SCN6
MCID: NTR034
MIFTS: 22

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

Categories: Blood diseases, Bone diseases, Genetic diseases, Immune 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 57 73
Severe Congenital Neutropenia 6, Autosomal Recessive 29 6
Scn6 57 75
Autosomal Recessive Severe Congenital Neutropenia Due to Jagn1 Deficiency 59
Neutropenia, Severe Congenital, Type 6, Autosomal Recessive 40
Neutropenia, Severe Congenital 6, Autosomal Recessive 75

Characteristics:

Orphanet epidemiological data:

59
autosomal recessive severe congenital neutropenia due to jagn1 deficiency
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM:

57
Inheritance:
autosomal recessive

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


HPO:

32
neutropenia, severe congenital, 6, autosomal recessive:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 59  
Rare immunological diseases


External Ids:

OMIM 57 616022
Orphanet 59 ORPHA423384
ICD10 via Orphanet 34 D70
MeSH 44 D009503
UMLS 73 C4014954

Summaries for Neutropenia, Severe Congenital, 6, Autosomal Recessive

UniProtKB/Swiss-Prot : 75 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 skin, and related phenotypes are failure to thrive and recurrent respiratory infections

Description from OMIM: 616022

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

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

Symptoms via clinical synopsis from OMIM:

57
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

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

32 (show all 6)
# Description HPO Frequency HPO Source Accession
1 failure to thrive 32 occasional (7.5%) HP:0001508
2 recurrent respiratory infections 32 HP:0002205
3 short stature 32 occasional (7.5%) HP:0004322
4 recurrent otitis media 32 HP:0000403
5 neutropenia 32 HP:0001875
6 recurrent bacterial infections 32 HP:0002718

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:

41
Neutrophil, Bone, Skin, Bone Marrow

Publications for Neutropenia, Severe Congenital, 6, Autosomal Recessive

Variations for Neutropenia, Severe Congenital, 6, Autosomal Recessive

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

75
# 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

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

6 (show all 32)
# Gene Variation Type Significance SNP ID Assembly Location
1 JAGN1 NM_032492.3(JAGN1): c.3G> A (p.Met1Ile) single nucleotide variant Pathogenic rs587777727 GRCh38 Chromosome 3, 9890725: 9890725
2 JAGN1 NM_032492.3(JAGN1): c.3G> A (p.Met1Ile) single nucleotide variant Pathogenic rs587777727 GRCh37 Chromosome 3, 9932409: 9932409
3 JAGN1 NM_032492.3(JAGN1): c.130C> T (p.His44Tyr) single nucleotide variant Pathogenic rs587777728 GRCh37 Chromosome 3, 9934639: 9934639
4 JAGN1 NM_032492.3(JAGN1): c.130C> T (p.His44Tyr) single nucleotide variant Pathogenic rs587777728 GRCh38 Chromosome 3, 9892955: 9892955
5 JAGN1 NM_032492.3(JAGN1): c.63G> T (p.Glu21Asp) single nucleotide variant Pathogenic rs587777729 GRCh38 Chromosome 3, 9890785: 9890785
6 JAGN1 NM_032492.3(JAGN1): c.63G> T (p.Glu21Asp) single nucleotide variant Pathogenic rs587777729 GRCh37 Chromosome 3, 9932469: 9932469
7 JAGN1 NM_032492.3(JAGN1): c.485A> G (p.Gln162Arg) single nucleotide variant Pathogenic rs587777730 GRCh38 Chromosome 3, 9893310: 9893310
8 JAGN1 NM_032492.3(JAGN1): c.485A> G (p.Gln162Arg) single nucleotide variant Pathogenic rs587777730 GRCh37 Chromosome 3, 9934994: 9934994
9 JAGN1 NM_032492.3(JAGN1): c.35_43delCCGACGGCA (p.Thr12_Gly14del) deletion Pathogenic rs587777731 GRCh38 Chromosome 3, 9890757: 9890765
10 JAGN1 NM_032492.3(JAGN1): c.35_43delCCGACGGCA (p.Thr12_Gly14del) deletion Pathogenic rs587777731 GRCh37 Chromosome 3, 9932441: 9932449
11 JAGN1 NM_032492.3(JAGN1): c.21G> C (p.Pro7=) single nucleotide variant Benign rs138937423 GRCh37 Chromosome 3, 9932427: 9932427
12 JAGN1 NM_032492.3(JAGN1): c.21G> C (p.Pro7=) single nucleotide variant Benign rs138937423 GRCh38 Chromosome 3, 9890743: 9890743
13 JAGN1 NM_032492.3(JAGN1): c.35C> T (p.Thr12Ile) single nucleotide variant Uncertain significance rs150797085 GRCh37 Chromosome 3, 9932441: 9932441
14 JAGN1 NM_032492.3(JAGN1): c.35C> T (p.Thr12Ile) single nucleotide variant Uncertain significance rs150797085 GRCh38 Chromosome 3, 9890757: 9890757
15 JAGN1 NM_032492.3(JAGN1): c.403G> A (p.Ala135Thr) single nucleotide variant Benign rs61746084 GRCh38 Chromosome 3, 9893228: 9893228
16 JAGN1 NM_032492.3(JAGN1): c.403G> A (p.Ala135Thr) single nucleotide variant Benign rs61746084 GRCh37 Chromosome 3, 9934912: 9934912
17 JAGN1 NM_032492.3(JAGN1): c.541A> C (p.Lys181Gln) single nucleotide variant Uncertain significance rs754191323 GRCh38 Chromosome 3, 9893366: 9893366
18 JAGN1 NM_032492.3(JAGN1): c.541A> C (p.Lys181Gln) single nucleotide variant Uncertain significance rs754191323 GRCh37 Chromosome 3, 9935050: 9935050
19 JAGN1 NM_032492.3(JAGN1): c.211C> A (p.Pro71Thr) single nucleotide variant Uncertain significance rs200023062 GRCh37 Chromosome 3, 9934720: 9934720
20 JAGN1 NM_032492.3(JAGN1): c.211C> A (p.Pro71Thr) single nucleotide variant Uncertain significance rs200023062 GRCh38 Chromosome 3, 9893036: 9893036
21 JAGN1 NM_032492.3(JAGN1): c.172G> A (p.Gly58Arg) single nucleotide variant Uncertain significance rs919986813 GRCh38 Chromosome 3, 9892997: 9892997
22 JAGN1 NM_032492.3(JAGN1): c.172G> A (p.Gly58Arg) single nucleotide variant Uncertain significance rs919986813 GRCh37 Chromosome 3, 9934681: 9934681
23 JAGN1 NM_032492.3(JAGN1): c.244A> G (p.Ile82Val) single nucleotide variant Benign rs35365817 GRCh38 Chromosome 3, 9893069: 9893069
24 JAGN1 NM_032492.3(JAGN1): c.244A> G (p.Ile82Val) single nucleotide variant Benign rs35365817 GRCh37 Chromosome 3, 9934753: 9934753
25 JAGN1 NM_032492.3(JAGN1): c.498C> T (p.Ser166=) single nucleotide variant Benign rs61738795 GRCh38 Chromosome 3, 9893323: 9893323
26 JAGN1 NM_032492.3(JAGN1): c.498C> T (p.Ser166=) single nucleotide variant Benign rs61738795 GRCh37 Chromosome 3, 9935007: 9935007
27 JAGN1 NM_032492.3(JAGN1): c.270C> T (p.Leu90=) single nucleotide variant Likely benign rs143617732 GRCh37 Chromosome 3, 9934779: 9934779
28 JAGN1 NM_032492.3(JAGN1): c.270C> T (p.Leu90=) single nucleotide variant Likely benign rs143617732 GRCh38 Chromosome 3, 9893095: 9893095
29 JAGN1 NC_000003.12: g.(?_9890703)_(9893397_?)dup duplication Uncertain significance GRCh37 Chromosome 3, 9932387: 9935081
30 JAGN1 NC_000003.12: g.(?_9890703)_(9893397_?)dup duplication Uncertain significance GRCh38 Chromosome 3, 9890703: 9893397
31 JAGN1 NM_032492.4(JAGN1): c.71C> T (p.Ala24Val) single nucleotide variant Uncertain significance rs377495463 GRCh37 Chromosome 3, 9932477: 9932477
32 JAGN1 NM_032492.4(JAGN1): c.71C> T (p.Ala24Val) single nucleotide variant Uncertain significance rs377495463 GRCh38 Chromosome 3, 9890793: 9890793

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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