SCN6
MCID: NTR034
MIFTS: 25

Neutropenia, Severe Congenital, 6, Autosomal Recessive (SCN6)

Categories: Blood diseases, Bone diseases, Cancer diseases, Endocrine diseases, Genetic diseases, Immune diseases, Infectious diseases, Neuronal diseases, Rare diseases, Respiratory diseases
Data Licensing
For inquiries, contact:

Aliases & Classifications for Neutropenia, Severe Congenital, 6, Autosomal Recessive

MalaCards integrated aliases for Neutropenia, Severe Congenital, 6, Autosomal Recessive:

Name: Neutropenia, Severe Congenital, 6, Autosomal Recessive 57 71
Scn6 57 73
Neutropenia, Severe Congenital, Type 6, Autosomal Recessive 38
Neutropenia, Severe Congenital 6, Autosomal Recessive 73
Severe Congenital Neutropenia 6, Autosomal Recessive 5

Characteristics:


Inheritance:

Autosomal recessive 57

OMIM®:

57 (Updated 08-Dec-2022)
Miscellaneous:
onset in early childhood
poor response to g-csf treatment


Classifications:



External Ids:

OMIM® 57 616022
OMIM Phenotypic Series 57 PS202700
MeSH 43 D009503
UMLS 71 C4014954

Summaries for Neutropenia, Severe Congenital, 6, Autosomal Recessive

UniProtKB/Swiss-Prot: 73 A disorder of hematopoiesis characterized by maturation arrest of granulopoiesis at the level of promyelocytes with peripheral blood absolute neutrophil counts below 0.5 x 10(9)/l and early onset of severe bacterial infections.

MalaCards based summary: Neutropenia, Severe Congenital, 6, Autosomal Recessive, also known as scn6, is related to severe congenital neutropenia 6. An important gene associated with Neutropenia, Severe Congenital, 6, Autosomal Recessive is JAGN1 (Jagunal Homolog 1). Affiliated tissues include neutrophil, bone marrow and bone, and related phenotypes are failure to thrive and short stature

More information from OMIM: 616022 PS202700

Related Diseases for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Symptoms & Phenotypes for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Human phenotypes related to Neutropenia, Severe Congenital, 6, Autosomal Recessive:

30 (show all 6)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 failure to thrive 30 Occasional (7.5%) HP:0001508
2 short stature 30 Occasional (7.5%) HP:0004322
3 recurrent respiratory infections 30 HP:0002205
4 recurrent otitis media 30 HP:0000403
5 neutropenia 30 HP:0001875
6 recurrent bacterial infections 30 HP:0002718

Symptoms via clinical synopsis from OMIM®:

57 (Updated 08-Dec-2022)
Respiratory:
recurrent respiratory infections

Immunology:
neutropenia
recurrent bacterial infections
maturational arrest of granulocytes at the promyelocyte/myelocyte stage seen on bone marrow biopsy

Skin Nails Hair Skin:
skin abscesses

Head And Neck Ears:
recurrent otitis media

Growth Height:
short stature (in some patients)

Growth Other:
failure to thrive (in some patients)

Clinical features from OMIM®:

616022 (Updated 08-Dec-2022)

Drugs & Therapeutics for Neutropenia, Severe Congenital, 6, Autosomal Recessive

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

Genetic Tests for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Anatomical Context for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Organs/tissues related to Neutropenia, Severe Congenital, 6, Autosomal Recessive:

MalaCards : Neutrophil, Bone Marrow, Bone, Lung, Skin, Myeloid
ODiseA: Blood And Bone Marrow, Respiratory System-Lung, Respiratory System

Publications for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Articles related to Neutropenia, Severe Congenital, 6, Autosomal Recessive:

# Title Authors PMID Year
1
JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia. 57 5
25129144 2014
2
[Application of subtractive hybridization in screening for colorectal cancer negatively related genes]. 62
9596923 1997

Variations for Neutropenia, Severe Congenital, 6, Autosomal Recessive

ClinVar genetic disease variations for Neutropenia, Severe Congenital, 6, Autosomal Recessive:

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.172G>A (p.Gly58Arg) SNV Uncertain Significance
475243 rs919986813 GRCh37: 3:9934681-9934681
GRCh38: 3:9892997-9892997
14 JAGN1 NM_032492.4(JAGN1):c.541A>C (p.Lys181Gln) SNV Uncertain Significance
475249 rs754191323 GRCh37: 3:9935050-9935050
GRCh38: 3:9893366-9893366
15 JAGN1 NM_032492.4(JAGN1):c.35C>T (p.Thr12Ile) SNV Uncertain Significance
475247 rs150797085 GRCh37: 3:9932441-9932441
GRCh38: 3:9890757-9890757
16 JAGN1 NM_032492.4(JAGN1):c.211C>A (p.Pro71Thr) SNV Uncertain Significance
475244 rs200023062 GRCh37: 3:9934720-9934720
GRCh38: 3:9893036-9893036
17 JAGN1 NM_032492.4(JAGN1):c.71C>T (p.Ala24Val) SNV Uncertain Significance
577875 rs377495463 GRCh37: 3:9932477-9932477
GRCh38: 3:9890793-9890793
18 JAGN1 NC_000003.11:g.(?_9932387)_(9935081_?)dup DUP Uncertain Significance
584197 GRCh37: 3:9932387-9935081
GRCh38: 3:9890703-9893397
19 JAGN1 NM_032492.4(JAGN1):c.41G>A (p.Gly14Asp) SNV Uncertain Significance
649136 rs1575466167 GRCh37: 3:9932447-9932447
GRCh38: 3:9890763-9890763
20 JAGN1 NM_032492.4(JAGN1):c.433G>A (p.Val145Ile) SNV Uncertain Significance
649445 rs759636820 GRCh37: 3:9934942-9934942
GRCh38: 3:9893258-9893258
21 JAGN1 NM_032492.4(JAGN1):c.46G>T (p.Asp16Tyr) SNV Uncertain Significance
658417 rs1177521463 GRCh37: 3:9932452-9932452
GRCh38: 3:9890768-9890768
22 JAGN1 NM_032492.4(JAGN1):c.11G>C (p.Arg4Pro) SNV Uncertain Significance
666030 rs569985954 GRCh37: 3:9932417-9932417
GRCh38: 3:9890733-9890733
23 JAGN1 NM_032492.4(JAGN1):c.179T>C (p.Leu60Pro) SNV Uncertain Significance
839671 rs1297627583 GRCh37: 3:9934688-9934688
GRCh38: 3:9893004-9893004
24 JAGN1 NM_032492.4(JAGN1):c.64C>T (p.Arg22Cys) SNV Uncertain Significance
841147 rs146967886 GRCh37: 3:9932470-9932470
GRCh38: 3:9890786-9890786
25 JAGN1 NM_032492.4(JAGN1):c.538AAG[1] (p.Lys181del) MICROSAT Uncertain Significance
843940 rs756989255 GRCh37: 3:9935045-9935047
GRCh38: 3:9893361-9893363
26 JAGN1 NM_032492.4(JAGN1):c.392G>A (p.Arg131His) SNV Uncertain Significance
847039 rs542419840 GRCh37: 3:9934901-9934901
GRCh38: 3:9893217-9893217
27 JAGN1 NM_032492.4(JAGN1):c.280C>G (p.Arg94Gly) SNV Uncertain Significance
848863 rs866176976 GRCh37: 3:9934789-9934789
GRCh38: 3:9893105-9893105
28 JAGN1 NM_032492.4(JAGN1):c.394C>T (p.His132Tyr) SNV Uncertain Significance
858153 rs1444848644 GRCh37: 3:9934903-9934903
GRCh38: 3:9893219-9893219
29 JAGN1 NM_032492.4(JAGN1):c.379C>T (p.Gln127Ter) SNV Uncertain Significance
939939 rs771407343 GRCh37: 3:9934888-9934888
GRCh38: 3:9893204-9893204
30 JAGN1 NM_032492.4(JAGN1):c.56A>G (p.His19Arg) SNV Uncertain Significance
943976 rs748123071 GRCh37: 3:9932462-9932462
GRCh38: 3:9890778-9890778
31 JAGN1 NM_032492.4(JAGN1):c.70_76del (p.Ala24fs) DEL Uncertain Significance
947595 rs2082557086 GRCh37: 3:9932475-9932481
GRCh38: 3:9890791-9890797
32 JAGN1 NM_032492.4(JAGN1):c.90T>C (p.Ser30=) SNV Uncertain Significance
966622 rs201225696 GRCh37: 3:9934599-9934599
GRCh38: 3:9892915-9892915
33 JAGN1 NM_032492.4(JAGN1):c.503A>G (p.Lys168Arg) SNV Uncertain Significance
1002786 rs749080431 GRCh37: 3:9935012-9935012
GRCh38: 3:9893328-9893328
