MCID: IMM034
MIFTS: 37

Immunodeficiency, Common Variable, 2

Categories: Genetic diseases, Immune diseases

Aliases & Classifications for Immunodeficiency, Common Variable, 2

MalaCards integrated aliases for Immunodeficiency, Common Variable, 2:

Name: Immunodeficiency, Common Variable, 2 57 75 13 73
Hypogammaglobulinemia Due to Taci Deficiency 57 75
Antibody Deficiency Due to Taci Defect 57 75
Common Variable Immunodeficiency 2 29 6
Cvid2 57 75
Immunodeficiency, Variable, Common, Type 2 40

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive
autosomal dominant

Miscellaneous:
onset in first or second decades


HPO:

32
immunodeficiency, common variable, 2:
Inheritance autosomal recessive inheritance autosomal dominant inheritance


Classifications:



Summaries for Immunodeficiency, Common Variable, 2

UniProtKB/Swiss-Prot : 75 Immunodeficiency, common variable, 2: A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low.

MalaCards based summary : Immunodeficiency, Common Variable, 2, also known as hypogammaglobulinemia due to taci deficiency, is related to primary agammaglobulinemia and cryptococcal meningitis, and has symptoms including diarrhea An important gene associated with Immunodeficiency, Common Variable, 2 is TNFRSF13B (TNF Receptor Superfamily Member 13B), and among its related pathways/superpathways are Allograft rejection and RANK Signaling in Osteoclasts. Affiliated tissues include b cells, t cells and lymph node, and related phenotypes are recurrent otitis media and conjunctivitis

Description from OMIM: 240500

Related Diseases for Immunodeficiency, Common Variable, 2

Diseases related to Immunodeficiency, Common Variable, 2 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 11)
# Related Disease Score Top Affiliating Genes
1 primary agammaglobulinemia 10.0 TNFRSF13B TNFRSF13C
2 cryptococcal meningitis 9.9 TNFRSF13B TNFRSF13C
3 lobomycosis 9.6 CD19 CR2
4 bladder lymphoma 9.5 CD19 CR2
5 lateral medullary syndrome 9.5 CD19 CR2
6 lung lymphoma 9.3 CD19 CR2
7 follicular lymphoma 9.0 CR2 TNFRSF13C
8 leukemia, chronic lymphocytic 8.6 CD19 CR2 TNFRSF13C
9 b cell deficiency 8.5 CD19 CR2 TNFRSF13B TNFRSF13C
10 lymphoma, non-hodgkin, familial 8.4 CD19 CR2 TNFRSF13B TNFRSF13C
11 common variable immunodeficiency 7.7 CD19 CR2 ICOS TNFRSF13B TNFRSF13C

Graphical network of the top 20 diseases related to Immunodeficiency, Common Variable, 2:



Diseases related to Immunodeficiency, Common Variable, 2

Symptoms & Phenotypes for Immunodeficiency, Common Variable, 2

Symptoms via clinical synopsis from OMIM:

57
AbdomenSpleen:
splenomegaly

Abdomen Gastrointestinal:
diarrhea
enteritis, recurrent

Neurologic Central Nervous System:
meningitis

Immunology:
lymphadenopathy
recurrent bacterial infections
autoimmune disorders
hypogammaglobulinemia
defective antibody production
more
Head And Neck Head:
sinusitis, recurrent

Respiratory Lung:
pneumonia, recurrent

Abdomen Liver:
hepatomegaly

Head And Neck Eyes:
conjunctivitis

Neoplasia:
lymphoma

Respiratory Airways:
bronchiectasis
bronchitis, recurrent

Head And Neck Ears:
otitis media, recurrent

Laboratory Abnormalities:
markedly reduced iga levels
markedly reduced igg levels
reduced igm levels
anti-iga antibodies commonly present


Clinical features from OMIM:

240500

Human phenotypes related to Immunodeficiency, Common Variable, 2:

