Aliases & Classifications for Specific Granule Deficiency

MalaCards integrated aliases for Specific Granule Deficiency:

Name: Specific Granule Deficiency 54 29 13 52 69
Specific Granule Deficiency 1 71
Sgd1 71

Characteristics:

OMIM:

54
Inheritance:
autosomal recessive


HPO:

32
specific granule deficiency:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 54 245480
MedGen 40 C0398593
MeSH 42 D007960
SNOMED-CT via HPO 65 258211005 85559002

Summaries for Specific Granule Deficiency

UniProtKB/Swiss-Prot : 71 Specific granule deficiency 1: An autosomal recessive disorder characterized by recurrent pyogenic infections, defective neutrophil chemotaxis and bactericidal activity, and lack of neutrophil secondary granule proteins. Neutrophils of affected individuals lack lactoferrin and show abnormal nuclear segmentation, bilobed nuclei, low alkaline phosphatase, and increased number of neutrophil mitochondria and ribosomes.

MalaCards based summary : Specific Granule Deficiency, also known as specific granule deficiency 1, is related to neutrophil-specific granule deficiency and specific granule deficiency 2, and has symptoms including recurrent infections, absent neutrophil specific granules and hyposegmentation of neutrophil nuclei. An important gene associated with Specific Granule Deficiency is CEBPE (CCAAT/Enhancer Binding Protein Epsilon), and among its related pathways/superpathways are C-MYB transcription factor network and Dendritic Cells Developmental Lineage Pathway. The drugs Iron and Anti-Infective Agents have been mentioned in the context of this disorder. Affiliated tissues include neutrophil, liver and testes, and related phenotypes are hematopoietic system and immune system

Description from OMIM: 245480

Related Diseases for Specific Granule Deficiency

Diseases related to Specific Granule Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

id Related Disease Score Top Affiliating Genes
1 neutrophil-specific granule deficiency 12.3
2 specific granule deficiency 2 12.3
3 chediak-higashi syndrome 9.6
4 cranioectodermal dysplasia 1 8.9 CEBPE GATA1 GFI1 SPI1
5 nguyen syndrome 7.8 CEBPE GATA1 SCARB1 SMARCD2 SPI1
6 autism 18 7.0 CEBPE GATA1 GFI1 LTF SCARB1 SMARCD2

Graphical network of the top 20 diseases related to Specific Granule Deficiency:



Diseases related to Specific Granule Deficiency

Symptoms & Phenotypes for Specific Granule Deficiency

Symptoms via clinical synopsis from OMIM:

54

Lab:
normal neutrophil count
normal degranulation of azurophil granules after phagocytosis
increased neutrophil mitochondria and ribosomes
low neutrophil alkaline phosphatase
neutrophil nuclear clefts
more
Misc:
recurrent infections


Clinical features from OMIM:

245480

Human phenotypes related to Specific Granule Deficiency:

32
id Description HPO Frequency HPO Source Accession
1 recurrent infections 32 HP:0002719
2 absent neutrophil specific granules 32 HP:0012551
3 hyposegmentation of neutrophil nuclei 32 HP:0011447

MGI Mouse Phenotypes related to Specific Granule Deficiency:

44
id Description MGI Source Accession Score Top Affiliating Genes
1 hematopoietic system MP:0005397 9.73 GFI1 LTF SCARB1 SPI1 CEBPE GATA1
2 immune system MP:0005387 9.63 CEBPE GATA1 GFI1 LTF SCARB1 SPI1
3 liver/biliary system MP:0005370 9.26 GATA1 LTF SCARB1 SPI1
4 mortality/aging MP:0010768 9.1 CEBPE GATA1 GFI1 SCARB1 SMARCD2 SPI1

Drugs & Therapeutics for Specific Granule Deficiency

Drugs for Specific Granule Deficiency (from DrugBank, HMDB, Dgidb, PharmGKB, IUPHAR, NovoSeek, BitterDB):

