SCN6
MCID: SVR108
MIFTS: 25

Severe Congenital Neutropenia 6 (SCN6)

Categories: Blood diseases, Bone diseases, Cancer diseases, Endocrine diseases, Genetic diseases, Immune diseases, Infectious diseases, Neuronal diseases, Rare diseases, Respiratory diseases
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Aliases & Classifications for Severe Congenital Neutropenia 6

MalaCards integrated aliases for Severe Congenital Neutropenia 6:

Name: Severe Congenital Neutropenia 6 11 14
Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency 11 58 28 5
Scn6 11

Characteristics:


Inheritance:

Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency: Autosomal recessive 58

Prevelance:

Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency: <1/1000000 (Worldwide) 58

Age Of Onset:

Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency: Infancy,Neonatal 58

Classifications:

Orphanet: 58  
Rare immunological diseases


External Ids:

Disease Ontology 11 DOID:0112134
ICD10 via Orphanet 32 D70
Orphanet 58 ORPHA423384

Summaries for Severe Congenital Neutropenia 6

Orphanet: 58 Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency is a rare, genetic, primary immunodeficiency disorder characterized by early-onset, recurrent, severe bacterial infections, granulopoiesis maturation arrest at the promyelocyte/myelocyte stage and markedly reduced absolute neutrophil counts, resulting from recessively inherited mutations in the JAGN1 gene. Mild facial dysmorphism (i.e. triangular face), short stature, failure to thrive, hypothyroidism, developmental delay, pancreatic insufficiency and coarctation of aorta, as well as bone and urogenital abnormalities, may also be associated.

MalaCards based summary: Severe Congenital Neutropenia 6, also known as autosomal recessive severe congenital neutropenia due to jagn1 deficiency, is related to neutropenia, severe congenital, 6, autosomal recessive and severe congenital neutropenia. An important gene associated with Severe Congenital Neutropenia 6 is JAGN1 (Jagunal Homolog 1). Affiliated tissues include neutrophil, bone and myeloid.

Disease Ontology: 11 A severe congenital neutropenia that has material basis in homozygous or compound heterozygous mutation in JAGN1 on chromosome 3p25.3.

Related Diseases for Severe Congenital Neutropenia 6

Diseases in the Neutropenia family:

Neutropenia, Chronic Familial Neutropenia, Severe Congenital, 1, Autosomal Dominant
Neutropenia, Severe Congenital, 3, Autosomal Recessive Neutropenia, Severe Congenital, 4, Autosomal Recessive
Neutropenia, Severe Congenital, 2, Autosomal Dominant Neutropenia, Severe Congenital, 5, Autosomal Recessive
Neutropenia, Severe Congenital, 6, Autosomal Recessive Neutropenia, Severe Congenital, 7, Autosomal Recessive
Neutropenia, Severe Congenital, 8, Autosomal Dominant Neutropenia, Severe Congenital, 9, Autosomal Dominant
Severe Congenital Neutropenia Severe Congenital Neutropenia 1
Severe Congenital Neutropenia 7 Autosomal Dominant Severe Congenital Neutropenia
Severe Congenital Neutropenia 2 Severe Congenital Neutropenia 5
Severe Congenital Neutropenia 3 Severe Congenital Neutropenia 6
Severe Congenital Neutropenia 8 Severe Congenital Neutropenia 4
Elane-Related Neutropenia Acquired Neutropenia
Autosomal Recessive Severe Congenital Neutropenia

Diseases related to Severe Congenital Neutropenia 6 via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 neutropenia, severe congenital, 6, autosomal recessive 11.3
2 severe congenital neutropenia 10.0 JAGN1 G6PC3
3 neutropenia 9.9 JAGN1 G6PC3
4 severe congenital neutropenia 7 9.9 JAGN1 G6PC3
5 severe congenital neutropenia 5 9.9 JAGN1 G6PC3
6 severe congenital neutropenia 3 9.9 JAGN1 G6PC3
7 poikiloderma with neutropenia 9.9 JAGN1 G6PC3
8 autosomal dominant severe congenital neutropenia 9.8 JAGN1 G6PC3
9 cohen syndrome 9.8 JAGN1 G6PC3
10 cyclic neutropenia 9.7 JAGN1 G6PC3

Graphical network of the top 20 diseases related to Severe Congenital Neutropenia 6:



