Database CD3Dbase
Version 1.0
File cd3dpub.html
Date 20-Jun-2007
Curator Mauno Vihinen
Address Protein Structure and Bioinformatics
Address Lund University, BMC D10, SE-22184 Lund, Sweden
Phone +46 72 526 0022
Fax +46 46 222 9328
Email Mauno Vihinen
URL http://structure.bmc.lu.se/idbase/CD3Dbase/
IDR factfile http://structure.bmc.lu.se/idbase/IDRefSeq/xml/idr/ff/FF111.html
Gene CD3D
Disease Autosomal recessive CD3delta deficiency
OMIM 186790
Sequence IDRefSeq:D0014; IDRefSeq:C0014; UniProt:P04234
Numbering start of the entry
Funding Tampere University Hospital Medical Research Fund
Funding European Union
Comments sequence entry reference in every entry
//
ID R68X(1a),R68X(1a); standard; MUTATION; EC,EC
Accession C0001
Systematic name Allele 1 and 2: g.2604C>T, c.202C>T, r.202c>u, p.Arg68X
Original code Patient 1
Description Allele 1 and 2: a point mutation in the exon 2 leading to a
Description premature stop codon in the EC domain
Date 13-Feb-2004 (Rel. 1, Created)
Date 13-Feb-2004 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 14602880
RefAuthors Dadi, H. K., Simon, A. J., Roifman, C. M.
RefTitle Effect of CD3delta deficiency on maturation of alpha/beta
RefTitle and gamma/delta T-cell lineages in severe combined
RefTitle immunodeficiency.
RefLoc N Engl J Med 349:1821-1828 (2003)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 3
Feature /rnalink: 2
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 6
Feature /rnalink: 5
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
Sex XX
Parents Consanguineous
IgA 0.3
IgG 4.7
IgM 0.4
CD3 0.3
CD4 0
CD8 0
Treatment Bone marrow transplantation: Yes
Treatment Outcome: alive and well
Relative CD3Dbase; C0002 cousin
Relative CD3Dbase; C0003 cousin
//
ID R68X(1b),R68X(1b); standard; MUTATION; EC,EC
Accession C0002
Systematic name Allele 1 and 2: g.2604C>T, c.202C>T, r.202c>u, p.Arg68X
Original code Patient 2
Description Allele 1 and 2: a point mutation in the exon 2 leading to a
Description premature stop codon in the EC domain
Date 13-Feb-2004 (Rel. 1, Created)
Date 13-Feb-2004 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 14602880
RefAuthors Dadi, H. K., Simon, A. J., Roifman, C. M.
RefTitle Effect of CD3delta deficiency on maturation of alpha/beta
RefTitle and gamma/delta T-cell lineages in severe combined
RefTitle immunodeficiency.
RefLoc N Engl J Med 349:1821-1828 (2003)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 3
Feature /rnalink: 2
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 6
Feature /rnalink: 5
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
Sex XY
Parents Consanguineous
IgA 0.5
IgG 3.8
IgM 0.3
CD3 0.1
CD4 0
CD8 0
Treatment No bone marrow transplantation
Relative CD3Dbase; C0001 cousin
Relative CD3Dbase; C0003 cousin
//
ID R68X(1c),R68X(1c); standard; MUTATION; EC,EC
Accession C0003
Systematic name Allele 1 and 2: g.2604C>T, c.202C>T, r.202c>u, p.Arg68X
Original code Patient 3
Description Allele 1 and 2: a point mutation in the exon 2 leading to a
Description premature stop codon in the EC domain
Date 13-Feb-2004 (Rel. 1, Created)
Date 13-Feb-2004 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 14602880
RefAuthors Dadi, H. K., Simon, A. J., Roifman, C. M.
RefTitle Effect of CD3delta deficiency on maturation of alpha/beta
RefTitle and gamma/delta T-cell lineages in severe combined
RefTitle immunodeficiency.
RefLoc N Engl J Med 349:1821-1828 (2003)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 3
Feature /rnalink: 2
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 6
Feature /rnalink: 5
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
Sex XY
Parents Consanguineous
IgA 0.2
IgG 2.5
IgM 0.6
CD3 0.6
CD4 0
CD8 0
Relative CD3Dbase; C0001 cousin
Relative CD3Dbase; C0002 cousin
//
ID R68X(2),R68X(2); standard; MUTATION; EC,EC
Accession C0007
Systematic name Allele 1 and 2: g.2604C>T, c.202C>T, r.202c>u, , p.Arg68X
Original code PIII-1
Description Allele 1 and 2: A point mutation in the exon 2 leading to a
Description premature stop codon in the EC domain
Date 13-Sep-2006 (Rel. 1, Created)
Date 13-Sep-2006 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 15546002
RefAuthors de Saint Basile, G., Geissmann, F., Flori, E., Uring-
RefAuthors Lambert, B., Soudais, C., Cavazzana-Calvo, M., Durandy,
RefAuthors A., Jabado, N., Fischer, A., Le Deist, F.