(show all 27)
id Name Status Phase Clinical Trials Cas Number PubChem Id
1
Iron Approved Phase 4 7439-89-6 23925
2 Anti-Infective Agents Phase 4
3 Lactoferrin Phase 4
4 Iron Supplement Nutraceutical Phase 4
5 Licorice Approved, Nutraceutical Phase 2, Phase 3
6 Orange Approved, Nutraceutical Phase 2, Phase 3
7 Liver Extracts Phase 2, Phase 3
8 Bitter Orange Nutraceutical Phase 2, Phase 3
9 Skullcap Nutraceutical Phase 2, Phase 3
10
Sunitinib Approved, Investigational Phase 1 341031-54-7, 557795-19-4 5329102
11 Angiogenesis Inhibitors Phase 1
12 Angiogenesis Modulating Agents Phase 1
13
Fludarabine Approved 21679-14-1, 75607-67-9 30751
14
Miconazole Approved, Investigational, Vet_approved 22916-47-8 4189
15
Mycophenolate mofetil Approved, Investigational 128794-94-5 5281078
16
Mycophenolic acid Approved 24280-93-1 446541
17 Anti-Bacterial Agents
18 Antibiotics, Antitubercular
19 Antifungal Agents
20 Antimetabolites
21 Antimetabolites, Antineoplastic
22 Antirheumatic Agents
23 Calcineurin Inhibitors
24 Cyclosporins
25 Dermatologic Agents
26 Immunosuppressive Agents
27 Vidarabine Phosphate

Interventional clinical trials:


id Name Status NCT ID Phase Drugs
1 Bovine Lactoferrin Versus Ferrous Sulphate In The Treatment Of Iron Deficiency Anemia During Pregnancy Recruiting NCT03202615 Phase 4 F (ferrous sulphate)
2 Traditional Chinese Medicine for Treatment of Irritable Bowel Syndrome Recruiting NCT03135821 Phase 2, Phase 3
3 Sunitinib Malate in Treating HIV-Positive Patients With Cancer Receiving Antiretroviral Therapy Completed NCT00890747 Phase 1 sunitinib malate
4 Study of Megakaryocytes From Patients With Abnormal Platelet Vesicles Completed NCT00086476
5 Fludarabine and Total-Body Irradiation Followed By Donor Stem Cell Transplant and Cyclosporine and Mycophenolate Mofetil in Treating HIV-Positive Patients With or Without Cancer Completed NCT00112593 fludarabine phosphate;cyclosporine;mycophenolate mofetil
6 Observational Study on the Long Term Safety of Kuvan® Treatment in Patients With Hyperphenylalaninemia (HPA) Due to Phenylketonuria (PKU) or BH4 Deficiency Recruiting NCT01016392

Search NIH Clinical Center for Specific Granule Deficiency

Genetic Tests for Specific Granule Deficiency

Genetic tests related to Specific Granule Deficiency:

id Genetic test Affiliating Genes
1 Specific Granule Deficiency 29

Anatomical Context for Specific Granule Deficiency

MalaCards organs/tissues related to Specific Granule Deficiency:

39
Neutrophil, Liver, Testes, Monocytes, Myeloid

Publications for Specific Granule Deficiency

Articles related to Specific Granule Deficiency:

(show all 18)
id Title Authors Year
1
Role of the Leucine Zipper Domain of CCAAT/ Enhancer Binding Protein-Epsilon (C/EBPI/) in Neutrophil-Specific Granule Deficiency. ( 28322138 )
2016
2
A Novel In-Frame Deletion in the Leucine Zipper Domain of C/EBPI/ Leads to Neutrophil-Specific Granule Deficiency. ( 26019275 )
2015
3
Clinical course in a patient with neutrophil-specific granule deficiency and rapid detection of neutrophil granules as a screening test. ( 25081842 )
2014
4
Neutrophil-specific granule deficiency. ( 23294125 )
2013
5
Growth factor independence-1 (Gfi-1) plays a role in mediating specific granule deficiency (SGD) in a patient lacking a gene-inactivating mutation in the C/EBPepsilon gene. ( 17244686 )
2007
6
Intractable diarrhoea of infancy caused by neutrophil specific granule deficiency and cured by stem cell transplantation. ( 16407388 )
2006
7
Aberrant expression of neutrophil and macrophage-related genes in a murine model for human neutrophil-specific granule deficiency. ( 16204633 )
2005
8
Phenotypic and functional alterations of peripheral blood monocytes in neutrophil-specific granule deficiency. ( 14576362 )
2004
9
Neutrophil specific granule deficiency and mutations in the gene encoding transcription factor C/EBP(epsilon). ( 11753076 )
2002
10
Neutrophil-specific granule deficiency: homozygous recessive inheritance of a frameshift mutation in the gene encoding transcription factor CCAAT/enhancer binding protein--epsilon. ( 11313242 )
2001
11
Neutrophil-specific granule deficiency results from a novel mutation with loss of function of the transcription factor CCAAT/enhancer binding protein epsilon. ( 10359588 )
1999
12
A marked decrease in defensin mRNA in the only case of congenital neutrophil-specific granule deficiency reported in Japan. ( 8018907 )
1994
13
Ultrastructure of neutrophilic phagosome of autologous platelet in vivo in specific granule deficiency. ( 8342544 )
1993
14
Neutrophil-specific granule deficiency includes eosinophils. ( 8324226 )
1993
15
Correlation of messenger RNA levels with protein defects in specific granule deficiency. ( 1327289 )
1992
16
Selective defect in myeloid cell lactoferrin gene expression in neutrophil specific granule deficiency. ( 2536400 )
1989
17
Neutrophil specific granule deficiency. ( 3888052 )
1985
18
Human neutrophil-specific granule deficiency: a model to assess the role of neutrophil-specific granules in the evolution of the inflammatory response. ( 7044447 )
1982