Diseases related to Severe Congenital Neutropenia 6

Symptoms & Phenotypes for Severe Congenital Neutropenia 6

Drugs & Therapeutics for Severe Congenital Neutropenia 6

Search Clinical Trials, NIH Clinical Center for Severe Congenital Neutropenia 6

Genetic Tests for Severe Congenital Neutropenia 6

Genetic tests related to Severe Congenital Neutropenia 6:

# Genetic test Affiliating Genes
1 Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency 28 JAGN1

Anatomical Context for Severe Congenital Neutropenia 6

Organs/tissues related to Severe Congenital Neutropenia 6:

MalaCards : Neutrophil, Bone, Myeloid

Publications for Severe Congenital Neutropenia 6

Articles related to Severe Congenital Neutropenia 6:

# Title Authors PMID Year
1
JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia. 5
25129144 2014
2
[Application of subtractive hybridization in screening for colorectal cancer negatively related genes]. 62
9596923 1997

Variations for Severe Congenital Neutropenia 6

ClinVar genetic disease variations for Severe Congenital Neutropenia 6:

5 (show top 50) (show all 86)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 JAGN1 NM_032492.4(JAGN1):c.485A>G (p.Gln162Arg) SNV Pathogenic
156116 rs587777730 GRCh37: 3:9934994-9934994
GRCh38: 3:9893310-9893310
2 JAGN1 NM_032492.4(JAGN1):c.130C>T (p.His44Tyr) SNV Pathogenic
156114 rs587777728 GRCh37: 3:9934639-9934639
GRCh38: 3:9892955-9892955
3 JAGN1 NM_032492.4(JAGN1):c.3G>A (p.Met1Ile) SNV Conflicting Interpretations Of Pathogenicity
156113 rs587777727 GRCh37: 3:9932409-9932409
GRCh38: 3:9890725-9890725
4 JAGN1 NM_032492.4(JAGN1):c.63G>T (p.Glu21Asp) SNV Uncertain Significance
156115 rs587777729 GRCh37: 3:9932469-9932469
GRCh38: 3:9890785-9890785
5 JAGN1 NM_032492.4(JAGN1):c.35_43del (p.Thr12_Gly14del) DEL Uncertain Significance
156117 rs587777731 GRCh37: 3:9932436-9932444
GRCh38: 3:9890752-9890760
6 JAGN1 NM_032492.4(JAGN1):c.519G>T (p.Trp173Cys) SNV Uncertain Significance
1370140 GRCh37: 3:9935028-9935028
GRCh38: 3:9893344-9893344
7 JAGN1 NM_032492.4(JAGN1):c.184C>T (p.Leu62Phe) SNV Uncertain Significance
1402910 GRCh37: 3:9934693-9934693
GRCh38: 3:9893009-9893009
8 JAGN1 NM_032492.4(JAGN1):c.542A>G (p.Lys181Arg) SNV Uncertain Significance
1361485 GRCh37: 3:9935051-9935051
GRCh38: 3:9893367-9893367
9 JAGN1 NM_032492.4(JAGN1):c.389A>G (p.Tyr130Cys) SNV Uncertain Significance
1366171 GRCh37: 3:9934898-9934898
GRCh38: 3:9893214-9893214
10 JAGN1 NM_032492.4(JAGN1):c.145C>G (p.Leu49Val) SNV Uncertain Significance
1480106 GRCh37: 3:9934654-9934654
GRCh38: 3:9892970-9892970
11 JAGN1 NM_032492.4(JAGN1):c.11G>T (p.Arg4Leu) SNV Uncertain Significance
1467577 GRCh37: 3:9932417-9932417
GRCh38: 3:9890733-9890733
12 JAGN1 NM_032492.4(JAGN1):c.260T>C (p.Leu87Ser) SNV Uncertain Significance
1499691 GRCh37: 3:9934769-9934769
GRCh38: 3:9893085-9893085
13 JAGN1 NM_032492.4(JAGN1):c.541A>C (p.Lys181Gln) SNV Uncertain Significance
475249 rs754191323 GRCh37: 3:9935050-9935050
GRCh38: 3:9893366-9893366