32 (show all 20)
# Description HPO Frequency HPO Source Accession
1 recurrent otitis media 32 HP:0000403
2 conjunctivitis 32 HP:0000509
3 meningitis 32 HP:0001287
4 splenomegaly 32 HP:0001744
5 diarrhea 32 HP:0002014
6 bronchiectasis 32 HP:0002110
7 hepatomegaly 32 HP:0002240
8 neoplasm 32 HP:0002664
9 lymphoma 32 HP:0002665
10 lymphadenopathy 32 HP:0002716
11 recurrent bacterial infections 32 HP:0002718
12 iga deficiency 32 HP:0002720
13 immunodeficiency 32 HP:0002721
14 recurrent bronchitis 32 HP:0002837
15 igm deficiency 32 HP:0002850
16 autoimmunity 32 HP:0002960
17 igg deficiency 32 HP:0004315
18 impaired t cell function 32 HP:0005435
19 recurrent pneumonia 32 HP:0006532
20 recurrent sinusitis 32 HP:0011108

UMLS symptoms related to Immunodeficiency, Common Variable, 2:


diarrhea

MGI Mouse Phenotypes related to Immunodeficiency, Common Variable, 2:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 hematopoietic system MP:0005397 9.65 CD19 CR2 ICOS TNFRSF13B TNFRSF13C
2 homeostasis/metabolism MP:0005376 9.55 TNFRSF13B TNFRSF13C CD19 CR2 ICOS
3 immune system MP:0005387 9.35 CD19 CR2 ICOS TNFRSF13B TNFRSF13C
4 neoplasm MP:0002006 8.8 CD19 ICOS TNFRSF13B

Drugs & Therapeutics for Immunodeficiency, Common Variable, 2

Search Clinical Trials , NIH Clinical Center for Immunodeficiency, Common Variable, 2

Genetic Tests for Immunodeficiency, Common Variable, 2

Genetic tests related to Immunodeficiency, Common Variable, 2:

# Genetic test Affiliating Genes
1 Common Variable Immunodeficiency 2 29 CD19 CR2 ICOS TNFRSF13B TNFRSF13C

Anatomical Context for Immunodeficiency, Common Variable, 2

MalaCards organs/tissues related to Immunodeficiency, Common Variable, 2:

41
B Cells, T Cells, Lymph Node

Publications for Immunodeficiency, Common Variable, 2

Variations for Immunodeficiency, Common Variable, 2

UniProtKB/Swiss-Prot genetic disease variations for Immunodeficiency, Common Variable, 2:

75
# Symbol AA change Variation ID SNP ID
1 TNFRSF13B p.Cys104Arg VAR_024027 rs34557412
2 TNFRSF13B p.Ala181Gly VAR_024028
3 TNFRSF13B p.Arg202His VAR_024029 rs104894649

ClinVar genetic disease variations for Immunodeficiency, Common Variable, 2:

6
(show top 50) (show all 55)
# Gene Variation Type Significance SNP ID Assembly Location
1 TNFRSF13B NM_012452.2(TNFRSF13B): c.310T> C (p.Cys104Arg) single nucleotide variant risk factor rs34557412 GRCh37 Chromosome 17, 16852187: 16852187
2 TNFRSF13B NM_012452.2(TNFRSF13B): c.310T> C (p.Cys104Arg) single nucleotide variant risk factor rs34557412 GRCh38 Chromosome 17, 16948873: 16948873
3 TNFRSF13B TNFRSF13B, 1-BP INS, 204A insertion Pathogenic
4 TNFRSF13B NM_012452.2(TNFRSF13B): c.581_582delCCinsAA (p.Ser194Ter) indel Pathogenic rs121908379 GRCh37 Chromosome 17, 16843689: 16843690
5 TNFRSF13B NM_012452.2(TNFRSF13B): c.581_582delCCinsAA (p.Ser194Ter) indel Pathogenic rs121908379 GRCh38 Chromosome 17, 16940375: 16940376
6 TNFRSF13B NM_012452.2(TNFRSF13B): c.431C> A (p.Ser144Ter) single nucleotide variant Pathogenic rs104894650 GRCh37 Chromosome 17, 16852066: 16852066
7 TNFRSF13B NM_012452.2(TNFRSF13B): c.431C> A (p.Ser144Ter) single nucleotide variant Pathogenic rs104894650 GRCh38 Chromosome 17, 16948752: 16948752
8 TNFRSF13B NM_012452.2(TNFRSF13B): c.492C> G (p.Tyr164Ter) single nucleotide variant Pathogenic rs72553882 GRCh38 Chromosome 17, 16940465: 16940465
9 TNFRSF13B NM_012452.2(TNFRSF13B): c.492C> G (p.Tyr164Ter) single nucleotide variant Pathogenic rs72553882 GRCh37 Chromosome 17, 16843779: 16843779
10 TNFRSF13B NM_012452.2(TNFRSF13B): c.453G> C (p.Pro151=) single nucleotide variant Uncertain significance rs768819413 GRCh38 Chromosome 17, 16940504: 16940504
11 TNFRSF13B NM_012452.2(TNFRSF13B): c.453G> C (p.Pro151=) single nucleotide variant Uncertain significance rs768819413 GRCh37 Chromosome 17, 16843818: 16843818
12 TNFRSF13B NM_012452.2(TNFRSF13B): c.563A> T (p.Lys188Met) single nucleotide variant Benign/Likely benign rs74811083 GRCh37 Chromosome 17, 16843708: 16843708
13 TNFRSF13B NM_012452.2(TNFRSF13B): c.563A> T (p.Lys188Met) single nucleotide variant Benign/Likely benign rs74811083 GRCh38 Chromosome 17, 16940394: 16940394
14 TNFRSF13B NM_012452.2(TNFRSF13B): c.291T> G (p.Pro97=) single nucleotide variant Benign/Likely benign rs35062843 GRCh38 Chromosome 17, 16948892: 16948892
15 TNFRSF13B NM_012452.2(TNFRSF13B): c.291T> G (p.Pro97=) single nucleotide variant Benign/Likely benign rs35062843 GRCh37 Chromosome 17, 16852206: 16852206
16 TNFRSF13B NM_012452.2(TNFRSF13B): c.236A> G (p.Tyr79Cys) single nucleotide variant Conflicting interpretations of pathogenicity rs72553876 GRCh37 Chromosome 17, 16852261: 16852261
17 TNFRSF13B NM_012452.2(TNFRSF13B): c.236A> G (p.Tyr79Cys) single nucleotide variant Conflicting interpretations of pathogenicity rs72553876 GRCh38 Chromosome 17, 16948947: 16948947
18 TNFRSF13B NM_012452.2(TNFRSF13B): c.592C> T (p.Arg198Cys) single nucleotide variant Uncertain significance rs140781824 GRCh37 Chromosome 17, 16843679: 16843679
19 TNFRSF13B NM_012452.2(TNFRSF13B): c.592C> T (p.Arg198Cys) single nucleotide variant Uncertain significance rs140781824 GRCh38 Chromosome 17, 16940365: 16940365
20 TNFRSF13B NM_012452.2(TNFRSF13B): c.215G> A (p.Arg72His) single nucleotide variant Likely benign rs55916807 GRCh37 Chromosome 17, 16852282: 16852282
21 TNFRSF13B NM_012452.2(TNFRSF13B): c.215G> A (p.Arg72His) single nucleotide variant Likely benign rs55916807 GRCh38 Chromosome 17, 16948968: 16948968
22 TNFRSF13B NM_012452.2(TNFRSF13B): c.204dupA (p.Leu69Thrfs) duplication Conflicting interpretations of pathogenicity rs72553875 GRCh37 Chromosome 17, 16852293: 16852293
23 TNFRSF13B NM_012452.2(TNFRSF13B): c.204dupA (p.Leu69Thrfs) duplication Conflicting interpretations of pathogenicity rs72553875 GRCh38 Chromosome 17, 16948979: 16948979
24 TNFRSF13B NM_012452.2(TNFRSF13B): c.61+10C> T single nucleotide variant Benign/Likely benign rs148297590 GRCh38 Chromosome 17, 16972005: 16972005
25 TNFRSF13B NM_012452.2(TNFRSF13B): c.61+10C> T single nucleotide variant Benign/Likely benign rs148297590 GRCh37 Chromosome 17, 16875319: 16875319
