SCN5
MCID: NTR031
MIFTS: 30

Neutropenia, Severe Congenital, 5, Autosomal Recessive (SCN5)

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 Neutropenia, Severe Congenital, 5, Autosomal Recessive

MalaCards integrated aliases for Neutropenia, Severe Congenital, 5, Autosomal Recessive:

Name: Neutropenia, Severe Congenital, 5, Autosomal Recessive 57 71
Scn5 57 73
Neutropenia, Congenital, Severe, Type 5, Autosomal Recessive 38
Neutropenia, Severe Congenital 5, Autosomal Recessive 73
Severe Congenital Neutropenia 5, Autosomal Recessive 5

Characteristics:


Inheritance:

Autosomal recessive 57

OMIM®:

57 (Updated 08-Dec-2022)
Miscellaneous:
onset in infancy
early death from infection may occur


Classifications:



Summaries for Neutropenia, Severe Congenital, 5, Autosomal Recessive

OMIM®: 57 Severe congenital neutropenia-5 is an autosomal recessive primary immunodeficiency disorder characterized primarily by neutropenia and neutrophil dysfunction, a lack of response to G-CSF, life-threatening infections, bone marrow fibrosis, and renal extramedullary hematopoiesis (summary by Vilboux et al., 2013). For a general phenotypic description and a discussion of genetic heterogeneity of severe congenital neutropenia, see SCN1 (202700). (615285) (Updated 08-Dec-2022)

MalaCards based summary: Neutropenia, Severe Congenital, 5, Autosomal Recessive, also known as scn5, is related to severe congenital neutropenia 5. An important gene associated with Neutropenia, Severe Congenital, 5, Autosomal Recessive is VPS45 (Vacuolar Protein Sorting 45 Homolog). Affiliated tissues include bone marrow, neutrophil and bone, and related phenotypes are global developmental delay and failure to thrive

UniProtKB/Swiss-Prot: 73 An autosomal recessive primary immunodeficiency disorder characterized primarily by neutropenia and neutrophil dysfunction, a lack of response to G-CSF, life-threatening infections, bone marrow fibrosis, and renal extramedullary hematopoiesis.

Related Diseases for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Symptoms & Phenotypes for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Human phenotypes related to Neutropenia, Severe Congenital, 5, Autosomal Recessive:

30 (show all 11)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 global developmental delay 30 Occasional (7.5%) HP:0001263
2 failure to thrive 30 HP:0001508
3 splenomegaly 30 HP:0001744
4 hepatomegaly 30 HP:0002240
5 anemia 30 HP:0001903
6 thrombocytopenia 30 HP:0001873
7 neutropenia 30 HP:0001875
8 recurrent infections 30 HP:0002719
9 leukopenia 30 HP:0001882
10 extramedullary hematopoiesis 30 HP:0001978
11 increased circulating antibody level 30 HP:0010702

Symptoms via clinical synopsis from OMIM®:

57 (Updated 08-Dec-2022)
Abdomen Spleen:
splenomegaly

Hematology:
anemia
thrombocytopenia
extramedullary hematopoiesis
nucleated red cells in peripheral blood
bone marrow fibrosis
more
Growth Weight:
poor weight gain

Neurologic Central Nervous System:
delayed psychomotor development (in 1 family)

Abdomen Liver:
hepatomegaly

Immunology:
neutropenia
leukopenia
hypergammaglobulinemia
recurrent infections, bacterial and fungal
neutrophil dysfunction

Genitourinary Kidneys:
enlarged kidneys due to extramedullary hematopoiesis

Clinical features from OMIM®:

615285 (Updated 08-Dec-2022)

Drugs & Therapeutics for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Search Clinical Trials, NIH Clinical Center for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Genetic Tests for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Anatomical Context for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Organs/tissues related to Neutropenia, Severe Congenital, 5, Autosomal Recessive:

MalaCards : Bone Marrow, Neutrophil, Bone, Cardiac Myocytes, Cortex
ODiseA: Blood And Bone Marrow

Publications for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Articles related to Neutropenia, Severe Congenital, 5, Autosomal Recessive:

