CGD3
MCID: GRN064
MIFTS: 38

Granulomatous Disease, Chronic, Autosomal Recessive, 3 (CGD3)

Categories: Blood diseases, Bone diseases, Eye diseases, Gastrointestinal diseases, Genetic diseases, Immune diseases, Infectious diseases, Rare diseases, Respiratory diseases, Skin diseases

Aliases & Classifications for Granulomatous Disease, Chronic, Autosomal Recessive, 3

MalaCards integrated aliases for Granulomatous Disease, Chronic, Autosomal Recessive, 3:

Name: Granulomatous Disease, Chronic, Autosomal Recessive, 3 57
Granulomatous Disease, Chronic, Autosomal Recessive, Cytochrome B-Positive, Type Iii 57 29 13 6
Autosomal Recessive Chronic Granulomatous Disease Cytochrome B-Positive Type Iii 12 15
Cgd3 57 72
Granulomatous Disease, Chronic, Autosomal Recessive Cytochrome B-Positive, Type 3 39
Chronic Granulomatous Disease Autosomal Recessive Cytochrome B-Positive Type Iii 72
Granulomatous Disease, Chronic, Cytochrome-B-Positive 3, Autosomal Recessive 72
Cgd, Autosomal Recessive Cytochrome B-Positive, Type Iii 57
Granulomatous Disease, Chronic, Due to Ncf4 Deficiency 57
Autosomal Recessive Cytochrome B-Positive Cgd Type Iii 12
Cgd Autosomal Recessive Cytochrome B-Positive Type Iii 72
Chronic Granulomatous Disease 3, Autosomal Recessive 57
Chronic Granulomatous Disease Due to Ncf4 Deficiency 12
Granulomatous Disease Chronic Due to Ncf4 Deficiency 72
Autosomal Recessive Chronic Granulomatous Disease 3 12
Cdg3 12

Characteristics:

OMIM®:

57 (Updated 05-Apr-2021)
Miscellaneous:
incomplete penetrance
variable phenotype
onset usually in first decade
invasive infections are uncommon

Inheritance:
autosomal recessive


HPO:

31
granulomatous disease, chronic, autosomal recessive, 3:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

Disease Ontology 12 DOID:0070194
OMIM® 57 613960
OMIM Phenotypic Series 57 PS306400
MeSH 44 D006105
MedGen 41 C3151409

Summaries for Granulomatous Disease, Chronic, Autosomal Recessive, 3

OMIM® : 57 Autosomal recessive chronic granulomatous disease-3 (CGD3) is an immunodeficiency disorder characterized by recurrent pyogenic infections and granulomatous inflammation with onset usually in the first decade of life. Most patients present with colitis and features of inflammatory bowel disease. Other common manifestations include lupus-like skin lesions, skin granulomas, Staphylococcal abscesses, oral ulcers, and periodontitis. Patients usually do not have invasive infections and are not markedly susceptible to fungal infections. The disorder results from variable loss of phagocyte superoxide production due to NADPH oxidase dysfunction; it is generally less severe than other genetic types of CGD (summary by Matute et al., 2009; van de Geer et al., 2018). For a general phenotypic description and a discussion of genetic heterogeneity of CGD, see the X-linked form (CGDX; 306400). (613960) (Updated 05-Apr-2021)

MalaCards based summary : Granulomatous Disease, Chronic, Autosomal Recessive, 3, also known as granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type iii, is related to granulomatous disease, chronic, autosomal recessive, 4 and congenital disorder of glycosylation, type iia. An important gene associated with Granulomatous Disease, Chronic, Autosomal Recessive, 3 is NCF4 (Neutrophil Cytosolic Factor 4), and among its related pathways/superpathways are Antigen processing-Cross presentation and Nur77 Signaling in T-Cell. Affiliated tissues include neutrophil, and related phenotypes are diarrhea and recurrent aphthous stomatitis

Disease Ontology : 12 A chronic granulomatous disease characterized by that autosomal recessive inheritance has material basis in mutation in the NCF4 gene on chromosome 22q12.

UniProtKB/Swiss-Prot : 72 Granulomatous disease, chronic, cytochrome-b-positive 3, autosomal recessive: A form of chronic granulomatous disease, a primary immunodeficiency characterized by severe recurrent bacterial and fungal infections, along with manifestations of chronic granulomatous inflammation. It results from an impaired ability of phagocytes to mount a burst of reactive oxygen species in response to pathogens.