26 TNFRSF13B NM_012452.2(TNFRSF13B): c.512T> G (p.Leu171Arg) single nucleotide variant Conflicting interpretations of pathogenicity rs143027621 GRCh37 Chromosome 17, 16843759: 16843759
27 TNFRSF13B NM_012452.2(TNFRSF13B): c.512T> G (p.Leu171Arg) single nucleotide variant Conflicting interpretations of pathogenicity rs143027621 GRCh38 Chromosome 17, 16940445: 16940445
28 TNFRSF13B NM_012452.2(TNFRSF13B): c.515G> A (p.Cys172Tyr) single nucleotide variant Uncertain significance rs751216929 GRCh37 Chromosome 17, 16843756: 16843756
29 TNFRSF13B NM_012452.2(TNFRSF13B): c.515G> A (p.Cys172Tyr) single nucleotide variant Uncertain significance rs751216929 GRCh38 Chromosome 17, 16940442: 16940442
30 TNFRSF13B NM_012452.2(TNFRSF13B): c.566G> T (p.Arg189Met) single nucleotide variant Uncertain significance rs199777698 GRCh38 Chromosome 17, 16940391: 16940391
31 TNFRSF13B NM_012452.2(TNFRSF13B): c.566G> T (p.Arg189Met) single nucleotide variant Uncertain significance rs199777698 GRCh37 Chromosome 17, 16843705: 16843705
32 TNFRSF13B NM_012452.2(TNFRSF13B): c.716C> T (p.Ala239Val) single nucleotide variant Uncertain significance rs375891337 GRCh38 Chromosome 17, 16939713: 16939713
33 TNFRSF13B NM_012452.2(TNFRSF13B): c.716C> T (p.Ala239Val) single nucleotide variant Uncertain significance rs375891337 GRCh37 Chromosome 17, 16843027: 16843027
34 TNFRSF13B NM_012452.2(TNFRSF13B): c.754G> A (p.Asp252Asn) single nucleotide variant Uncertain significance rs111439115 GRCh38 Chromosome 17, 16939675: 16939675
35 TNFRSF13B NM_012452.2(TNFRSF13B): c.754G> A (p.Asp252Asn) single nucleotide variant Uncertain significance rs111439115 GRCh37 Chromosome 17, 16842989: 16842989
36 TNFRSF13B NM_012452.2(TNFRSF13B): c.641T> C (p.Met214Thr) single nucleotide variant Uncertain significance rs144560464 GRCh37 Chromosome 17, 16843102: 16843102
37 TNFRSF13B NM_012452.2(TNFRSF13B): c.641T> C (p.Met214Thr) single nucleotide variant Uncertain significance rs144560464 GRCh38 Chromosome 17, 16939788: 16939788
38 TNFRSF13B NM_012452.2(TNFRSF13B): c.563_565delAGA (p.Lys188del) deletion Benign GRCh38 Chromosome 17, 16940392: 16940394
39 TNFRSF13B NM_012452.2(TNFRSF13B): c.563_565delAGA (p.Lys188del) deletion Benign GRCh37 Chromosome 17, 16843706: 16843708
40 TNFRSF13B NM_012452.2(TNFRSF13B): c.49delC (p.Gln17Argfs) deletion Pathogenic GRCh37 Chromosome 17, 16875341: 16875341
41 TNFRSF13B NM_012452.2(TNFRSF13B): c.49delC (p.Gln17Argfs) deletion Pathogenic GRCh38 Chromosome 17, 16972027: 16972027
42 TNFRSF13B NM_012452.2(TNFRSF13B): c.532T> C (p.Phe178Leu) single nucleotide variant Uncertain significance rs764319738 GRCh37 Chromosome 17, 16843739: 16843739
43 TNFRSF13B NM_012452.2(TNFRSF13B): c.532T> C (p.Phe178Leu) single nucleotide variant Uncertain significance rs764319738 GRCh38 Chromosome 17, 16940425: 16940425
44 TNFRSF13B NM_012452.2(TNFRSF13B): c.165C> T (p.Asn55=) single nucleotide variant Likely benign rs756655390 GRCh38 Chromosome 17, 16952480: 16952480
45 TNFRSF13B NM_012452.2(TNFRSF13B): c.165C> T (p.Asn55=) single nucleotide variant Likely benign rs756655390 GRCh37 Chromosome 17, 16855794: 16855794
46 TNFRSF13B NM_012452.2(TNFRSF13B): c.828C> G (p.Asp276Glu) single nucleotide variant Uncertain significance rs144383122 GRCh37 Chromosome 17, 16842915: 16842915
47 TNFRSF13B NM_012452.2(TNFRSF13B): c.828C> G (p.Asp276Glu) single nucleotide variant Uncertain significance rs144383122 GRCh38 Chromosome 17, 16939601: 16939601
48 TNFRSF13B NM_012452.2(TNFRSF13B): c.706G> T (p.Glu236Ter) single nucleotide variant Uncertain significance rs201021960 GRCh37 Chromosome 17, 16843037: 16843037
49 TNFRSF13B NM_012452.2(TNFRSF13B): c.706G> T (p.Glu236Ter) single nucleotide variant Uncertain significance rs201021960 GRCh38 Chromosome 17, 16939723: 16939723
50 TNFRSF13B NM_012452.2(TNFRSF13B): c.17G> A (p.Arg6Gln) single nucleotide variant Uncertain significance rs747078163 GRCh38 Chromosome 17, 16972059: 16972059