RefTitle Severe combined immunodeficiency caused by deficiency in
RefTitle either the delta or the epsilon subunit of CD3.
RefLoc J Clin Invest:1512-1517 (2004)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 3
Feature /rnalink: 2
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 2604
Feature /change: c -> t
Feature /CpG; 1
Feature /genomic_region: exon; 2
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 202
Feature /codon: cga -> tga; 1
Feature aa; 6
Feature /rnalink: 5
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 68
Feature /change: R -> X
Feature /domain: EC
Symptoms T-B+NK+ SCID phenotype
Sex XY
Parents Consanguineous
Treatment Bone marrow transplantation: Yes
Comment The patient received a haploidentical BMT from his mother
Comment but died from EBV infection 30 days after BMT.
//
ID C93X(1),C93X(1); standard; MUTATION; EC,EC
Accession C0004
Systematic name Allele 1 and 2: g.3149C>A, c.279C>A, r.279c>a, p.Cys93X
Original code PII-2
Description Allele 1 and 2: a point mutation in the exon 3 leading to a
Description premature stop codon in the EC domain
Date 17-May-2005 (Rel. 1, Created)
Date 17-May-2005 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 15546002
RefAuthors de Saint Basile, G., Geissmann, F., Flori, E., Uring-
RefAuthors Lambert, B., Soudais, C., Cavazzana-Calvo, M., Durandy,
RefAuthors A., Jabado, N., Fischer, A., Le Deist, F.
RefTitle Severe combined immunodeficiency caused by deficiency in
RefTitle either the delta or the epsilon subunit of CD3.
RefLoc J Clin Invest 114:1512-1517 (2004)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 3149
Feature /change: c -> a
Feature /genomic_region: exon; 3
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 279
Feature /codon: tgc -> tga; 3
Feature aa; 3
Feature /rnalink: 2
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 93
Feature /change: C -> X
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 3149
Feature /change: c -> a
Feature /genomic_region: exon; 3
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: nonsense
Feature /loc: IDRefSeq: C0014: 279
Feature /codon: tgc -> tga; 3
Feature aa; 6
Feature /rnalink: 5
Feature /name: out of frame translation; premature termination
Feature /loc: UniProt: P04234; CD3D_HUMAN: 93
Feature /change: C -> X
Feature /domain: EC
Sex XX
Parents Consanguineous
CD3 <1
CD4 <1
CD8 17
CD19 55
Treatment Bone marrow transplantation: Yes
Comment Patient died 6 months after BMT from a disseminated
Comment Aspergillus infection.
//
ID Intron 2(1a),Intron 2(1a); standard; MUTATION;
Accession C0005
Systematic name Allele 1 and 2: g.IVS2-2A>G, c.275-2A>G, r.275-2a>g,
Original code Patient 1
Description Allele 1 and 2: a point mutation in the intron 2 leading to
Description an amino acid change
Date 23-Sep-2005 (Rel. 1, Created)
Date 23-Sep-2005 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 15729559
RefAuthors Takada, H., Nomura, A., Roifman, C. M., Hara, T.
RefTitle Severe combined immunodeficiency caused by a splicing
RefTitle abnormality of the CD3delta gene.