Related Diseases for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Graphical network of the top 20 diseases related to Granulomatous Disease, Chronic, Autosomal Recessive, 3:



Diseases related to Granulomatous Disease, Chronic, Autosomal Recessive, 3

Symptoms & Phenotypes for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Human phenotypes related to Granulomatous Disease, Chronic, Autosomal Recessive, 3:

31
# Description HPO Frequency HPO Source Accession
1 diarrhea 31 HP:0002014
2 recurrent aphthous stomatitis 31 HP:0011107
3 colitis 31 HP:0002583
4 perioral eczema 31 HP:0011127
5 recurrent sinusitis 31 HP:0011108

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Respiratory:
recurrent respiratory infections

Head And Neck Eyes:
conjunctivitis
blepharitis

Immunology:
recurrent infections
lymphadenitis
staphylococcal infections
neutrophils show defective intracellular nadph oxidase function
impaired respiratory burst
more
Head And Neck Mouth:
periodontitis
perioral eczema
aphthous ulcers
thrush

Skin Nails Hair Skin:
eczema
recurrent skin infections
abscesses
lupus-like lesions
cutaneous lesions
more
Abdomen Gastrointestinal:
diarrhea
esophageal ulceration
chronic granulomatous colitis
perianal infections and fistula

Clinical features from OMIM®:

613960 (Updated 05-Apr-2021)

Drugs & Therapeutics for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Search Clinical Trials , NIH Clinical Center for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Genetic Tests for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Genetic tests related to Granulomatous Disease, Chronic, Autosomal Recessive, 3:

# Genetic test Affiliating Genes
1 Granulomatous Disease, Chronic, Autosomal Recessive, Cytochrome B-Positive, Type Iii 29 NCF4

Anatomical Context for Granulomatous Disease, Chronic, Autosomal Recessive, 3

MalaCards organs/tissues related to Granulomatous Disease, Chronic, Autosomal Recessive, 3:

40
Neutrophil

Publications for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Articles related to Granulomatous Disease, Chronic, Autosomal Recessive, 3:

# Title Authors PMID Year
1
Inherited p40phox deficiency differs from classic chronic granulomatous disease. 6 57
29969437 2018
2
A new genetic subgroup of chronic granulomatous disease with autosomal recessive mutations in p40 phox and selective defects in neutrophil NADPH oxidase activity. 6 57
19692703 2009
3
Clinical and molecular findings of chronic granulomatous disease in Oman: family studies. 6
24446915 2015
4
Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. 57
17435756 2007
5
Neutrophils from p40phox-/- mice exhibit severe defects in NADPH oxidase regulation and oxidant-dependent bacterial killing. 57
16880254 2006
6
Characterization of INS-15, A Metalloprotease Potentially Involved in the Invasion of Cryptosporidium parvum. 61
31615118 2019
7
Herpes simplex virus glycoprotein D is recognized as antigen by CD4+ and CD8+ T lymphocytes from infected mice. Characterization of T cell clones. 61
1973187 1990

Variations for Granulomatous Disease, Chronic, Autosomal Recessive, 3

ClinVar genetic disease variations for Granulomatous Disease, Chronic, Autosomal Recessive, 3:

6 (show top 50) (show all 97)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 NCF4 NM_000631.5(NCF4):c.758+50C>T SNV Pathogenic 652770 rs201021542 GRCh37: 22:37271875-37271875
GRCh38: 22:36875833-36875833
2 NCF4 NM_000631.5(NCF4):c.716G>A (p.Trp239Ter) SNV Pathogenic 932309 GRCh37: 22:37271783-37271783
GRCh38: 22:36875741-36875741
3 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.32+2T>G SNV Pathogenic 932310 GRCh37: 22:37257247-37257247
GRCh38: 22:36861205-36861205
4 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.143_152del (p.Lys48fs) Deletion Pathogenic 30193 rs876657377 GRCh37: 22:37260986-37260995
GRCh38: 22:36864944-36864953
5 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.118-1G>A SNV Pathogenic 425281 rs28445840 GRCh37: 22:37260960-37260960
GRCh38: 22:36864918-36864918
6 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.314G>A (p.Arg105Gln) SNV Pathogenic 30194 rs387906808 GRCh37: 22:37263476-37263476
GRCh38: 22:36867434-36867434
7 LOC106029312 , NCF1 NM_000265.6(NCF1):c.579G>A (p.Trp193Ter) SNV Pathogenic 426990 rs145360423 GRCh37: 7:74197872-74197872
GRCh38: 7:74783529-74783529
8 NCF4-AS1 , NCF4 NC_000022.11:g.36864921_36864935del Deletion Likely pathogenic 803685 rs1200078508 GRCh37: 22:37260959-37260973
GRCh38: 22:36864917-36864931
9 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.270_271+16del Deletion Likely pathogenic 842976 GRCh37: 22:37261106-37261123
GRCh38: 22:36865064-36865081
10 NCF4 NM_000631.5(NCF4):c.759-97C>T SNV Uncertain significance 848741 GRCh37: 22:37271974-37271974
GRCh38: 22:36875932-36875932
11 NCF4 and overlap with 1 gene(s) NC_000022.11:g.(?_36864025)_(36870562_?)del Deletion Uncertain significance 584111 GRCh37: 22:37260067-37266604
GRCh38: 22:36864025-36870562
12 NCF4 NM_000631.5(NCF4):c.758+51G>A SNV Uncertain significance 576370 rs150640467 GRCh37: 22:37271876-37271876
GRCh38: 22:36875834-36875834
13 NCF4 NM_000631.5(NCF4):c.499G>A (p.Val167Ile) SNV Uncertain significance 837549 GRCh37: 22:37267722-37267722
GRCh38: 22:36871680-36871680
14 NCF4 NM_000631.5(NCF4):c.451C>T (p.Arg151Cys) SNV Uncertain significance 839355 GRCh37: 22:37266565-37266565
GRCh38: 22:36870523-36870523
15 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.311T>C (p.Met104Thr) SNV Uncertain significance 846758 GRCh37: 22:37263473-37263473
GRCh38: 22:36867431-36867431
16 NCF4 NM_000631.5(NCF4):c.759-7C>G SNV Uncertain significance 848725 GRCh37: 22:37272064-37272064
GRCh38: 22:36876022-36876022
17 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.229A>G (p.Ser77Gly) SNV Uncertain significance 852015 GRCh37: 22:37261072-37261072
GRCh38: 22:36865030-36865030
18 NCF4 NM_000631.5(NCF4):c.758+12G>C SNV Uncertain significance 853742 GRCh37: 22:37271837-37271837
GRCh38: 22:36875795-36875795
19 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.304G>A (p.Ala102Thr) SNV Uncertain significance 857766 GRCh37: 22:37263466-37263466
GRCh38: 22:36867424-36867424
20 NCF4 NM_000631.5(NCF4):c.774G>A (p.Glu258=) SNV Uncertain significance 944277 GRCh37: 22:37272086-37272086
GRCh38: 22:36876044-36876044
21 NCF4 NM_000631.5(NCF4):c.758+87T>G SNV Uncertain significance 948699 GRCh37: 22:37271912-37271912
GRCh38: 22:36875870-36875870
22 NCF4 NM_000631.5(NCF4):c.485C>T (p.Pro162Leu) SNV Uncertain significance 1000083 GRCh37: 22:37267708-37267708
GRCh38: 22:36871666-36871666
23 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.256C>G (p.Leu86Val) SNV Uncertain significance 1004127 GRCh37: 22:37261099-37261099
GRCh38: 22:36865057-36865057
24 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.270A>T (p.Pro90=) SNV Uncertain significance 341551 rs370754874 GRCh37: 22:37261113-37261113
GRCh38: 22:36865071-36865071
25 NCF4 NM_000631.5(NCF4):c.758+32G>A SNV Uncertain significance 539177 rs148129899 GRCh37: 22:37271857-37271857
GRCh38: 22:36875815-36875815
26 NCF4 NM_000631.5(NCF4):c.458G>A (p.Arg153His) SNV Uncertain significance 660663 rs35160112 GRCh37: 22:37266572-37266572
GRCh38: 22:36870530-36870530
27 NCF4 NM_000631.5(NCF4):c.506G>A (p.Arg169His) SNV Uncertain significance 846603 GRCh37: 22:37267729-37267729
GRCh38: 22:36871687-36871687
28 NCF4 NM_000631.5(NCF4):c.758+69C>T SNV Uncertain significance 853449 GRCh37: 22:37271894-37271894
GRCh38: 22:36875852-36875852
29 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.170G>T (p.Arg57Leu) SNV Uncertain significance 853519 GRCh37: 22:37261013-37261013
GRCh38: 22:36864971-36864971
30 NCF4 NM_000631.5(NCF4):c.758+62C>T SNV Uncertain significance 854352 GRCh37: 22:37271887-37271887
GRCh38: 22:36875845-36875845
31 NCF4 NM_000631.5(NCF4):c.670G>A (p.Val224Met) SNV Uncertain significance 945677 GRCh37: 22:37271737-37271737
GRCh38: 22:36875695-36875695
32 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.248C>A (p.Ala83Asp) SNV Uncertain significance 953788 GRCh37: 22:37261091-37261091
GRCh38: 22:36865049-36865049
33 NCF4 NM_000631.5(NCF4):c.759-7C>A SNV Uncertain significance 968988 GRCh37: 22:37272064-37272064
GRCh38: 22:36876022-36876022
34 NCF4 NC_000022.10:g.(?_37260067)_(37266604_?)del Deletion Uncertain significance 1024936 GRCh37: 22:37260067-37266604
GRCh38:
35 NCF4 NM_000631.5(NCF4):c.655T>C (p.Phe219Leu) SNV Uncertain significance 341556 rs761212596 GRCh37: 22:37271722-37271722
GRCh38: 22:36875680-36875680
36 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.111C>A (p.Ser37Arg) SNV Uncertain significance 1025577 GRCh37: 22:37260165-37260165
GRCh38: 22:36864123-36864123
37 NCF4 NM_000631.5(NCF4):c.665C>T (p.Ser222Phe) SNV Uncertain significance 1025976 GRCh37: 22:37271732-37271732
GRCh38: 22:36875690-36875690
38 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.58G>A (p.Val20Ile) SNV Uncertain significance 1027045 GRCh37: 22:37260112-37260112
GRCh38: 22:36864070-36864070
39 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.179G>A (p.Arg60His) SNV Uncertain significance 539179 rs369847561 GRCh37: 22:37261022-37261022
GRCh38: 22:36864980-36864980
40 NCF4 NM_000631.5(NCF4):c.647C>T (p.Thr216Met) SNV Uncertain significance 341555 rs146911421 GRCh37: 22:37271714-37271714
GRCh38: 22:36875672-36875672
41 NCF4 NM_000631.5(NCF4):c.638G>A (p.Arg213Gln) SNV Uncertain significance 643606 rs376569226 GRCh37: 22:37271705-37271705
GRCh38: 22:36875663-36875663
42 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.50C>T (p.Pro17Leu) SNV Uncertain significance 661385 rs147322774 GRCh37: 22:37260104-37260104
GRCh38: 22:36864062-36864062
43 NCF4 NM_000631.5(NCF4):c.759-6C>A SNV Uncertain significance 855161 GRCh37: 22:37272065-37272065
GRCh38: 22:36876023-36876023
44 NCF4 NM_000631.5(NCF4):c.798A>G (p.Leu266=) SNV Uncertain significance 856467 GRCh37: 22:37272110-37272110
GRCh38: 22:36876068-36876068
45 NCF4 NM_000631.5(NCF4):c.628-3C>T SNV Uncertain significance 859548 GRCh37: 22:37271692-37271692
GRCh38: 22:36875650-36875650
46 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.28G>A (p.Glu10Lys) SNV Uncertain significance 341546 rs756372095 GRCh37: 22:37257241-37257241
GRCh38: 22:36861199-36861199
47 NCF4-AS1 , NCF4 NM_000631.5(NCF4):c.178C>T (p.Arg60Cys) SNV Uncertain significance 970787 GRCh37: 22:37261021-37261021
GRCh38: 22:36864979-36864979
48 NCF4 NM_000631.5(NCF4):c.544A>C (p.Thr182Pro) SNV Uncertain significance 539175 rs1168414742 GRCh37: 22:37268384-37268384
GRCh38: 22:36872342-36872342
49 NCF4 NM_000631.5(NCF4):c.562G>C (p.Glu188Gln) SNV Uncertain significance 566597 rs1569114734 GRCh37: 22:37268402-37268402
GRCh38: 22:36872360-36872360
50 NCF4 NM_000631.5(NCF4):c.388C>T (p.Arg130Trp) SNV Uncertain significance 570297 rs868444265 GRCh37: 22:37266502-37266502
GRCh38: 22:36870460-36870460

