SGD1
MCID: SPC026
MIFTS: 31

Specific Granule Deficiency 1 (SGD1)

Categories: Genetic diseases

Aliases & Classifications for Specific Granule Deficiency 1

MalaCards integrated aliases for Specific Granule Deficiency 1:

Name: Specific Granule Deficiency 1 56 73 29 6
Specific Granule Deficiency 56 13 54 6 39 71
Sgd1 56 73
Lactoferrin-Deficient Neutrophils 56
Neutrophil Lactoferrin Deficiency 56

Characteristics:

OMIM:

56
Inheritance:
autosomal recessive


HPO:

31
specific granule deficiency 1:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 56 245480
OMIM Phenotypic Series 56 PS245480
MeSH 43 D007960
SNOMED-CT via HPO 68 258211005 428875002 85559002
UMLS 71 C0398593

Summaries for Specific Granule Deficiency 1

UniProtKB/Swiss-Prot : 73 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 1, also known as specific granule deficiency, is related to neutrophil-specific granule deficiency and specific granule deficiency 2. An important gene associated with Specific Granule Deficiency 1 is CEBPE (CCAAT Enhancer Binding Protein Epsilon). Affiliated tissues include neutrophil, myeloid and monocytes, and related phenotypes are recurrent bacterial infections and hyposegmentation of neutrophil nuclei

Wikipedia : 74 Specific granules are secretory vesicles found exclusively in cells of the immune system called... more...

More information from OMIM: 245480 PS245480

Related Diseases for Specific Granule Deficiency 1

Diseases related to Specific Granule Deficiency 1 via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 neutrophil-specific granule deficiency 31.4 SMARCD2 CEBPE
2 specific granule deficiency 2 11.3
3 bacterial infectious disease 10.2
4 monocytic leukemia 10.0
5 chediak-higashi syndrome 9.8
6 lymphoproliferative syndrome 9.8
7 diarrhea 9.8
8 cellulitis 9.8
9 impetigo 9.8
10 severe congenital neutropenia 9.2 SMARCD2 CEBPE

Graphical network of the top 20 diseases related to Specific Granule Deficiency 1:



Diseases related to Specific Granule Deficiency 1

Symptoms & Phenotypes for Specific Granule Deficiency 1

Human phenotypes related to Specific Granule Deficiency 1:

31 (show all 8)
# Description HPO Frequency HPO Source Accession
1 recurrent bacterial infections 31 HP:0002718
2 hyposegmentation of neutrophil nuclei 31 HP:0011447
3 impaired neutrophil bactericidal activity 31 HP:0011993
4 absent neutrophil lactoferrin 31 HP:0041042
5 neutrophil nuclear clefts 31 HP:0041043
6 low neutrophil alkaline phosphatase 31 HP:0041044
7 increased neutrophil mitochondria 31 HP:0041045
8 increased neutrophil ribosomes 31 HP:0041046

Symptoms via clinical synopsis from OMIM:

56
Misc:
recurrent infections

Lab:
absent neutrophil lactoferrin
neutrophil nuclear clefts
low neutrophil alkaline phosphatase
absent neutrophil specific granules
abnormal neutrophil nuclear segmentation
more

Clinical features from OMIM:

245480

Drugs & Therapeutics for Specific Granule Deficiency 1

Search Clinical Trials , NIH Clinical Center for Specific Granule Deficiency 1

Genetic Tests for Specific Granule Deficiency 1

Genetic tests related to Specific Granule Deficiency 1:

# Genetic test Affiliating Genes
1 Specific Granule Deficiency 1 29 CEBPE

Anatomical Context for Specific Granule Deficiency 1

MalaCards organs/tissues related to Specific Granule Deficiency 1:

40
Neutrophil, Myeloid, Monocytes, Brain, Testes

Publications for Specific Granule Deficiency 1

Articles related to Specific Granule Deficiency 1:

(show top 50) (show all 64)
# Title Authors PMID Year
1
Neutrophil-specific granule deficiency: homozygous recessive inheritance of a frameshift mutation in the gene encoding transcription factor CCAAT/enhancer binding protein--epsilon. 61 56 6
11313242 2001
2
Neutrophil-specific granule deficiency results from a novel mutation with loss of function of the transcription factor CCAAT/enhancer binding protein epsilon. 56 6 61
10359588 1999
3
Selective defect in myeloid cell lactoferrin gene expression in neutrophil specific granule deficiency. 56 61
2536400 1989
4
Microbicidal/cytotoxic proteins of neutrophils are deficient in two disorders: Chediak-Higashi syndrome and "specific" granule deficiency. 61 56
2841356 1988
5
Lactoferrin deficiency as a consequence of a lack of specific granules in neutrophils from a patient with recurrent infections. Detection by immunoperoxidase staining for lactoferrin and cytochemical electron microscopy. 61 56
6155073 1980
6
Lactoferrin deficiency associated with altered granulocyte function. 56
7088114 1982
7
An anomaly of neutrophil morphology with impaired function. 56
4129798 1974
8
Stimulus-dependent impairment of the neutrophil oxidative burst response in lactoferrin-deficient mice. 54 61
18321995 2008
9
Highly glycosylated alpha1-acid glycoprotein is synthesized in myelocytes, stored in secondary granules, and released by activated neutrophils. 54 61
15941779 2005
10
Neutrophil Defects and Diagnosis Disorders of Neutrophil Function: An Overview. 61
31728980 2020
11
Brain Abscess as Severe Presentation of Specific Granule Deficiency. 61
32391290 2020
12
Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy. 61
31201888 2019
13
C/EBPε ΔRS derived from a neutrophil-specific granule deficiency patient interacts with HDAC1 and its dysfunction is restored by trichostatin A. 61
31256937 2019
14
Identification of a novel enhancer of CEBPE essential for granulocytic differentiation. 61
30952671 2019
15
CEBPE-Mutant Specific Granule Deficiency Correlates With Aberrant Granule Organization and Substantial Proteome Alterations in Neutrophils. 61
29651288 2018
16
SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. 61
28369034 2017
17
Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. 61
28369036 2017
18
c-Myb acts in parallel and cooperatively with Cebp1 to regulate neutrophil maturation in zebrafish. 61
27268086 2016
19
Role of the Leucine Zipper Domain of CCAAT/ Enhancer Binding Protein-Epsilon (C/EBPε) in Neutrophil-Specific Granule Deficiency. 61
28322138 2016
20
A Novel In-Frame Deletion in the Leucine Zipper Domain of C/EBPε Leads to Neutrophil-Specific Granule Deficiency. 61
26019275 2015
21
The antimicrobial propeptide hCAP-18 plasma levels in neutropenia of various aetiologies: a prospective study. 61
26119962 2015
22
Clinical course in a patient with neutrophil-specific granule deficiency and rapid detection of neutrophil granules as a screening test. 61
25081842 2014
23
Congenital candidiasis as a subject of research in medicine and human ecology. 61
25281815 2014
24
Disorders of neutrophil function: an overview. 61
24504971 2014
25
Human α-defensin expression is not dependent on CCAAT/enhancer binding protein-ε in a murine model. 61
24658030 2014
26
Impaired neutrophil function in 24p3 null mice contributes to enhanced susceptibility to bacterial infections. 61
23543755 2013
27
Neutrophil-specific granule deficiency. 61
23294125 2013
28
C/EBPε mediates nicotinamide-enhanced clearance of Staphylococcus aureus in mice. 61
22922257 2012
29
C/EBPepsilon directs granulocytic-vs-monocytic lineage determination and confers chemotactic function via Hlx. 61
19925846 2010
30
Derangement of transcription factor profiles during in vitro differentiation of HL60 and NB4 cells. 61
16942795 2007
31
Expression of bactericidal/permeability-increasing protein requires C/EBP epsilon. 61
17483073 2007
32
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. 61
17244686 2007
33
Disorders of neutrophil function: an overview. 61
18453130 2007
34
All-trans retinoic acid-induced expression of bactericidal/permeability-increasing protein (BPI) in human myeloid cells correlates to binding of C/EBPbeta and C/EBPepsilon to the BPI promoter. 61
16684888 2006
35
Haptoglobin is synthesized during granulocyte differentiation, stored in specific granules, and released by neutrophils in response to activation. 61
16543473 2006
36
Intractable diarrhoea of infancy caused by neutrophil specific granule deficiency and cured by stem cell transplantation. 61
16407388 2006
37
Aberrant expression of neutrophil and macrophage-related genes in a murine model for human neutrophil-specific granule deficiency. 61
16204633 2005
38
Phenotypic and functional alterations of peripheral blood monocytes in neutrophil-specific granule deficiency. 61
14576362 2004
39
White blood cell defects: molecular discoveries and clinical management. 61
12165204 2002
40
Neutrophil specific granule deficiency and mutations in the gene encoding transcription factor C/EBP(epsilon). 61
11753076 2002
41
Deficiency of the specific granule proteins, R-binder/transcobalamin I and lactoferrin, in plasma and saliva: a new disorder. 61
11298376 2001
42
The role of C/EBP(epsilon) in the terminal stages of granulocyte differentiation. 61
11239167 2001
43
Inherited Neutrophil Disorders: Molecular Basis and New Therapies. 61
11701548 2000
44
CCAAT/enhancer binding protein epsilon is critical for effective neutrophil-mediated response to inflammatory challenge. 61
10216107 1999
45
[Neutrophil lactoferrin deficiency]. 54
9833431 1998
46
CCAAT displacement protein (CDP/cut) recognizes a silencer element within the lactoferrin gene promoter. 61
9326246 1997
47
Heterogeneity of peroxidase positive granules in normal and pathologic human neutrophils. 61
9293701 1997
48
A marked decrease in defensin mRNA in the only case of congenital neutrophil-specific granule deficiency reported in Japan. 61
8018907 1994
49
Neutrophil-specific granule deficiency includes eosinophils. 61
8324226 1993
50
Ultrastructure of neutrophilic phagosome of autologous platelet in vivo in specific granule deficiency. 61
8342544 1993