Expression for Immunodeficiency, Common Variable, 2

Search GEO for disease gene expression data for Immunodeficiency, Common Variable, 2.

Pathways for Immunodeficiency, Common Variable, 2

GO Terms for Immunodeficiency, Common Variable, 2

Cellular components related to Immunodeficiency, Common Variable, 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 integral component of membrane GO:0016021 9.55 CD19 CR2 ICOS TNFRSF13B TNFRSF13C
2 plasma membrane GO:0005886 9.35 CD19 CR2 ICOS TNFRSF13B TNFRSF13C
3 external side of plasma membrane GO:0009897 8.8 CD19 ICOS TNFRSF13C

Biological processes related to Immunodeficiency, Common Variable, 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 positive regulation of protein kinase B signaling GO:0051897 9.4 CD19 ICOS
2 tumor necrosis factor-mediated signaling pathway GO:0033209 9.37 TNFRSF13B TNFRSF13C
3 immune system process GO:0002376 9.33 CR2 TNFRSF13B TNFRSF13C
4 regulation of complement activation GO:0030449 9.32 CD19 CR2
5 phosphatidylinositol phosphorylation GO:0046854 9.26 CD19 ICOS
6 T cell costimulation GO:0031295 8.96 ICOS TNFRSF13C
7 B cell homeostasis GO:0001782 8.62 TNFRSF13B TNFRSF13C

Molecular functions related to Immunodeficiency, Common Variable, 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 phosphatidylinositol-4,5-bisphosphate 3-kinase activity GO:0046934 8.62 CD19 ICOS

Sources for Immunodeficiency, Common Variable, 2

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
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54 NINDS
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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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