(show all 13)
# Title Authors PMID Year
1
A congenital neutrophil defect syndrome associated with mutations in VPS45. 57 5
23738510 2013
2
The Thr224Asn mutation in the VPS45 gene is associated with the congenital neutropenia and primary myelofibrosis of infancy. 57 5
23599270 2013
3
A rare form of congenital neutropenia: VPS45 deficiency. 5
32037586 2020
4
Severe congenital neutropenia with neurological impairment due to a homozygous VPS45 p.E238K mutation: A case report suggesting a genotype-phenotype correlation. 5
26358756 2015
5
Gene variant effects across sodium channelopathies predict function and guide precision therapy. 62
35037686 2022
6
Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response. 62
35665156 2022
7
[Discovery and study on potential effect of herbal pair of Uncariae Ramulus cum Uncis-Eucommiae Cortex on pregnancy hypertension based on network pharmacology and molecular docking]. 62
33350198 2020
8
Periodontal Disease in Two Siblings with VPS45-associated Severe Congenital Neutropenia Type V: A Case Report. 62
33623350 2020
9
Preparation and characterization of chemically TEMPO-oxidized and mechanically disintegrated sacchachitin nanofibers (SCNF) for enhanced diabetic wound healing. 62
31826505 2020
10
Reliability of breeding values for feed intake and feed efficiency traits in dairy cattle: When dry matter intake recordings are sparse under different scenarios. 62
31155258 2019
11
[Adverse reactions analysis of Aconiti Lateralis Radix Praeparata and mechanism prediction of cardiac toxicity by network pharmacology]. 62
30989863 2019
12
Effects of seasonal acclimatization on thermal tolerance of inward currents in roach (Rutilus rutilus) cardiac myocytes. 62
28942482 2018
13
Direct activation of the Mauthner cell by electric field pulses drives ultrarapid escape responses. 62
24848468 2014

Variations for Neutropenia, Severe Congenital, 5, Autosomal Recessive

ClinVar genetic disease variations for Neutropenia, Severe Congenital, 5, Autosomal Recessive:

5 (show top 50) (show all 289)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 VPS45 NM_007259.5(VPS45):c.671C>A (p.Thr224Asn) SNV Pathogenic
55906 rs879255237 GRCh37: 1:150049841-150049841
GRCh38: 1:150077763-150077763
2 VPS45 NM_007259.5(VPS45):c.712G>A (p.Glu238Lys) SNV Likely Pathogenic
55907 rs782269909 GRCh37: 1:150053448-150053448
GRCh38: 1:150081366-150081366
3 VPS45 NM_007259.5(VPS45):c.758C>T (p.Pro253Leu) SNV Conflicting Interpretations Of Pathogenicity
791006 rs143828923 GRCh37: 1:150053494-150053494
GRCh38: 1:150081412-150081412
4 VPS45 NM_007259.5(VPS45):c.475A>G (p.Thr159Ala) SNV Uncertain Significance
1384010 GRCh37: 1:150049208-150049208
GRCh38: 1:150077130-150077130
5 VPS45 NM_007259.5(VPS45):c.352G>A (p.Val118Ile) SNV Uncertain Significance
1402871 GRCh37: 1:150048373-150048373
GRCh38: 1:150076295-150076295
6 VPS45 NM_007259.5(VPS45):c.115T>A (p.Tyr39Asn) SNV Uncertain Significance
1379915 GRCh37: 1:150040708-150040708
GRCh38: 1:150068651-150068651
7 VPS45 NM_007259.5(VPS45):c.1141G>A (p.Glu381Lys) SNV Uncertain Significance
1411706 GRCh37: 1:150064067-150064067
GRCh38: 1:150091973-150091973
8 VPS45 NM_007259.5(VPS45):c.926C>T (p.Ala309Val) SNV Uncertain Significance
1362175 GRCh37: 1:150054069-150054069
GRCh38: 1:150081987-150081987
9 overlap with 230 genes NC_000001.10:g.(?_149895434)_(156851434_?)dup DUP Uncertain Significance
1445481 GRCh37: 1:149895434-156851434
GRCh38:
10 VPS45 NM_007259.5(VPS45):c.690G>T (p.Trp230Cys) SNV Uncertain Significance
1437134 GRCh37: 1:150053426-150053426
GRCh38: 1:150081344-150081344
11 VPS45 NM_007259.5(VPS45):c.1186G>A (p.Glu396Lys) SNV Uncertain Significance
1470258 GRCh37: 1:150064112-150064112
GRCh38: 1:150092018-150092018
12 VPS45 NM_007259.5(VPS45):c.93G>A (p.Thr31=) SNV Uncertain Significance
1475739 GRCh37: 1:150040007-150040007
GRCh38: 1:150067950-150067950
13 VPS45 NM_007259.5(VPS45):c.1412A>G (p.His471Arg) SNV Uncertain Significance
1469181 GRCh37: 1:150065663-150065663
GRCh38: 1:150093567-150093567
14 VPS45 NM_007259.5(VPS45):c.319G>C (p.Val107Leu) SNV Uncertain Significance
1505696 GRCh37: 1:150048340-150048340
GRCh38: 1:150076262-150076262
15 VPS45 NM_007259.5(VPS45):c.404A>G (p.His135Arg) SNV Uncertain Significance
1488243 GRCh37: 1:150049028-150049028
GRCh38: 1:150076950-150076950
16 VPS45 NM_007259.5(VPS45):c.461A>T (p.Gln154Leu) SNV Uncertain Significance
1480942 GRCh37: 1:150049194-150049194
GRCh38: 1:150077116-150077116
17 VPS45 NM_007259.5(VPS45):c.1543G>A (p.Ala515Thr) SNV Uncertain Significance
1512288 GRCh37: 1:150082660-150082660
GRCh38: 1:150110545-150110545
18 VPS45 NM_007259.5(VPS45):c.821A>G (p.Asn274Ser) SNV Uncertain Significance
1514881 GRCh37: 1:150053557-150053557
GRCh38: 1:150081475-150081475
19 VPS45 NM_007259.5(VPS45):c.38A>G (p.Lys13Arg) SNV Uncertain Significance
1506686 GRCh37: 1:150039952-150039952
GRCh38: 1:150067895-150067895
20 VPS45 NM_007259.5(VPS45):c.1568G>T (p.Arg523Leu) SNV Uncertain Significance
1352799 GRCh37: 1:150082685-150082685
GRCh38: 1:150110570-150110570
21 VPS45 NM_007259.5(VPS45):c.187A>G (p.Met63Val) SNV Uncertain Significance
1352996 GRCh37: 1:150040780-150040780
GRCh38: 1:150068723-150068723
22 VPS45 NM_007259.5(VPS45):c.220C>T (p.Pro74Ser) SNV Uncertain Significance
1346302 GRCh37: 1:150040813-150040813
GRCh38: 1:150068756-150068756
23 VPS45 NM_007259.5(VPS45):c.614G>A (p.Arg205His) SNV Uncertain Significance
474245 rs146660821 GRCh37: 1:150049784-150049784
GRCh38: 1:150077706-150077706
24 VPS45 NM_007259.5(VPS45):c.566A>G (p.Glu189Gly) SNV Uncertain Significance
541273 rs144659538 GRCh37: 1:150049299-150049299
GRCh38: 1:150077221-150077221
25 VPS45 NM_007259.5(VPS45):c.1535A>G (p.Tyr512Cys) SNV Uncertain Significance
626050 rs782797599 GRCh37: 1:150082652-150082652
GRCh38: 1:150110537-150110537
26 VPS45 NM_007259.5(VPS45):c.319G>A (p.Val107Met) SNV Uncertain Significance
639607 rs782553177 GRCh37: 1:150048340-150048340
GRCh38: 1:150076262-150076262
27 VPS45 NM_007259.5(VPS45):c.1664G>A (p.Arg555Gln) SNV Uncertain Significance
647655 rs142968690 GRCh37: 1:150116925-150116925
GRCh38: 1:150144747-150144747
28 VPS45 NM_007259.5(VPS45):c.1174G>A (p.Ala392Thr) SNV Uncertain Significance
658240 rs782059726 GRCh37: 1:150064100-150064100
GRCh38: 1:150092006-150092006
29 VPS45 NM_007259.5(VPS45):c.170C>A (p.Ser57Tyr) SNV Uncertain Significance
659879 rs782358688 GRCh37: 1:150040763-150040763
GRCh38: 1:150068706-150068706
30 VPS45 NM_007259.5(VPS45):c.1190G>A (p.Arg397Gln) SNV Uncertain Significance
