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, Neuronal diseases, Rare diseases

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 56 71
Severe Congenital Neutropenia 6, Autosomal Recessive 29 6
Scn6 56 73
Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency 58
Neutropenia, Severe Congenital, Type 6, Autosomal Recessive 39
Neutropenia, Severe Congenital 6, Autosomal Recessive 73

Characteristics:

Orphanet epidemiological data:

58
autosomal recessive severe congenital neutropenia due to jagn1 deficiency
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM:

56
Inheritance:
autosomal recessive

Miscellaneous:
onset in early childhood
poor response to g-csf treatment


HPO:

31
neutropenia, severe congenital, 6, autosomal recessive:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare immunological diseases


External Ids:

OMIM 56 616022
OMIM Phenotypic Series 56 PS202700
MeSH 43 D009503
ICD10 via Orphanet 33 D70
Orphanet 58 ORPHA423384
UMLS 71 C4014954

Summaries for Neutropenia, Severe Congenital, 6, Autosomal Recessive

UniProtKB/Swiss-Prot : 73 Neutropenia, severe congenital 6, autosomal recessive: 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, is also known as severe congenital neutropenia 6, autosomal recessive. An important gene associated with Neutropenia, Severe Congenital, 6, Autosomal Recessive is JAGN1 (Jagunal Homolog 1). Affiliated tissues include neutrophil, bone and bone marrow, and related phenotypes are failure to thrive and short stature

More information from OMIM: 616022 PS202700

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

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

31 (show all 6)
# Description HPO Frequency HPO Source Accession
1 failure to thrive 31 occasional (7.5%) HP:0001508
2 short stature 31 occasional (7.5%) HP:0004322
3 recurrent respiratory infections 31 HP:0002205
4 recurrent otitis media 31 HP:0000403
5 neutropenia 31 HP:0001875
6 recurrent bacterial infections 31 HP:0002718

Symptoms via clinical synopsis from OMIM:

56
Respiratory:
recurrent respiratory infections

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

Growth Other:
failure to thrive (in some patients)

Head And Neck Ears:
recurrent otitis media

Growth Height:
short stature (in some patients)

Skin Nails Hair Skin:
skin abscesses

Clinical features from OMIM:

616022

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

Genetic tests related to Neutropenia, Severe Congenital, 6, Autosomal Recessive:

# Genetic test Affiliating Genes
1 Severe Congenital Neutropenia 6, Autosomal Recessive 29 JAGN1

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

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

40
Neutrophil, Bone, Bone Marrow, Skin, Myeloid

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. 56 6
25129144 2014
2
[Application of subtractive hybridization in screening for colorectal cancer negatively related genes]. 61
9596923 1997

Variations for Neutropenia, Severe Congenital, 6, Autosomal Recessive

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

6 (show all 17) ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 JAGN1 NM_032492.4(JAGN1):c.3G>A (p.Met1Ile)SNV Pathogenic 156113 rs587777727 3:9932409-9932409 3:9890725-9890725
2 JAGN1 NM_032492.4(JAGN1):c.130C>T (p.His44Tyr)SNV Pathogenic 156114 rs587777728 3:9934639-9934639 3:9892955-9892955
3 JAGN1 NM_032492.4(JAGN1):c.63G>T (p.Glu21Asp)SNV Pathogenic 156115 rs587777729 3:9932469-9932469 3:9890785-9890785
4 JAGN1 NM_032492.4(JAGN1):c.485A>G (p.Gln162Arg)SNV Pathogenic 156116 rs587777730 3:9934994-9934994 3:9893310-9893310
5 JAGN1 NM_032492.4(JAGN1):c.35_43del (p.Thr12_Gly14del)deletion Pathogenic 156117 rs587777731 3:9932436-9932444 3:9890752-9890760
6 JAGN1 NM_032492.4(JAGN1):c.35C>T (p.Thr12Ile)SNV Uncertain significance 475247 rs150797085 3:9932441-9932441 3:9890757-9890757
7 JAGN1 NM_032492.4(JAGN1):c.541A>C (p.Lys181Gln)SNV Uncertain significance 475249 rs754191323 3:9935050-9935050 3:9893366-9893366
8 JAGN1 NM_032492.4(JAGN1):c.211C>A (p.Pro71Thr)SNV Uncertain significance 475244 rs200023062 3:9934720-9934720 3:9893036-9893036
9 JAGN1 NM_032492.4(JAGN1):c.172G>A (p.Gly58Arg)SNV Uncertain significance 475243 rs919986813 3:9934681-9934681 3:9892997-9892997
10 JAGN1 NC_000003.11:g.(?_9932387)_(9935081_?)dupduplication Uncertain significance 584197 3:9932387-9935081 3:9890703-9893397
11 JAGN1 NM_032492.4(JAGN1):c.71C>T (p.Ala24Val)SNV Uncertain significance 577875 rs377495463 3:9932477-9932477 3:9890793-9890793
12 JAGN1 NM_032492.4(JAGN1):c.11G>C (p.Arg4Pro)SNV Uncertain significance 666030 3:9932417-9932417 3:9890733-9890733
13 JAGN1 NM_032492.4(JAGN1):c.41G>A (p.Gly14Asp)SNV Uncertain significance 649136 3:9932447-9932447 3:9890763-9890763
14 JAGN1 NM_032492.4(JAGN1):c.46G>T (p.Asp16Tyr)SNV Uncertain significance 658417 3:9932452-9932452 3:9890768-9890768
15 JAGN1 NM_032492.4(JAGN1):c.433G>A (p.Val145Ile)SNV Uncertain significance 649445 3:9934942-9934942 3:9893258-9893258
16 JAGN1 NM_032492.4(JAGN1):c.244A>G (p.Ile82Val)SNV Benign 475246 rs35365817 3:9934753-9934753 3:9893069-9893069
17 JAGN1 NM_032492.4(JAGN1):c.21G>C (p.Pro7=)SNV Benign 475245 rs138937423 3:9932427-9932427 3:9890743-9890743

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

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30 HMDB
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32 ICD10
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43 MeSH
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53 NINDS
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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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