Variations for Specific Granule Deficiency 1

ClinVar genetic disease variations for Specific Granule Deficiency 1:

6 (show all 39) ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 CEBPE NM_001805.3(CEBPE):c.391C>T (p.Arg131Ter)SNV Pathogenic 530667 rs760325316 14:23587910-23587910 14:23118701-23118701
2 CEBPE CEBPE, 5-BP DEL, NT224deletion Pathogenic 8854
3 CEBPE CEBPE, 1-BP INS, 1113Ainsertion Pathogenic 8855
4 SMARCD2 NM_001098426.2(SMARCD2):c.1181+1G>ASNV Pathogenic 369729 rs1057518731 17:61911268-61911268 17:63833908-63833908
5 SMARCD2 NM_001098426.2(SMARCD2):c.414_438dup (p.Gln147delinsGluAspGlyArgTer)duplication Pathogenic 369730 rs1555580263 17:61914560-61914561 17:63837200-63837201
6 SMARCD2 NM_001098426.2(SMARCD2):c.401+2T>CSNV Pathogenic 369731 rs1057518733 17:61914799-61914799 17:63837439-63837439
7 CEBPE NC_000014.9:g.23117555G>ASNV Uncertain significance 855048 14:23586764-23586764 14:23117555-23117555
8 CEBPE NC_000014.9:g.23117676G>ASNV Uncertain significance 842523 14:23586885-23586885 14:23117676-23117676
9 CEBPE NC_000014.9:g.23117768G>ASNV Uncertain significance 850508 14:23586977-23586977 14:23117768-23117768
10 CEBPE NC_000014.9:g.23117797G>ASNV Uncertain significance 834881 14:23587006-23587006 14:23117797-23117797
11 CEBPE NC_000014.9:g.23118736G>TSNV Uncertain significance 841081 14:23587945-23587945 14:23118736-23118736
12 CEBPE NC_000014.9:g.23118806C>TSNV Uncertain significance 863274 14:23588015-23588015 14:23118806-23118806
13 CEBPE NC_000014.9:g.23118875C>TSNV Uncertain significance 836534 14:23588084-23588084 14:23118875-23118875
14 CEBPE NC_000014.9:g.23118992A>TSNV Uncertain significance 847959 14:23588201-23588201 14:23118992-23118992
15 CEBPE NM_001805.3(CEBPE):c.205C>T (p.Leu69Phe)SNV Uncertain significance 530665 rs146580935 14:23588096-23588096 14:23118887-23118887
16 CEBPE NM_001805.3(CEBPE):c.496C>G (p.Leu166Val)SNV Uncertain significance 461467 rs1273577069 14:23587805-23587805 14:23118596-23118596
17 CEBPE NM_001805.3(CEBPE):c.487G>A (p.Gly163Ser)SNV Uncertain significance 530666 rs762842144 14:23587814-23587814 14:23118605-23118605
18 CEBPE NM_001805.3(CEBPE):c.662G>A (p.Ser221Asn)SNV Uncertain significance 565423 rs1566773059 14:23586880-23586880 14:23117671-23117671
19 CEBPE NM_001805.3(CEBPE):c.349G>A (p.Ala117Thr)SNV Uncertain significance 582470 rs1566773537 14:23587952-23587952 14:23118743-23118743
20 CEBPE NM_001805.3(CEBPE):c.611G>C (p.Ser204Thr)SNV Uncertain significance 658176 14:23586931-23586931 14:23117722-23117722
21 CEBPE NM_001805.3(CEBPE):c.551T>C (p.Leu184Pro)SNV Uncertain significance 664942 14:23586991-23586991 14:23117782-23117782
22 CEBPE NM_001805.3(CEBPE):c.502G>A (p.Val168Ile)SNV Uncertain significance 657093 14:23587799-23587799 14:23118590-23118590