665526 rs373735080 GRCh37: 1:150064116-150064116
GRCh38: 1:150092022-150092022
31 VPS45 NM_007259.5(VPS45):c.1567C>T (p.Arg523Cys) SNV Uncertain Significance
841086 rs782426640 GRCh37: 1:150082684-150082684
GRCh38: 1:150110569-150110569
32 VPS45 NM_007259.5(VPS45):c.778A>G (p.Arg260Gly) SNV Uncertain Significance
850179 rs587646859 GRCh37: 1:150053514-150053514
GRCh38: 1:150081432-150081432
33 VPS45 NM_007259.5(VPS45):c.1162G>A (p.Val388Met) SNV Uncertain Significance
851006 rs782104716 GRCh37: 1:150064088-150064088
GRCh38: 1:150091994-150091994
34 VPS45 NM_007259.5(VPS45):c.257T>C (p.Leu86Pro) SNV Uncertain Significance
863733 rs782513242 GRCh37: 1:150044261-150044261
GRCh38: 1:150072194-150072194
35 VPS45 NM_007259.5(VPS45):c.695_696del (p.Tyr232fs) MICROSAT Uncertain Significance
864158 rs782700993 GRCh37: 1:150053429-150053430
GRCh38: 1:150081347-150081348
36 VPS45 NM_007259.5(VPS45):c.617G>A (p.Arg206Gln) SNV Uncertain Significance
952644 rs782495021 GRCh37: 1:150049787-150049787
GRCh38: 1:150077709-150077709
37 VPS45 NM_007259.5(VPS45):c.481G>A (p.Gly161Arg) SNV Uncertain Significance
960979 rs200134576 GRCh37: 1:150049214-150049214
GRCh38: 1:150077136-150077136
38 VPS45 NM_007259.5(VPS45):c.687G>C (p.Gln229His) SNV Uncertain Significance
966855 rs200019200 GRCh37: 1:150049857-150049857
GRCh38: 1:150077779-150077779
39 VPS45 NM_007259.5(VPS45):c.580G>A (p.Val194Met) SNV Uncertain Significance
970136 rs587713385 GRCh37: 1:150049750-150049750
GRCh38: 1:150077672-150077672
40 VPS45 NM_007259.5(VPS45):c.173A>G (p.Gln58Arg) SNV Uncertain Significance
991391 rs1654862605 GRCh37: 1:150040766-150040766
GRCh38: 1:150068709-150068709
41 VPS45 NM_007259.5(VPS45):c.353T>G (p.Val118Gly) SNV Uncertain Significance
991392 rs1298740891 GRCh37: 1:150048374-150048374
GRCh38: 1:150076296-150076296
42 VPS45 NM_007259.5(VPS45):c.419A>G (p.Asn140Ser) SNV Uncertain Significance
991394 rs782339252 GRCh37: 1:150049043-150049043
GRCh38: 1:150076965-150076965
43 VPS45 NM_007259.5(VPS45):c.443G>A (p.Arg148Gln) SNV Uncertain Significance
991395 rs370166172 GRCh37: 1:150049176-150049176
GRCh38: 1:150077098-150077098
44 VPS45 NM_007259.5(VPS45):c.462G>A (p.Gln154=) SNV Uncertain Significance
991396 rs781792682 GRCh37: 1:150049195-150049195
GRCh38: 1:150077117-150077117
45 VPS45 NM_007259.5(VPS45):c.739A>G (p.Ile247Val) SNV Uncertain Significance
991397 rs1553799320 GRCh37: 1:150053475-150053475
GRCh38: 1:150081393-150081393
46 VPS45 NM_007259.5(VPS45):c.1033C>T (p.Arg345Trp) SNV Uncertain Significance
991398 rs782225422 GRCh37: 1:150054896-150054896
GRCh38: 1:150082812-150082812
47 VPS45 NM_007259.5(VPS45):c.1133A>G (p.Lys378Arg) SNV Uncertain Significance
991399 rs190896405 GRCh37: 1:150064059-150064059
GRCh38: 1:150091965-150091965
48 VPS45 NM_007259.5(VPS45):c.1181A>G (p.His394Arg) SNV Uncertain Significance
991400 rs1486347658 GRCh37: 1:150064107-150064107
GRCh38: 1:150092013-150092013
49 VPS45 NM_007259.5(VPS45):c.613C>T (p.Arg205Cys) SNV Uncertain Significance
1020881 rs908608470 GRCh37: 1:150049783-150049783
GRCh38: 1:150077705-150077705
50 VPS45 NM_007259.5(VPS45):c.223A>G (p.Thr75Ala) SNV Uncertain Significance
1029151 rs782052786 GRCh37: 1:150040816-150040816
GRCh38: 1:150068759-150068759

UniProtKB/Swiss-Prot genetic disease variations for Neutropenia, Severe Congenital, 5, Autosomal Recessive:

73
# Symbol AA change Variation ID SNP ID
1 VPS45 p.Thr224Asn VAR_069865 rs879255237
2 VPS45 p.Glu238Lys VAR_069866 rs782269909

Expression for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Search GEO for disease gene expression data for Neutropenia, Severe Congenital, 5, Autosomal Recessive.

Pathways for Neutropenia, Severe Congenital, 5, Autosomal Recessive

GO Terms for Neutropenia, Severe Congenital, 5, Autosomal Recessive

Sources for Neutropenia, Severe Congenital, 5, Autosomal Recessive

2 CDC
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8 Cosmic
9 dbSNP
10 DGIdb
16 EFO
17 ExPASy
18 FMA
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29 HMDB
30 HPO
31 ICD10
32 ICD10 via Orphanet
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43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
52 NINDS
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56 OMIM via Orphanet
57 OMIM® (Updated 08-Dec-2022)
61 PubChem
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 Tocris
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72 UMLS via Orphanet
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