR2, Exon 14, c.2685G>T (p.Trp895Cys), heterozygous, Uncertain Significance
• This sequence change replaces tryptophan with cysteine at codon 895 of the CR2 protein (p.Trp895Cys). The
tryptophan residue is highly conserved and there is a large physicochemical difference between tryptophan and
cysteine.
• This variant is not present in population databases (ExAC no frequency).
• This variant has not been reported in the literature in individuals with CR2-related disease.
• Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT,
PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not
been confirmed by published functional studies and their clinical significance is uncertain.
• Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may
create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies.
• In summary, the available evidence is currently insufficient to determine the role of this variant in disease.
Therefore, it has been classified as a Variant of Uncertain Significance.
PSTPIP1, Exon 15, c.1213C>T (p.Arg405Cys), heterozygous, Uncertain Significance
• This sequence change replaces arginine with cysteine at codon 405 of the PSTPIP1 protein (p.Arg405Cys). The
arginine residue is moderately conserved and there is a large physicochemical difference between arginine and
cysteine.
• This variant is present in population databases (rs201253322, ExAC 0.1%), and has an allele count higher than
expected for a pathogenic variant (PMID: 28166811).
• This variant has been reported in individuals affected with pyoderma gangrenosum (PMID: 24421327,
26713508). ClinVar contains an entry for this variant (Variation ID: 242307).
• Experimental studies have shown that this missense change causes filipodia like projections in macrophage
podosomes and that macrophages are more chemotactic and invasive in patients with pyoderma gangrenosum.
In addition, in vitro studies have shown that this variant leads to increased WASP activity and induces more
membrane degradation compared to control macrophages (PMID: 24421327).
• In summary, the available evidence is currently insufficient to determine the role of this variant in disease.
Therefore, it has been classified as a Variant of Uncertain Significance.
Labor
Laboraatory DDir
irect
ector
or Swaroop Aradhya, Ph.D., FACMG 3/6
Invitae 1400 16th Street, San Francisco, CA 94103
E: clientservices@invitae.com P: 415.374.7782 or 800.436.3037
Name DOB
Simón Leiva 01.22.2009
Labor
Laboraatory DDir
irect
ector
or Swaroop Aradhya, Ph.D., FACMG 4/6
Invitae 1400 16th Street, San Francisco, CA 94103
E: clientservices@invitae.com P: 415.374.7782 or 800.436.3037
Name DOB
Simón Leiva 01.22.2009
LAMTOR2 (NM_014017.3), LCK (NM_001042771.2), LIG4 (NM_002312.3), LPIN2 (NM_014646.2), LRBA (NM_006726.4), LYST
(NM_000081.3), MAGT1 (NM_032121.5), MALT1 (NM_006785.3), MAP3K14 (NM_003954.4), MEFV (NM_000243.2), MOGS
(NM_006302.2), MVK (NM_000431.3), MYD88 (NM_002468.4), NBN (NM_002485.4), NCF2 (NM_000433.3), NCF4
(NM_013416.3), NFAT5 (NM_138714.3), NFKB2 (NM_001077494.3), NFKBIA (NM_020529.2), NHEJ1 (NM_024782.2), NHP2
(NM_017838.3), NLRC4 (NM_021209.4), NLRP12 (NM_144687.3), NLRP3 (NM_004895.4), NOD2 (NM_022162.2), NOP10
(NM_018648.3), ORAI1 (NM_032790.3), PARN (NM_002582.3), PGM3 (NM_001199917.1), PIK3CD (NM_005026.3), PIK3R1
(NM_181523.2), PLCG2 (NM_002661.4), PMS2 (NM_000535.5), PNP (NM_000270.3), POLE (NM_006231.3), PRF1
(NM_001083116.1), PRKCD (NM_006254.3), PRKDC (NM_006904.6), PSMB8 (NM_148919.3), PSTPIP1 (NM_003978.3), PTPRC
(NM_002838.4), RAB27A (NM_004580.4), RAC2 (NM_002872.4), RAG1 (NM_000448.2), RAG2 (NM_000536.3), RBCK1
(NM_031229.3), RFX5 (NM_000449.3), RFXANK (NM_003721.3), RFXAP (NM_000538.3), RHOH (NM_004310.4), RMRP
(NR_003051.3), RNASEH2A (NM_006397.2), RNASEH2B (NM_024570.3), RNASEH2C (NM_032193.3), RORC (NM_005060.3),
RTEL1 (NM_032957.4), SAMHD1 (NM_015474.3), SEMA3E (NM_012431.2), SH2D1A (NM_002351.4), SH3BP2 (NM_003023.4),
SLC29A3 (NM_018344.5), SLC35C1 (NM_018389.4), SLC37A4 (NM_001164277.1), SLC7A7 (NM_001126106.2), SMARCAL1
(NM_014140.3), SP110 (NM_004509.3), SPINK5 (NM_006846.3), STAT1 (NM_007315.3), STAT2 (NM_005419.3), STAT3