UniProtKB/Swiss-Prot genetic disease variations for Granulomatous Disease, Chronic, Autosomal Recessive, 3:

72
# Symbol AA change Variation ID SNP ID
1 NCF4 p.Arg105Gln VAR_065949 rs387906808

Expression for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Search GEO for disease gene expression data for Granulomatous Disease, Chronic, Autosomal Recessive, 3.

Pathways for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Pathways related to Granulomatous Disease, Chronic, Autosomal Recessive, 3 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
11.37 NCF4 NCF1 CD3G CD3D
2 10.8 CD3G CD3D
3 10.6 CD3G CD3D
4 10.07 NCF4 NCF1

GO Terms for Granulomatous Disease, Chronic, Autosomal Recessive, 3

Cellular components related to Granulomatous Disease, Chronic, Autosomal Recessive, 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 NADPH oxidase complex GO:0043020 9.16 NCF4 NCF1
2 alpha-beta T cell receptor complex GO:0042105 8.96 CD3G CD3D
3 phagolysosome GO:0032010 8.62 NCF4 NCF1

Biological processes related to Granulomatous Disease, Chronic, Autosomal Recessive, 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 superoxide metabolic process GO:0006801 9.16 NCF4 NCF1
2 respiratory burst GO:0045730 8.96 NCF4 NCF1
3 positive thymic T cell selection GO:0045059 8.62 CD3G CD3D

Molecular functions related to Granulomatous Disease, Chronic, Autosomal Recessive, 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 superoxide-generating NADPH oxidase activity GO:0016175 8.96 NCF4 NCF1
2 superoxide-generating NADPH oxidase activator activity GO:0016176 8.62 NCF4 NCF1

Sources for Granulomatous Disease, Chronic, Autosomal Recessive, 3

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Apr-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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