T B NK SCID
MCID: SVR098
MIFTS: 40

Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive (T B NK SCID)

Categories: Blood diseases, Genetic diseases, Immune diseases, Rare diseases

Aliases & Classifications for Severe Combined Immunodeficiency, Autosomal Recessive, T...

MalaCards integrated aliases for Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

Name: Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive 57 12 29 6 40
Severe Combined Immunodeficiency, T Cell-Negative, B-Cell/natural Killer-Cell Positive 57 13
Severe Combined Immunodeficiency Autosomal Recessive T-Cell-Negative/b-Cell-Positive/nk-Cell-Positive 75
Severe Combined Immunodeficiency Autosomal Recessive T Cell-Negative/b Cell-Positive/nk Cell-Positive 75
Severe Combined Immunodeficiency Autosomal Recessive T-Cell Negative/b-Cell Positive/nk-Cell Positive 75
Severe Combined Immunodeficiency, T-Cell Negative, B-Cell/natural Killer Cell-Positive Type 57
Scid, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive 57
Autosomal Recessive T Cell-Negative, B-Cell Positive, Nk Cell-Positive Scid 12
T-B+ Severe Combined Immunodeficiency Due to Il-7ralpha Deficiency 59
T-B+ Severe Combined Immunodeficiency Due to Cd45 Deficiency 59
T-B+ Scid Due to Il-7ralpha Deficiency 59
T-B+ Scid Due to Cd45 Deficiency 59
T B Nk Scid 75
Scidbnk 75

Characteristics:

Orphanet epidemiological data:

59

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
presents at 2 to 3 months of age
death within several months if untreated


HPO:

32
severe combined immunodeficiency, autosomal recessive, t cell-negative, b cell-positive, nk cell-positive:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 59  
Rare immunological diseases


External Ids:

OMIM 57 608971
Disease Ontology 12 DOID:0090014
ICD10 33 D81.2
UMLS via Orphanet 74 C1837028
ICD10 via Orphanet 34 D81.2
MedGen 42 C1837028
MeSH 44 D016511

Summaries for Severe Combined Immunodeficiency, Autosomal Recessive, T...

UniProtKB/Swiss-Prot : 75 Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive: A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development.

MalaCards based summary : Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive, also known as severe combined immunodeficiency, t cell-negative, b-cell/natural killer-cell positive, is related to severe combined immunodeficiency and severe combined immunodeficiency, autosomal recessive, t cell-negative, b cell-positive, nk cell-negative. An important gene associated with Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive is IL7R (Interleukin 7 Receptor), and among its related pathways/superpathways are T cell receptor signaling pathway and JAK-STAT signaling pathway (KEGG). Affiliated tissues include t cells, b cells and nk cells, and related phenotypes are splenomegaly and hepatomegaly

Disease Ontology : 12 A severe combined immunodeficiency characterized by being T cell-negative, B cell-positive and natural killer cell-positive and that has material basis in homozygous or compound heterozygous mutation in the IL7R gene on chromosome 5p13 or the CD45 gene on chromosome 1q31.

Description from OMIM: 608971

Related Diseases for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Diseases related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 severe combined immunodeficiency 29.4 CD3D IL7R PTPRC
2 severe combined immunodeficiency, autosomal recessive, t cell-negative, b cell-positive, nk cell-negative 11.9
3 jak3-deficient severe combined immunodeficiency 11.5
4 interleukin-7 receptor alpha deficiency 11.4
5 combined t cell and b cell immunodeficiency 10.0
6 t cell deficiency 9.8 IL7R PTPRC
7 immunodeficiency 18 9.8 CD3D PTPRC
8 immunodeficiency 17 9.8 CD3D PTPRC
9 demyelinating disease 9.8 IL7R PTPRC

Graphical network of the top 20 diseases related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:



Diseases related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive

Symptoms & Phenotypes for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Symptoms via clinical synopsis from OMIM:

57
Abdomen Spleen:
splenomegaly

Abdomen Gastrointestinal:
diarrhea

Immunology:
lymphadenopathy
frequent opportunistic infections
normal or elevated numbers of functional natural killer cells (nk)
normal or elevated number of peripheral blood b cells
absent peripheral blood t cells
more
Growth Other:
failure to thrive secondary to recurrent infections

Respiratory Lung:
recurrent acute pneumonia

Abdomen Liver:
hepatomegaly

Head And Neck Ears:
otitis media

Skin Nails Hair Skin:
dermatitis

Head And Neck Mouth:
candida albicans infection
thrush


Clinical features from OMIM:

608971

Human phenotypes related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

32 (show all 11)
# Description HPO Frequency HPO Source Accession
1 splenomegaly 32 HP:0001744
2 hepatomegaly 32 HP:0002240
3 diarrhea 32 HP:0002014
4 otitis media 32 HP:0000388
5 eczema 32 HP:0000964
6 lymphadenopathy 32 HP:0002716
7 decrease in t cell count 32 HP:0005403
8 oral ulcer 32 HP:0000155
9 severe combined immunodeficiency 32 HP:0004430
10 recurrent opportunistic infections 32 HP:0005390
11 failure to thrive secondary to recurrent infections 32 HP:0008866

GenomeRNAi Phenotypes related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive according to GeneCards Suite gene sharing:

26 (show all 12)
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Increased shRNA abundance (Z-score > 2) GR00366-A-105 9.44 PTPRC
2 Increased shRNA abundance (Z-score > 2) GR00366-A-121 9.44 PTPRC
3 Increased shRNA abundance (Z-score > 2) GR00366-A-143 9.44 IL7R
4 Increased shRNA abundance (Z-score > 2) GR00366-A-149 9.44 PTPRC
5 Increased shRNA abundance (Z-score > 2) GR00366-A-156 9.44 IL7R
6 Increased shRNA abundance (Z-score > 2) GR00366-A-189 9.44 IL7R
7 Increased shRNA abundance (Z-score > 2) GR00366-A-197 9.44 IL7R
8 Increased shRNA abundance (Z-score > 2) GR00366-A-2 9.44 IL7R PTPRC
9 Increased shRNA abundance (Z-score > 2) GR00366-A-214 9.44 PTPRC
10 Increased shRNA abundance (Z-score > 2) GR00366-A-41 9.44 PTPRC
11 Increased shRNA abundance (Z-score > 2) GR00366-A-43 9.44 IL7R
12 Increased shRNA abundance (Z-score > 2) GR00366-A-50 9.44 PTPRC

Drugs & Therapeutics for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Search Clinical Trials , NIH Clinical Center for Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive

Genetic Tests for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Genetic tests related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

# Genetic test Affiliating Genes
1 Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive 29 IL7R PTPRC

Anatomical Context for Severe Combined Immunodeficiency, Autosomal Recessive, T...

MalaCards organs/tissues related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

41
T Cells, B Cells, Nk Cells, Bone, Bone Marrow

Publications for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Articles related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

# Title Authors Year
1
A novel pathogenic frameshift variant of CD3E gene in two T-B+ NK+ SCID patients from Turkey. ( 28597365 )
2017
2
Genotype, phenotype, and outcomes of nine patients with T-B+NK+ SCID. ( 21883749 )
2011
3
A novel missense RAG-1 mutation results in T-B-NK+ SCID in Athabascan-speaking Dine Indians from the Canadian Northwest Territories. ( 18701881 )
2009
4
A novel DKC1 mutation, severe combined immunodeficiency (T+B-NK-SCID) and bone marrow transplantation in an infant with Hoyeraal-Hreidarsson syndrome. ( 12437656 )
2002

Variations for Severe Combined Immunodeficiency, Autosomal Recessive, T...