14 JAGN1 NM_032492.4(JAGN1):c.35C>T (p.Thr12Ile) SNV Uncertain Significance
475247 rs150797085 GRCh37: 3:9932441-9932441
GRCh38: 3:9890757-9890757
15 JAGN1 NM_032492.4(JAGN1):c.211C>A (p.Pro71Thr) SNV Uncertain Significance
475244 rs200023062 GRCh37: 3:9934720-9934720
GRCh38: 3:9893036-9893036
16 JAGN1 NM_032492.4(JAGN1):c.71C>T (p.Ala24Val) SNV Uncertain Significance
577875 rs377495463 GRCh37: 3:9932477-9932477
GRCh38: 3:9890793-9890793
17 JAGN1 NM_032492.4(JAGN1):c.41G>A (p.Gly14Asp) SNV Uncertain Significance
649136 rs1575466167 GRCh37: 3:9932447-9932447
GRCh38: 3:9890763-9890763
18 JAGN1 NM_032492.4(JAGN1):c.433G>A (p.Val145Ile) SNV Uncertain Significance
649445 rs759636820 GRCh37: 3:9934942-9934942
GRCh38: 3:9893258-9893258
19 JAGN1 NM_032492.4(JAGN1):c.46G>T (p.Asp16Tyr) SNV Uncertain Significance
658417 rs1177521463 GRCh37: 3:9932452-9932452
GRCh38: 3:9890768-9890768
20 JAGN1 NM_032492.4(JAGN1):c.11G>C (p.Arg4Pro) SNV Uncertain Significance
666030 rs569985954 GRCh37: 3:9932417-9932417
GRCh38: 3:9890733-9890733
21 JAGN1 NM_032492.4(JAGN1):c.179T>C (p.Leu60Pro) SNV Uncertain Significance
839671 rs1297627583 GRCh37: 3:9934688-9934688
GRCh38: 3:9893004-9893004
22 JAGN1 NM_032492.4(JAGN1):c.64C>T (p.Arg22Cys) SNV Uncertain Significance
841147 rs146967886 GRCh37: 3:9932470-9932470
GRCh38: 3:9890786-9890786
23 JAGN1 NM_032492.4(JAGN1):c.538AAG[1] (p.Lys181del) MICROSAT Uncertain Significance
843940 rs756989255 GRCh37: 3:9935045-9935047
GRCh38: 3:9893361-9893363
24 JAGN1 NM_032492.4(JAGN1):c.392G>A (p.Arg131His) SNV Uncertain Significance
847039 rs542419840 GRCh37: 3:9934901-9934901
GRCh38: 3:9893217-9893217
25 JAGN1 NM_032492.4(JAGN1):c.394C>T (p.His132Tyr) SNV Uncertain Significance
858153 rs1444848644 GRCh37: 3:9934903-9934903
GRCh38: 3:9893219-9893219
26 JAGN1 NM_032492.4(JAGN1):c.379C>T (p.Gln127Ter) SNV Uncertain Significance
939939 rs771407343 GRCh37: 3:9934888-9934888
GRCh38: 3:9893204-9893204
27 JAGN1 NM_032492.4(JAGN1):c.56A>G (p.His19Arg) SNV Uncertain Significance
943976 rs748123071 GRCh37: 3:9932462-9932462
GRCh38: 3:9890778-9890778
28 JAGN1 NM_032492.4(JAGN1):c.70_76del (p.Ala24fs) DEL Uncertain Significance
947595 rs2082557086 GRCh37: 3:9932475-9932481
GRCh38: 3:9890791-9890797
29 JAGN1 NM_032492.4(JAGN1):c.90T>C (p.Ser30=) SNV Uncertain Significance
966622 rs201225696 GRCh37: 3:9934599-9934599
GRCh38: 3:9892915-9892915
30 JAGN1 NM_032492.4(JAGN1):c.503A>G (p.Lys168Arg) SNV Uncertain Significance
1002786 rs749080431 GRCh37: 3:9935012-9935012
GRCh38: 3:9893328-9893328
31 JAGN1 NM_032492.4(JAGN1):c.346A>G (p.Ile116Val) SNV Uncertain Significance
1006422 rs1467031121 GRCh37: 3:9934855-9934855
GRCh38: 3:9893171-9893171
32 JAGN1 NM_032492.4(JAGN1):c.317G>A (p.Ser106Asn) SNV Uncertain Significance
1011467 rs2082574453 GRCh37: 3:9934826-9934826
GRCh38: 3:9893142-9893142
33 JAGN1 NM_032492.4(JAGN1):c.517T>A (p.Trp173Arg) SNV Uncertain Significance
1017842 rs2082575975 GRCh37: 3:9935026-9935026
GRCh38: 3:9893342-9893342
34 JAGN1 NM_032492.4(JAGN1):c.127G>A (p.Val43Ile) SNV Uncertain Significance