Variations for Specific Granule Deficiency

ClinVar genetic disease variations for Specific Granule Deficiency:

6
id Gene Variation Type Significance SNP ID Assembly Location
1 CEBPE CEBPE, 5-BP DEL, NT224 deletion Pathogenic
2 CEBPE CEBPE, 1-BP INS, 1113A insertion Pathogenic
3 SMARCD2 NM_001098426.1(SMARCD2): c.1181+1G> A single nucleotide variant Pathogenic rs1057518731 GRCh37 Chromosome 17, 61911268: 61911268
4 SMARCD2 NM_001098426.1(SMARCD2): c.414_438dup25 (p.Gln147Glufs) duplication Pathogenic rs1057518732 GRCh37 Chromosome 17, 61914561: 61914585
5 SMARCD2 NM_001098426.1(SMARCD2): c.401+2T> C single nucleotide variant Pathogenic rs1057518733 GRCh38 Chromosome 17, 63837439: 63837439

Expression for Specific Granule Deficiency

Search GEO for disease gene expression data for Specific Granule Deficiency.

Pathways for Specific Granule Deficiency

Pathways related to Specific Granule Deficiency according to GeneCards Suite gene sharing:

id Super pathways Score Top Affiliating Genes
1 11.15 GATA1 SPI1
2 11.04 GFI1 SPI1
3 10.74 GFI1 SPI1
4 10.3 GATA1 SPI1

GO Terms for Specific Granule Deficiency

Cellular components related to Specific Granule Deficiency according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 transcriptional repressor complex GO:0017053 8.62 GATA1 GFI1

Biological processes related to Specific Granule Deficiency according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 regulation of transcription, DNA-templated GO:0006355 9.73 CEBPE GATA1 GFI1 LTF SMARCD2 SPI1
2 transcription, DNA-templated GO:0006351 9.63 CEBPE GATA1 GFI1 LTF SMARCD2 SPI1
3 transcription from RNA polymerase II promoter GO:0006366 9.61 CEBPE GATA1 SPI1
4 cellular response to lipopolysaccharide GO:0071222 9.46 CEBPE GFI1
5 erythrocyte differentiation GO:0030218 9.4 GATA1 SPI1
6 myeloid cell differentiation GO:0030099 9.37 CEBPE GATA1
7 macrophage differentiation GO:0030225 9.32 CEBPE SPI1
8 positive regulation of osteoblast proliferation GO:0033690 8.96 GATA1 LTF
9 granulocyte differentiation GO:0030851 8.32 SPI1

Molecular functions related to Specific Granule Deficiency according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 DNA binding GO:0003677 9.8 CEBPE GATA1 GFI1 LTF SPI1
2 RNA polymerase II distal enhancer sequence-specific DNA binding GO:0000980 9.46 SMARCD2 SPI1
3 core promoter binding GO:0001047 9.43 GATA1 SPI1
4 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0001077 9.43 CEBPE GATA1 SPI1
5 RNA polymerase II core promoter sequence-specific DNA binding GO:0000979 9.37 GATA1 SPI1
6 RNA polymerase II transcription factor binding GO:0001085 9.32 GATA1 SPI1
7 lipopolysaccharide binding GO:0001530 9.16 LTF SCARB1
8 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0001078 9.13 GATA1 GFI1 SPI1
9 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000978 8.92 CEBPE GATA1 SMARCD2 SPI1

Sources for Specific Granule Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 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 MedGen
42 MeSH
43 MESH via Orphanet
44 MGI
46 NCI
47 NCIt
48 NDF-RT
51 NINDS
52 Novoseek
54 OMIM
55 OMIM via Orphanet
59 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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