UniProtKB/Swiss-Prot genetic disease variations for Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

75
# Symbol AA change Variation ID SNP ID
1 IL7R p.Pro132Ser VAR_034870

ClinVar genetic disease variations for Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive:

6 (show top 50) (show all 216)
# Gene Variation Type Significance SNP ID Assembly Location
1 PTPRC PTPRC, IVS13DS, G-A, +1 single nucleotide variant Pathogenic
2 PTPRC PTPRC, 6-BP DEL, NT1168 deletion Pathogenic
3 IL7R NM_002185.3(IL7R): c.197T> C (p.Ile66Thr) single nucleotide variant Benign rs1494558 GRCh37 Chromosome 5, 35861068: 35861068
4 IL7R NM_002185.3(IL7R): c.197T> C (p.Ile66Thr) single nucleotide variant Benign rs1494558 GRCh38 Chromosome 5, 35860966: 35860966
5 IL7R NM_002185.3(IL7R): c.412G> A (p.Val138Ile) single nucleotide variant Benign rs1494555 GRCh37 Chromosome 5, 35871190: 35871190
6 IL7R NM_002185.3(IL7R): c.412G> A (p.Val138Ile) single nucleotide variant Benign rs1494555 GRCh38 Chromosome 5, 35871088: 35871088
7 IL7R IL7R, IVS4, G-A, -1 single nucleotide variant Pathogenic
8 IL7R NM_002185.4(IL7R): c.651G> A (p.Trp217Ter) single nucleotide variant Pathogenic rs104893893 GRCh37 Chromosome 5, 35873695: 35873695
9 IL7R NM_002185.4(IL7R): c.651G> A (p.Trp217Ter) single nucleotide variant Pathogenic rs104893893 GRCh38 Chromosome 5, 35873593: 35873593
10 IL7R NM_002185.4(IL7R): c.394C> T (p.Pro132Ser) single nucleotide variant Pathogenic rs104893894 GRCh37 Chromosome 5, 35871172: 35871172
11 IL7R NM_002185.4(IL7R): c.394C> T (p.Pro132Ser) single nucleotide variant Pathogenic rs104893894 GRCh38 Chromosome 5, 35871070: 35871070
12 IL7R NM_002185.4(IL7R): c.617G> A (p.Arg206Gln) single nucleotide variant Conflicting interpretations of pathogenicity rs193922644 GRCh37 Chromosome 5, 35873661: 35873661
13 IL7R NM_002185.4(IL7R): c.617G> A (p.Arg206Gln) single nucleotide variant Conflicting interpretations of pathogenicity rs193922644 GRCh38 Chromosome 5, 35873559: 35873559
14 PTPRC NM_002838.4(PTPRC): c.1624A> T (p.Lys542Ter) single nucleotide variant Pathogenic rs398122383 GRCh37 Chromosome 1, 198687396: 198687396
15 PTPRC NM_002838.4(PTPRC): c.1624A> T (p.Lys542Ter) single nucleotide variant Pathogenic rs398122383 GRCh38 Chromosome 1, 198718267: 198718267
16 IL7R NM_002185.4(IL7R): c.662G> T (p.Ser221Ile) single nucleotide variant Conflicting interpretations of pathogenicity rs587778405 GRCh37 Chromosome 5, 35873706: 35873706
17 IL7R NM_002185.4(IL7R): c.662G> T (p.Ser221Ile) single nucleotide variant Conflicting interpretations of pathogenicity rs587778405 GRCh38 Chromosome 5, 35873604: 35873604
18 IL7R NM_002185.4(IL7R): c.760G> A (p.Ala254Thr) single nucleotide variant Uncertain significance rs137868226 GRCh37 Chromosome 5, 35874604: 35874604
19 IL7R NM_002185.4(IL7R): c.760G> A (p.Ala254Thr) single nucleotide variant Uncertain significance rs137868226 GRCh38 Chromosome 5, 35874502: 35874502
20 IL7R NM_002185.4(IL7R): c.1043A> C (p.Asn348Thr) single nucleotide variant Benign rs41270321 GRCh37 Chromosome 5, 35876251: 35876251
21 IL7R NM_002185.4(IL7R): c.1043A> C (p.Asn348Thr) single nucleotide variant Benign rs41270321 GRCh38 Chromosome 5, 35876149: 35876149
22 IL7R NM_002185.4(IL7R): c.1231A> G (p.Thr411Ala) single nucleotide variant Benign/Likely benign rs115316501 GRCh37 Chromosome 5, 35876439: 35876439
23 IL7R NM_002185.4(IL7R): c.1231A> G (p.Thr411Ala) single nucleotide variant Benign/Likely benign rs115316501 GRCh38 Chromosome 5, 35876337: 35876337
24 IL7R NM_002185.4(IL7R): c.1241C> T (p.Thr414Met) single nucleotide variant Benign/Likely benign rs2229232 GRCh37 Chromosome 5, 35876449: 35876449