1020952 rs778975542 GRCh37: 3:9934636-9934636
GRCh38: 3:9892952-9892952
35 JAGN1 NM_032492.4(JAGN1):c.43A>G (p.Ser15Gly) SNV Uncertain Significance
1055949 GRCh37: 3:9932449-9932449
GRCh38: 3:9890765-9890765
36 JAGN1 NM_032492.4(JAGN1):c.421G>C (p.Gly141Arg) SNV Uncertain Significance
1388265 GRCh37: 3:9934930-9934930
GRCh38: 3:9893246-9893246
37 JAGN1 NM_032492.4(JAGN1):c.111C>G (p.Ile37Met) SNV Uncertain Significance
1371122 GRCh37: 3:9934620-9934620
GRCh38: 3:9892936-9892936
38 JAGN1 NM_032492.4(JAGN1):c.496A>T (p.Ser166Cys) SNV Uncertain Significance
1403166 GRCh37: 3:9935005-9935005
GRCh38: 3:9893321-9893321
39 JAGN1 NM_032492.4(JAGN1):c.334A>G (p.Ile112Val) SNV Uncertain Significance
1409634 GRCh37: 3:9934843-9934843
GRCh38: 3:9893159-9893159
40 JAGN1 NM_032492.4(JAGN1):c.522C>G (p.Phe174Leu) SNV Uncertain Significance
1400765 GRCh37: 3:9935031-9935031
GRCh38: 3:9893347-9893347
41 JAGN1 NM_032492.4(JAGN1):c.319A>G (p.Met107Val) SNV Uncertain Significance
1489464 GRCh37: 3:9934828-9934828
GRCh38: 3:9893144-9893144
42 JAGN1 NM_032492.4(JAGN1):c.163A>T (p.Met55Leu) SNV Uncertain Significance
1486200 GRCh37: 3:9934672-9934672
GRCh38: 3:9892988-9892988
43 JAGN1 NM_032492.4(JAGN1):c.193C>T (p.His65Tyr) SNV Uncertain Significance
1480459 GRCh37: 3:9934702-9934702
GRCh38: 3:9893018-9893018
44 JAGN1 NM_032492.4(JAGN1):c.124T>C (p.Tyr42His) SNV Uncertain Significance
1512903 GRCh37: 3:9934633-9934633
GRCh38: 3:9892949-9892949
45 JAGN1 NM_032492.4(JAGN1):c.443T>C (p.Met148Thr) SNV Uncertain Significance
1503991 GRCh37: 3:9934952-9934952
GRCh38: 3:9893268-9893268
46 JAGN1 NC_000003.11:g.(?_9932387)_(9935081_?)del DEL Uncertain Significance
1052604 GRCh37: 3:9932387-9935081
GRCh38:
47 JAGN1 NM_032492.4(JAGN1):c.211C>T (p.Pro71Ser) SNV Uncertain Significance
1009400 rs200023062 GRCh37: 3:9934720-9934720
GRCh38: 3:9893036-9893036
48 JAGN1 NM_032492.4(JAGN1):c.77A>T (p.His26Leu) SNV Uncertain Significance
1060531 GRCh37: 3:9932483-9932483
GRCh38: 3:9890799-9890799
49 JAGN1 NM_032492.4(JAGN1):c.89+4T>C SNV Uncertain Significance
1057517 GRCh37: 3:9932499-9932499
GRCh38: 3:9890815-9890815
50 JAGN1 NM_032492.4(JAGN1):c.205G>A (p.Ala69Thr) SNV Uncertain Significance
1047313 rs2082573376 GRCh37: 3:9934714-9934714
GRCh38: 3:9893030-9893030

Expression for Severe Congenital Neutropenia 6

Search GEO for disease gene expression data for Severe Congenital Neutropenia 6.

Pathways for Severe Congenital Neutropenia 6

GO Terms for Severe Congenital Neutropenia 6

Sources for Severe Congenital Neutropenia 6

2 CDC
6 CNVD
8 Cosmic
9 dbSNP
10 DGIdb
16 EFO
17 ExPASy
18 FMA
19 GARD
27 GO
28 GTR
29 HMDB
30 HPO
31 ICD10
32 ICD10 via Orphanet
33 ICD11
34 ICD9CM
35 IUPHAR
36 LifeMap
38 LOVD
40 MedGen
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
52 NINDS
53 Novoseek
55 ODiseA
56 OMIM via Orphanet
57 OMIM® (Updated 08-Dec-2022)
61 PubChem
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 Tocris
71 UMLS
72 UMLS via Orphanet
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