RefLoc Eur J Pediatr 164:311-314 (2005)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 3143
Feature /change: a -> g
Feature /genomic_region: intron; 2
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: inframe deletion
Feature /loc: IDRefSeq: C0014: 275..406
Feature /change: -tgtgccagag ctgtgtggag ctggatccag ccaccgtggc
Feature /change: tggcatcatt gtcactgatg tcattgccac tctgctcctt
Feature /change: gctttgggag tcttctgctt tgctggacat gagactggaa
Feature /change: ggctgtctgg gg
Feature /note: skipping of exon 3
Feature /inexloc: -2
Feature aa; 3
Feature /rnalink: 2
Feature /name: deletion; inframe
Feature /loc: UniProt: P04234; CD3D_HUMAN: 92..136
Feature /change: MCQSCVELDP ATVAGIIVTD VIATLLLALG VFCFAGHETG
Feature /change: RLSGA
Feature /change: ->
Feature /change: T
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 3143
Feature /change: a -> g
Feature /genomic_region: intron; 2
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: inframe deletion
Feature /loc: IDRefSeq: C0014: 275..406
Feature /change: -tgtgccagag ctgtgtggag ctggatccag ccaccgtggc
Feature /change: tggcatcatt gtcactgatg tcattgccac tctgctcctt
Feature /change: gctttgggag tcttctgctt tgctggacat gagactggaa
Feature /change: ggctgtctgg gg
Feature /note: skipping of exon 3
Feature /inexloc: -2
Feature aa; 6
Feature /rnalink: 5
Feature /name: deletion; inframe
Feature /loc: UniProt: P04234; CD3D_HUMAN: 92..136
Feature /change: MCQSCVELDP ATVAGIIVTD VIATLLLALG VFCFAGHETG
Feature /change: RLSGA
Feature /change: ->
Feature /change: T
Feature /domain: EC
Symptoms SCID accompanied with severe cytomegalovirus pneumonitis
Sex XX
Ethnic origin Mongoloid; Japan
Parents Non-consanguineous
Relative CD3Dbase; C0006 brother
Comment Although the patient received stem cell transplantation,
Comment she died from generalized cytomegalovirus infection
//
ID Intron 2(1b),Intron 2(1b); standard; MUTATION;
Accession C0006
Systematic name Allele 1 and 2: g.IVS2-2A>G, c.275-2A>G, r.275-2a>g,
Original code Patient 2
Description Allele 1 and 2: a point mutation in the intron 2 leading to
Description an amino acid change
Date 23-Sep-2005 (Rel. 1, Created)
Date 23-Sep-2005 (Rel. 1, Last updated, Version 1)
RefNumber [1]
RefCrossRef PUBMED; 15729559
RefAuthors Takada, H., Nomura, A., Roifman, C. M., Hara, T.
RefTitle Severe combined immunodeficiency caused by a splicing
RefTitle abnormality of the CD3delta gene.
RefLoc Eur J Pediatr 164:311-314 (2005)
FeatureHeader allele; 1
Feature dna; 1
Feature /rnalink: 2
Feature /name: point
Feature /loc: IDRefSeq: D0014: 3143
Feature /change: a -> g
Feature /genomic_region: intron; 2
Feature rna; 2
Feature /dnalink: 1
Feature /aalink: 3
Feature /name: inframe deletion
Feature /loc: IDRefSeq: C0014: 275..406
Feature /change: -tgtgccagag ctgtgtggag ctggatccag ccaccgtggc
Feature /change: tggcatcatt gtcactgatg tcattgccac tctgctcctt
Feature /change: gctttgggag tcttctgctt tgctggacat gagactggaa
Feature /change: ggctgtctgg gg
Feature /note: skipping of exon 3
Feature /inexloc: -2
Feature aa; 3
Feature /rnalink: 2
Feature /name: deletion; inframe
Feature /loc: UniProt: P04234; CD3D_HUMAN: 92..136
Feature /change: MCQSCVELDP ATVAGIIVTD VIATLLLALG VFCFAGHETG
Feature /change: RLSGA
Feature /change: ->
Feature /change: T
Feature /domain: EC
FeatureHeader allele; 2
Feature dna; 4
Feature /rnalink: 5
Feature /name: point
Feature /loc: IDRefSeq: D0014: 3143
Feature /change: a -> g
Feature /genomic_region: intron; 2
Feature rna; 5
Feature /dnalink: 4
Feature /aalink: 6
Feature /name: inframe deletion
Feature /loc: IDRefSeq: C0014: 275..406
Feature /change: -tgtgccagag ctgtgtggag ctggatccag ccaccgtggc
Feature /change: tggcatcatt gtcactgatg tcattgccac tctgctcctt
Feature /change: gctttgggag tcttctgctt tgctggacat gagactggaa
Feature /change: ggctgtctgg gg
Feature /note: skipping of exon 3
Feature /inexloc: -2
Feature aa; 6
Feature /rnalink: 5
Feature /name: deletion; inframe
Feature /loc: UniProt: P04234; CD3D_HUMAN: 92..136
Feature /change: MCQSCVELDP ATVAGIIVTD VIATLLLALG VFCFAGHETG
Feature /change: RLSGA
Feature /change: ->
Feature /change: T
Feature /domain: EC
Symptoms SCID
Sex XY
Ethnic origin Mongoloid; Japan
Parents Non-consanguineous
Relative CD3Dbase; C0005 sister
Comment Patient is doing well after the cord blood stem cell
Comment transplantation
//
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