25 IL7R NM_002185.4(IL7R): c.1241C> T (p.Thr414Met) single nucleotide variant Benign/Likely benign rs2229232 GRCh38 Chromosome 5, 35876347: 35876347
26 IL7R NM_002185.4(IL7R): c.1096T> C (p.Ser366Pro) single nucleotide variant Uncertain significance rs201671392 GRCh37 Chromosome 5, 35876304: 35876304
27 IL7R NM_002185.4(IL7R): c.1096T> C (p.Ser366Pro) single nucleotide variant Uncertain significance rs201671392 GRCh38 Chromosome 5, 35876202: 35876202
28 IL7R NM_002185.4(IL7R): c.1357T> C (p.Ser453Pro) single nucleotide variant Uncertain significance rs141919625 GRCh37 Chromosome 5, 35876565: 35876565
29 IL7R NM_002185.4(IL7R): c.1357T> C (p.Ser453Pro) single nucleotide variant Uncertain significance rs141919625 GRCh38 Chromosome 5, 35876463: 35876463
30 IL7R NM_002185.4(IL7R): c.561G> A (p.Lys187=) single nucleotide variant Benign/Likely benign rs11567764 GRCh38 Chromosome 5, 35873503: 35873503
31 IL7R NM_002185.4(IL7R): c.561G> A (p.Lys187=) single nucleotide variant Benign/Likely benign rs11567764 GRCh37 Chromosome 5, 35873605: 35873605
32 PTPRC NM_002838.4(PTPRC): c.3402C> T (p.Pro1134=) single nucleotide variant Benign rs61757805 GRCh37 Chromosome 1, 198721794: 198721794
33 PTPRC NM_002838.4(PTPRC): c.3402C> T (p.Pro1134=) single nucleotide variant Benign rs61757805 GRCh38 Chromosome 1, 198752665: 198752665
34 PTPRC NM_002838.4(PTPRC): c.367G> C (p.Asp123His) single nucleotide variant Benign rs41269905 GRCh37 Chromosome 1, 198668761: 198668761
35 PTPRC NM_002838.4(PTPRC): c.367G> C (p.Asp123His) single nucleotide variant Benign rs41269905 GRCh38 Chromosome 1, 198699632: 198699632
36 PTPRC NM_002838.4(PTPRC): c.886A> C (p.Ile296Leu) single nucleotide variant Benign rs2230606 GRCh37 Chromosome 1, 198676063: 198676063
37 PTPRC NM_002838.4(PTPRC): c.886A> C (p.Ile296Leu) single nucleotide variant Benign rs2230606 GRCh38 Chromosome 1, 198706934: 198706934
38 PTPRC NM_002838.4(PTPRC): c.1029G> A (p.Gln343=) single nucleotide variant Benign rs41314043 GRCh37 Chromosome 1, 198677386: 198677386
39 PTPRC NM_002838.4(PTPRC): c.1029G> A (p.Gln343=) single nucleotide variant Benign rs41314043 GRCh38 Chromosome 1, 198708257: 198708257
40 PTPRC NM_002838.4(PTPRC): c.1710T> A (p.His570Gln) single nucleotide variant Benign rs12136658 GRCh37 Chromosome 1, 198691595: 198691595
41 PTPRC NM_002838.4(PTPRC): c.1710T> A (p.His570Gln) single nucleotide variant Benign rs12136658 GRCh38 Chromosome 1, 198722466: 198722466
42 PTPRC NM_002838.4(PTPRC): c.3545T> C (p.Leu1182Ser) single nucleotide variant Uncertain significance rs114970039 GRCh38 Chromosome 1, 198754304: 198754304
43 PTPRC NM_002838.4(PTPRC): c.3545T> C (p.Leu1182Ser) single nucleotide variant Uncertain significance rs114970039 GRCh37 Chromosome 1, 198723433: 198723433
44 IL7R NM_002185.4(IL7R): c.333T> A (p.Val111=) single nucleotide variant Pathogenic rs199641706 GRCh37 Chromosome 5, 35867519: 35867519
45 IL7R NM_002185.4(IL7R): c.333T> A (p.Val111=) single nucleotide variant Pathogenic rs199641706 GRCh38 Chromosome 5, 35867417: 35867417
46 IL7R NM_002185.4(IL7R): c.361dup (p.Ile121Asnfs) duplication Pathogenic rs869312857 GRCh38 Chromosome 5, 35867445: 35867445
47 IL7R NM_002185.4(IL7R): c.361dup (p.Ile121Asnfs) duplication Pathogenic rs869312857 GRCh37 Chromosome 5, 35867547: 35867547
48 IL7R NC_000005.9 deletion Pathogenic GRCh37 Chromosome 5, 35862009: 35867620
49 IL7R NM_002185.4(IL7R): c.153G> A (p.Ser51=) single nucleotide variant Benign/Likely benign rs149235072 GRCh37 Chromosome 5, 35861024: 35861024
50 IL7R NM_002185.4(IL7R): c.153G> A (p.Ser51=) single nucleotide variant Benign/Likely benign rs149235072 GRCh38 Chromosome 5, 35860922: 35860922