34 JAGN1 NM_032492.4(JAGN1):c.346A>G (p.Ile116Val) SNV Uncertain Significance
1006422 rs1467031121 GRCh37: 3:9934855-9934855
GRCh38: 3:9893171-9893171
35 JAGN1 NM_032492.4(JAGN1):c.317G>A (p.Ser106Asn) SNV Uncertain Significance
1011467 rs2082574453 GRCh37: 3:9934826-9934826
GRCh38: 3:9893142-9893142
36 JAGN1 NM_032492.4(JAGN1):c.517T>A (p.Trp173Arg) SNV Uncertain Significance
1017842 rs2082575975 GRCh37: 3:9935026-9935026
GRCh38: 3:9893342-9893342
37 JAGN1 NM_032492.4(JAGN1):c.127G>A (p.Val43Ile) SNV Uncertain Significance
1020952 rs778975542 GRCh37: 3:9934636-9934636
GRCh38: 3:9892952-9892952
38 JAGN1 NM_032492.4(JAGN1):c.205G>A (p.Ala69Thr) SNV Uncertain Significance
1047313 rs2082573376 GRCh37: 3:9934714-9934714
GRCh38: 3:9893030-9893030
39 JAGN1 NM_032492.4(JAGN1):c.43A>G (p.Ser15Gly) SNV Uncertain Significance
1055949 GRCh37: 3:9932449-9932449
GRCh38: 3:9890765-9890765
40 JAGN1 NM_032492.4(JAGN1):c.89+4T>C SNV Uncertain Significance
1057517 GRCh37: 3:9932499-9932499
GRCh38: 3:9890815-9890815
41 JAGN1 NM_032492.4(JAGN1):c.77A>T (p.His26Leu) SNV Uncertain Significance
1060531 GRCh37: 3:9932483-9932483
GRCh38: 3:9890799-9890799
42 JAGN1 NM_032492.4(JAGN1):c.421G>C (p.Gly141Arg) SNV Uncertain Significance
1388265 GRCh37: 3:9934930-9934930
GRCh38: 3:9893246-9893246
43 JAGN1 NM_032492.4(JAGN1):c.111C>G (p.Ile37Met) SNV Uncertain Significance
1371122 GRCh37: 3:9934620-9934620
GRCh38: 3:9892936-9892936
44 JAGN1 NM_032492.4(JAGN1):c.496A>T (p.Ser166Cys) SNV Uncertain Significance
1403166 GRCh37: 3:9935005-9935005
GRCh38: 3:9893321-9893321
45 JAGN1 NM_032492.4(JAGN1):c.334A>G (p.Ile112Val) SNV Uncertain Significance
1409634 GRCh37: 3:9934843-9934843
GRCh38: 3:9893159-9893159
46 JAGN1 NM_032492.4(JAGN1):c.522C>G (p.Phe174Leu) SNV Uncertain Significance
1400765 GRCh37: 3:9935031-9935031
GRCh38: 3:9893347-9893347
47 JAGN1 NM_032492.4(JAGN1):c.319A>G (p.Met107Val) SNV Uncertain Significance
1489464 GRCh37: 3:9934828-9934828
GRCh38: 3:9893144-9893144
48 JAGN1 NM_032492.4(JAGN1):c.163A>T (p.Met55Leu) SNV Uncertain Significance
1486200 GRCh37: 3:9934672-9934672
GRCh38: 3:9892988-9892988
49 JAGN1 NM_032492.4(JAGN1):c.193C>T (p.His65Tyr) SNV Uncertain Significance
1480459 GRCh37: 3:9934702-9934702
GRCh38: 3:9893018-9893018
50 JAGN1 NM_032492.4(JAGN1):c.124T>C (p.Tyr42His) SNV Uncertain Significance
1512903 GRCh37: 3:9934633-9934633
GRCh38: 3:9892949-9892949

UniProtKB/Swiss-Prot genetic disease variations for Neutropenia, Severe Congenital, 6, Autosomal Recessive:

73
# Symbol AA change Variation ID SNP ID
1 JAGN1 p.Gly14Ser VAR_071795 rs786205704
2 JAGN1 p.Arg20Gln VAR_071796 rs777966677
3 JAGN1 p.Glu21Asp VAR_071797 rs587777729
4 JAGN1 p.His44Tyr VAR_071798 rs587777728
5 JAGN1 p.Gln162Arg VAR_071799 rs587777730

Expression for Neutropenia, Severe Congenital, 6, Autosomal Recessive

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

Pathways for Neutropenia, Severe Congenital, 6, Autosomal Recessive

GO Terms for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Sources for Neutropenia, Severe Congenital, 6, Autosomal Recessive

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
Content
Loading form....