23 CEBPE NM_001805.3(CEBPE):c.499C>T (p.Arg167Cys)SNV Uncertain significance 659768 14:23587802-23587802 14:23118593-23118593
24 CEBPE NM_001805.3(CEBPE):c.404G>A (p.Arg135Gln)SNV Uncertain significance 650956 14:23587897-23587897 14:23118688-23118688
25 CEBPE NM_001805.3(CEBPE):c.373C>T (p.Arg125Trp)SNV Uncertain significance 662588 14:23587928-23587928 14:23118719-23118719
26 CEBPE NM_001805.3(CEBPE):c.223C>A (p.Pro75Thr)SNV Uncertain significance 663169 14:23588078-23588078 14:23118869-23118869
27 CEBPE NM_001805.3(CEBPE):c.66G>T (p.Gly22=)SNV Uncertain significance 640081 14:23588235-23588235 14:23119026-23119026
28 CEBPE NM_001805.3(CEBPE):c.64G>A (p.Gly22Arg)SNV Uncertain significance 640442 14:23588237-23588237 14:23119028-23119028
29 CEBPE NM_001805.3(CEBPE):c.828C>T (p.Gly276=)SNV Likely benign 787006 14:23586714-23586714 14:23117505-23117505
30 CEBPE NM_001805.3(CEBPE):c.842G>A (p.Ser281Asn)SNV Likely benign 714668 14:23586700-23586700 14:23117491-23117491
31 CEBPE NM_001805.3(CEBPE):c.303G>A (p.Ala101=)SNV Likely benign 461466 rs149752323 14:23587998-23587998 14:23118789-23118789
32 CEBPE NM_001805.3(CEBPE):c.357G>T (p.Ala119=)SNV Likely benign 530668 rs202220573 14:23587944-23587944 14:23118735-23118735
33 CEBPE NM_001805.3(CEBPE):c.177C>G (p.Ala59=)SNV Likely benign 732426 14:23588124-23588124 14:23118915-23118915
34 CEBPE NM_001805.3(CEBPE):c.357G>A (p.Ala119=)SNV Likely benign 762741 14:23587944-23587944 14:23118735-23118735
35 CEBPE NM_001805.3(CEBPE):c.789C>G (p.Leu263=)SNV Likely benign 795218 14:23586753-23586753 14:23117544-23117544
36 CEBPE NM_001805.3(CEBPE):c.463C>A (p.Leu155Met)SNV Benign 530670 rs141903485 14:23587838-23587838 14:23118629-23118629
37 CEBPE NM_001805.3(CEBPE):c.747C>T (p.Arg249=)SNV Benign 461468 rs55722931 14:23586795-23586795 14:23117586-23117586
38 CEBPE NM_001805.3(CEBPE):c.234C>T (p.Pro78=)SNV Benign 530669 rs114913626 14:23588067-23588067 14:23118858-23118858
39 CEBPE NM_001805.3(CEBPE):c.558G>A (p.Ala186=)SNV Benign 727768 14:23586984-23586984 14:23117775-23117775

Expression for Specific Granule Deficiency 1

Search GEO for disease gene expression data for Specific Granule Deficiency 1.

Pathways for Specific Granule Deficiency 1

GO Terms for Specific Granule Deficiency 1

Biological processes related to Specific Granule Deficiency 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 defense response to bacterium GO:0042742 8.62 LTF CEBPE

Molecular functions related to Specific Granule Deficiency 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 RNA polymerase II proximal promoter sequence-specific DNA binding GO:0000978 8.62 SMARCD2 CEBPE

Sources for Specific Granule Deficiency 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
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43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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