MCID: SVR098
MIFTS: 39

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

Categories: Genetic diseases, Blood diseases, Rare diseases, Immune 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 Negative, 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, autosomal recessive, t cell-negative, b cell-positive, nk cell-negative and immunodeficiency 18. 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 ICos-ICosL Pathway in T-Helper Cell. 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, autosomal recessive, t cell-negative, b cell-positive, nk cell-negative 11.9
2 immunodeficiency 18 9.7 CD3D PTPRC
3 immunodeficiency 17 9.6 CD3D PTPRC
4 t cell deficiency 9.5 IL7R PTPRC
5 demyelinating disease 9.2 IL7R PTPRC
6 combined immunodeficiency, x-linked 9.1 CD3D IL7R PTPRC
7 severe combined immunodeficiency 9.1 CD3D 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
AbdomenSpleen:
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.Thr66Ile VAR_021286 rs1494558
2 IL7R p.Ile138Val VAR_021288 rs1494555
3 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 122)
# 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 IL7R, IVS4, G-A, -1 single nucleotide variant Pathogenic
4 IL7R NM_002185.4(IL7R): c.651G> A (p.Trp217Ter) single nucleotide variant Pathogenic rs104893893 GRCh37 Chromosome 5, 35873695: 35873695
5 IL7R NM_002185.4(IL7R): c.651G> A (p.Trp217Ter) single nucleotide variant Pathogenic rs104893893 GRCh38 Chromosome 5, 35873593: 35873593
6 IL7R NM_002185.4(IL7R): c.394C> T (p.Pro132Ser) single nucleotide variant Pathogenic rs104893894 GRCh37 Chromosome 5, 35871172: 35871172
7 IL7R NM_002185.4(IL7R): c.394C> T (p.Pro132Ser) single nucleotide variant Pathogenic rs104893894 GRCh38 Chromosome 5, 35871070: 35871070
8 PTPRC NM_002838.4(PTPRC): c.1624A> T (p.Lys542Ter) single nucleotide variant Pathogenic rs398122383 GRCh37 Chromosome 1, 198687396: 198687396
9 PTPRC NM_002838.4(PTPRC): c.1624A> T (p.Lys542Ter) single nucleotide variant Pathogenic rs398122383 GRCh38 Chromosome 1, 198718267: 198718267
10 IL7R NM_002185.4(IL7R): c.333T> A (p.Val111=) single nucleotide variant Pathogenic rs199641706 GRCh37 Chromosome 5, 35867519: 35867519
11 IL7R NM_002185.4(IL7R): c.333T> A (p.Val111=) single nucleotide variant Pathogenic rs199641706 GRCh38 Chromosome 5, 35867417: 35867417
12 IL7R NM_002185.4(IL7R): c.361dup (p.Ile121Asnfs) duplication Pathogenic rs869312857 GRCh38 Chromosome 5, 35867445: 35867445
13 IL7R NM_002185.4(IL7R): c.361dup (p.Ile121Asnfs) duplication Pathogenic rs869312857 GRCh37 Chromosome 5, 35867547: 35867547
14 IL7R NC_000005.9 deletion Pathogenic GRCh37 Chromosome 5, 35862009: 35867620
15 IL7R NM_002185.4(IL7R): c.153G> A (p.Ser51=) single nucleotide variant Benign/Likely benign rs149235072 GRCh37 Chromosome 5, 35861024: 35861024
16 IL7R NM_002185.4(IL7R): c.153G> A (p.Ser51=) single nucleotide variant Benign/Likely benign rs149235072 GRCh38 Chromosome 5, 35860922: 35860922
17 IL7R NM_002185.4(IL7R): c.1165G> C (p.Asp389His) single nucleotide variant Uncertain significance rs143596606 GRCh37 Chromosome 5, 35876373: 35876373
18 IL7R NM_002185.4(IL7R): c.1165G> C (p.Asp389His) single nucleotide variant Uncertain significance rs143596606 GRCh38 Chromosome 5, 35876271: 35876271
19 PTPRC NM_002838.4(PTPRC): c.1268C> T (p.Thr423Ile) single nucleotide variant Benign/Likely benign rs6696162 GRCh37 Chromosome 1, 198682178: 198682178
20 PTPRC NM_002838.4(PTPRC): c.1268C> T (p.Thr423Ile) single nucleotide variant Benign/Likely benign rs6696162 GRCh38 Chromosome 1, 198713049: 198713049
21 PTPRC NM_002838.4(PTPRC): c.177C> G (p.Pro59=) single nucleotide variant Benign/Likely benign rs17612648 GRCh37 Chromosome 1, 198665917: 198665917
22 PTPRC NM_002838.4(PTPRC): c.177C> G (p.Pro59=) single nucleotide variant Benign/Likely benign rs17612648 GRCh38 Chromosome 1, 198696788: 198696788
23 PTPRC NM_002838.4(PTPRC): c.3780T> C (p.Asn1260=) single nucleotide variant Benign rs1058191 GRCh37 Chromosome 1, 198725169: 198725169