Expression for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Search GEO for disease gene expression data for Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive.

Pathways for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Pathways related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive according to GeneCards Suite gene sharing:

(show all 16)
# Super pathways Score Top Affiliating Genes
1
Show member pathways
11.96 CD3D PTPRC
2
Show member pathways
11.92 IL7R PTPRC
3
Show member pathways
11.92 CD3D PTPRC
4
Show member pathways
11.87 CD3D PTPRC
5
Show member pathways
11.84 CD3D PTPRC
6 11.52 IL7R PTPRC
7
Show member pathways
11.47 CD3D PTPRC
8
Show member pathways
11.44 CD3D PTPRC
9 11.42 IL7R PTPRC
10 11.35 CD3D IL7R
11 11.22 IL7R PTPRC
12 11.14 CD3D PTPRC
13 11.1 CD3D PTPRC
14 11.02 IL7R PTPRC
15 10.68 IL7R PTPRC
16 10.37 CD3D IL7R PTPRC

GO Terms for Severe Combined Immunodeficiency, Autosomal Recessive, T...

Cellular components related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 clathrin-coated vesicle membrane GO:0030665 8.96 CD3D IL7R
2 external side of plasma membrane GO:0009897 8.8 CD3D IL7R PTPRC

Biological processes related to Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Positive, Nk Cell-Positive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 cell surface receptor signaling pathway GO:0007166 9.43 CD3D IL7R PTPRC
2 membrane organization GO:0061024 9.4 CD3D IL7R
3 T cell receptor signaling pathway GO:0050852 9.37 CD3D PTPRC
4 B cell proliferation GO:0042100 9.32 IL7R PTPRC
5 positive thymic T cell selection GO:0045059 9.16 CD3D PTPRC
6 negative regulation of T cell mediated cytotoxicity GO:0001915 8.96 IL7R PTPRC
7 T cell differentiation GO:0030217 8.8 CD3D IL7R PTPRC

Sources for Severe Combined Immunodeficiency, Autosomal Recessive, T...

3 CDC
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9 Cosmic
10 dbSNP
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17 ExPASy
19 FMA
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29 GTR
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34 ICD10 via Orphanet
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44 MeSH
45 MESH via Orphanet
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58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
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74 UMLS via Orphanet
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