Immunodeficiency, Common Variable, 2 disease: Malacards - Research Articles, Drugs, Genes, Clinical Trials

MCID: IMM034 MIFTS: 37	Immunodeficiency, Common Variable, 2 Categories: Genetic diseases, Immune diseases
Genes Variations Tissues Related diseases Pathways Symptoms & Phenotypes Download Expand all tables

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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:

MalaCards categories:
Global: Genetic diseases
Anatomical: Immune diseases

See all MalaCards categories (disease lists)

External Ids:

OMIM ⁵⁷ 240500

MedGen ⁴² C3150354

MeSH ⁴⁴ D017074

UMLS ⁷³ C3150354

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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

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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:

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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 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

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Drugs & Therapeutics for Immunodeficiency, Common Variable, 2

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

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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

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Anatomical Context for Immunodeficiency, Common Variable, 2

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

⁴¹

B Cells, T Cells, Lymph Node

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Publications for Immunodeficiency, Common Variable, 2

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Genes for Immunodeficiency, Common Variable, 2

Genes related to Immunodeficiency, Common Variable, 2 (5 elite genes):

- Elite gene

- Cancer Census gene in COSMIC

#	Symbol	Description	Category	Score	Evidence	PubmedIds
1	TNFRSF13B	TNF Receptor Superfamily Member 13B	Protein Coding	1352.91	Molecular basis known ⁵⁷ Pathogenic ⁶ Causative variation ⁷⁵ Genetic Tests ²⁹ Risk factor ⁶ GeneCards inferred via : Disorders Variants (show sections)	16007087 16007086 17492055 (more) 19605846
2	TNFRSF13C	TNF Receptor Superfamily Member 13C	Protein Coding	100	Genetic Tests ²⁹
3	ICOS	Inducible T Cell Costimulator	Protein Coding	100	Genetic Tests ²⁹
4	CR2	Complement C3d Receptor 2	Protein Coding	100	Genetic Tests ²⁹
5	CD19	CD19 Molecule	Protein Coding	100	Genetic Tests ²⁹

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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

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Expression for Immunodeficiency, Common Variable, 2

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

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Pathways for Immunodeficiency, Common Variable, 2

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

#	Super pathways	Score	Top Affiliating Genes
1	Allograft rejection ¹ ³⁷ Show member pathways Antigen processing and presentation ³⁷ Asthma ³⁷ Autoimmune thyroid disease ³⁷ CTL Mediated Apoptosis ⁶⁴ Graft-versus-host disease ³⁷ Intestinal immune network for IgA production ³⁷ THC Differentiation Pathway ⁶⁴ Type I diabetes mellitus ³⁷ Viral myocarditis ³⁷	12.24	ICOS TNFRSF13B TNFRSF13C
2	RANK Signaling in Osteoclasts ⁶⁴ Show member pathways Apoptosis and survival APRIL and BAFF signaling ²² APRIL Pathway ⁶⁴ BAFF in B-Cell Signaling ⁶⁴ RANK Pathway ⁶⁴ RANKL/RANK (Receptor activator of NFKB (ligand)) Signaling Pathway ¹	11.73	CR2 TNFRSF13B TNFRSF13C
3	Epstein-Barr virus infection ³⁷	11.67	CD19 CR2
4	Hematopoietic cell lineage ³⁷	11.24	CD19 CR2
5	B Cell Development Pathways ⁶⁵	10.98	CD19 CR2 ICOS TNFRSF13B
6	Primary immunodeficiency ³⁷	10.49	CD19 ICOS TNFRSF13B TNFRSF13C

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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

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Sources for Immunodeficiency, Common Variable, 2

¹ BioSystems

² BitterDB

³ CDC

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²¹ GeneCards

²² GeneGo (Thomson Reuters)

²³ GeneHancer via GeneCards

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²⁷ GEO DataSets

²⁸ GO

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³³ ICD10

³⁴ ICD10 via Orphanet

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⁴¹ MalaCards

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⁵⁵ Novoseek

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⁵⁷ OMIM

⁵⁸ OMIM via Orphanet

⁵⁹ Orphanet

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⁶¹ PharmGKB

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⁶⁸ SNOMED-CT

⁶⁹ SNOMED-CT via HPO

⁷⁰ SNOMED-CT via Orphanet

⁷¹ TGDB

⁷² Tocris

⁷³ UMLS

⁷⁴ UMLS via Orphanet

⁷⁵ UniProtKB/Swiss-Prot

⁷⁶ Wikipedia