24 PTPRC NM_002838.4(PTPRC): c.3780T> C (p.Asn1260=) single nucleotide variant Benign rs1058191 GRCh38 Chromosome 1, 198756040: 198756040
25 PTPRC NM_002838.4(PTPRC): c.132A> G (p.Pro44=) single nucleotide variant Benign/Likely benign rs115797104 GRCh37 Chromosome 1, 198665872: 198665872
26 PTPRC NM_002838.4(PTPRC): c.132A> G (p.Pro44=) single nucleotide variant Benign/Likely benign rs115797104 GRCh38 Chromosome 1, 198696743: 198696743
27 PTPRC NM_002838.4(PTPRC): c.1052A> G (p.Asn351Ser) single nucleotide variant Benign rs79141749 GRCh37 Chromosome 1, 198678834: 198678834
28 PTPRC NM_002838.4(PTPRC): c.1052A> G (p.Asn351Ser) single nucleotide variant Benign rs79141749 GRCh38 Chromosome 1, 198709705: 198709705
29 PTPRC NM_002838.4(PTPRC): c.3510-3T> C single nucleotide variant Likely benign rs142096878 GRCh37 Chromosome 1, 198723395: 198723395
30 PTPRC NM_002838.4(PTPRC): c.3510-3T> C single nucleotide variant Likely benign rs142096878 GRCh38 Chromosome 1, 198754266: 198754266
31 IL7R NM_002185.4(IL7R): c.132C> T (p.Ser44=) single nucleotide variant Benign rs11567704 GRCh38 Chromosome 5, 35860901: 35860901
32 IL7R NM_002185.4(IL7R): c.132C> T (p.Ser44=) single nucleotide variant Benign rs11567704 GRCh37 Chromosome 5, 35861003: 35861003
33 IL7R NM_002185.4(IL7R): c.339A> C (p.Glu113Asp) single nucleotide variant Likely benign rs11567735 GRCh37 Chromosome 5, 35867525: 35867525
34 IL7R NM_002185.4(IL7R): c.339A> C (p.Glu113Asp) single nucleotide variant Likely benign rs11567735 GRCh38 Chromosome 5, 35867423: 35867423
35 IL7R NM_002185.4(IL7R): c.778G> A (p.Ala260Thr) single nucleotide variant Conflicting interpretations of pathogenicity rs147153824 GRCh38 Chromosome 5, 35874520: 35874520
36 IL7R NM_002185.4(IL7R): c.778G> A (p.Ala260Thr) single nucleotide variant Conflicting interpretations of pathogenicity rs147153824 GRCh37 Chromosome 5, 35874622: 35874622
37 PTPRC NM_002838.4(PTPRC): c.3670G> A (p.Val1224Ile) single nucleotide variant Conflicting interpretations of pathogenicity rs150672767 GRCh37 Chromosome 1, 198725059: 198725059
38 PTPRC NM_002838.4(PTPRC): c.3670G> A (p.Val1224Ile) single nucleotide variant Conflicting interpretations of pathogenicity rs150672767 GRCh38 Chromosome 1, 198755930: 198755930
39 PTPRC NM_002838.4(PTPRC): c.982A> G (p.Ile328Val) single nucleotide variant Uncertain significance rs41314039 GRCh37 Chromosome 1, 198677339: 198677339
40 PTPRC NM_002838.4(PTPRC): c.982A> G (p.Ile328Val) single nucleotide variant Uncertain significance rs41314039 GRCh38 Chromosome 1, 198708210: 198708210
41 PTPRC NM_002838.4(PTPRC): c.1297G> A (p.Asp433Asn) single nucleotide variant Uncertain significance rs140403368 GRCh37 Chromosome 1, 198685816: 198685816
42 PTPRC NM_002838.4(PTPRC): c.1297G> A (p.Asp433Asn) single nucleotide variant Uncertain significance rs140403368 GRCh38 Chromosome 1, 198716687: 198716687
43 PTPRC NM_002838.4(PTPRC): c.1737G> T (p.Leu579=) single nucleotide variant Likely benign rs112713919 GRCh37 Chromosome 1, 198697485: 198697485
44 PTPRC NM_002838.4(PTPRC): c.1737G> T (p.Leu579=) single nucleotide variant Likely benign rs112713919 GRCh38 Chromosome 1, 198728356: 198728356
45 PTPRC NM_002838.4(PTPRC): c.2395A> T (p.Ile799Phe) single nucleotide variant Uncertain significance rs185420520 GRCh37 Chromosome 1, 198704373: 198704373
46 PTPRC NM_002838.4(PTPRC): c.2395A> T (p.Ile799Phe) single nucleotide variant Uncertain significance rs185420520 GRCh38 Chromosome 1, 198735244: 198735244
47 PTPRC NM_002838.4(PTPRC): c.577A> G (p.Thr193Ala) single nucleotide variant Benign rs4915154 GRCh37 Chromosome 1, 198671653: 198671653
48 PTPRC NM_002838.4(PTPRC): c.577A> G (p.Thr193Ala) single nucleotide variant Benign rs4915154 GRCh38 Chromosome 1, 198702524: 198702524
49 PTPRC NM_002838.4(PTPRC): c.1456A> G (p.Ser486Gly) single nucleotide variant Uncertain significance GRCh37 Chromosome 1, 198687228: 198687228
50 PTPRC NM_002838.4(PTPRC): c.1456A> G (p.Ser486Gly) single nucleotide variant Uncertain significance GRCh38 Chromosome 1, 198718099: 198718099