(NM_139276.2), STAT5B (NM_012448.3), STIM1 (NM_003156.3), STK4 (NM_006282.3), STX11 (NM_003764.3), STXBP2
(NM_006949.3), TAP1 (NM_000593.5), TAP2 (NM_000544.3), TAPBP (NM_003190.4), TAZ (NM_000116.4), TBK1 (NM_013254.3),
TCN2 (NM_000355.3), TERC (NR_001566.1), TERT (NM_198253.2), TICAM1 (NM_182919.3), TINF2 (NM_001099274.1), TLR3
(NM_003265.2), TMC6 (NM_007267.7), TMC8 (NM_152468.4), TMEM173 (NM_198282.3), TNFRSF13B (NM_012452.2), TNFRSF13C
(NM_052945.3), TNFRSF1A (NM_001065.3), TNFRSF4 (NM_003327.3), TNFSF12 (NM_003809.2), TPP2 (NM_003291.2), TRAF3
(NM_003300.3), TRAF3IP2 (NM_147686.3), TREX1 (NM_033629.4), TRNT1 (NM_182916.2), TTC7A (NM_020458.3), TYK2
(NM_003331.4), UNC13D (NM_199242.2), UNC93B1 (NM_030930.3), UNG (NM_080911.2), VPS13B (NM_017890.4), VPS45
(NM_007259.4), WAS (NM_000377.2), WIPF1 (NM_001077269.1), XIAP (NM_001167.3), ZAP70 (NM_001079.3), ZBTB24
(NM_014797.2).
• A PMID is a unique identifier referring to a published, scientific paper. Search by PMID at http://www.ncbi.nlm.nih.gov/pubmed.
• An rsID is a unique identifier referring to a single genomic position, and is used to associate population frequency information with
sequence changes at that position. Reported population frequencies are derived from a number of public sites that aggregate data from
large-scale population sequencing projects, including ExAC (http://exac.broadinstitute.org) and dbSNP (http://ncbi.nlm.nih.gov/SNP).
• A MedGen ID is a unique identifier referring to an article in MedGen, NCBI's centralized database of information about genetic disorders
and phenotypes. Search by MedGen ID at http://www.ncbi.nlm.nih.gov/medgen. An OMIM number is a unique identifier referring to a
comprehensive entry in Online Mendelian Inheritance of Man (OMIM). Search by OMIM number at http://omim.org/.
• This assay achieves >99% sensitivity and specificity for single nucleotide variants and insertions and deletions <15bp indels, based on
Limita
Limitations
tions
validation study results. Sensitivity to detect insertions and deletions larger than 15bp but smaller than a full exon may be marginally
reduced. Expansions and contractions within trinucleotide repeat regions may not be detected unless specified. Invitae's deletion/
duplication analysis determines copy number with high confidence at >95% of targeted exons. This methodology may not detect low-
level mosaicism. This report reflects the analysis of an extracted DNA sample. In very rare cases, (circulating hematolymphoid
neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional
genome.
• CORO1A: Deletion/duplication and sequencing analysis is not offered for exon 11 (NM_007074.3).
This rreport
eport has been rreeview
viewed
ed and appr
approoved b
by:
y:
Labor
Laboraatory DDir
irect
ector
or Swaroop Aradhya, Ph.D., FACMG 5/6
Invitae 1400 16th Street, San Francisco, CA 94103
E: clientservices@invitae.com P: 415.374.7782 or 800.436.3037
Name DOB
Simón Leiva 01.22.2009
Disclaimer DNA studies do not constitute a definitive test for the selected condition(s) in all individuals. It should be realized that there are possible
sources of error. Errors can result from trace contamination, rare technical errors, rare genetic variants that interfere with analysis, recent
scientific developments, and alternative classification systems. This test should be one of many aspects used by the healthcare provider to
help with a diagnosis and treatment plan, but it is not a diagnosis itself. This test was developed and its performance characteristics
determined by Invitae. It has not been cleared or approved by the FDA. The laboratory is regulated under the Clinical Laboratory Improvement
Act (CLIA) as qualified to perform high-complexity clinical tests (CLIA IDs: 05D2040778). This test is used for clinical purposes. It should not
be regarded as investigational or for research.
Labor
Laboraatory DDir
irect
ector
or Swaroop Aradhya, Ph.D., FACMG 6/6
Invitae 1400 16th Street, San Francisco, CA 94103
E: clientservices@invitae.com P: 415.374.7782 or 800.436.3037
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