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 14)
# Super pathways Score Top Affiliating Genes
1
Show member pathways
11.94 CD3D PTPRC
2
Show member pathways
11.9 CD3D PTPRC
3
Show member pathways
11.86 CD3D PTPRC
4
Show member pathways
11.83 CD3D PTPRC
5 11.52 IL7R PTPRC
6
Show member pathways
11.47 CD3D PTPRC
7
Show member pathways
11.44 CD3D PTPRC
8 11.42 IL7R PTPRC
9 11.35 CD3D IL7R
10 11.22 IL7R PTPRC
11 11.14 CD3D PTPRC
12 11.02 IL7R PTPRC
13 10.68 IL7R PTPRC
14 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 external side of plasma membrane GO:0009897 8.96 IL7R PTPRC
2 clathrin-coated vesicle membrane GO:0030665 8.62 CD3D IL7R

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 T cell receptor signaling pathway GO:0050852 9.37 CD3D PTPRC
2 cell surface receptor signaling pathway GO:0007166 9.33 CD3D IL7R PTPRC
3 membrane organization GO:0061024 9.32 CD3D IL7R
4 B cell proliferation GO:0042100 9.26 IL7R PTPRC
5 negative regulation of T cell mediated cytotoxicity GO:0001915 8.96 IL7R PTPRC
6 T cell differentiation GO:0030217 8.8 CD3D IL7R PTPRC

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

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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