MCID: LYM106
MIFTS: 31

Lymphoproliferative Syndrome 1

Categories: Genetic diseases, Immune diseases, Rare diseases, Blood diseases, Gastrointestinal diseases

Aliases & Classifications for Lymphoproliferative Syndrome 1

MalaCards integrated aliases for Lymphoproliferative Syndrome 1:

Name: Lymphoproliferative Syndrome 1 57 12 75 37 29 13 6 73
Lpfs1 57 12 75
Lymphoproliferative Syndrome, Ebv-Associated, Autosomal, 1 75 40

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
onset in childhood
fatal without bone marrow transplantation


HPO:

32
lymphoproliferative syndrome 1:
Onset and clinical course juvenile onset
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Lymphoproliferative Syndrome 1

OMIM : 57 Lymphoproliferative syndrome-1 is an autosomal recessive primary immunodeficiency characterized by onset in early childhood of Epstein-Barr virus (EBV)-associated immune dysregulation, manifest as lymphoma, lymphomatoid granulomatosis, hemophagocytic lymphohistiocytosis, Hodgkin disease, and/or hypogammaglobulinemia. Autoimmune disorders, such as autoimmune hemolytic anemia or renal disease, may also occur. Patients show a high EBV viral load and decreased invariant natural killer T cells. It is unknown whether patients with ITK mutations are intrinsically susceptible to development of lymphoma or dysgammaglobulinemia in the absence of EBV infection (summary by Stepensky et al., 2011; Linka et al., 2012). For a discussion of genetic heterogeneity of lymphoproliferative syndrome, see XLP1 (308240). (613011)

MalaCards based summary : Lymphoproliferative Syndrome 1, also known as lpfs1, is related to lymphoproliferative syndrome, x-linked, 1 and selective immunoglobulin deficiency disease. An important gene associated with Lymphoproliferative Syndrome 1 is ITK (IL2 Inducible T Cell Kinase), and among its related pathways/superpathways are T cell receptor signaling pathway and NF-kappaB Signaling. Affiliated tissues include t cells, liver and bone, and related phenotypes are splenomegaly and hepatomegaly

Disease Ontology : 12 A lymphoproliferative syndrome characterized by autosomal recessive inheritance, early childhood onset of Epstein-Barr virus-associated immune dysregulation typically manifesting as lymphoma, lymphomatoid granulomatosis, hemophagocytic lymphohistiocytosis, Hodgkin disease, and-or hypogammaglobulinemia and that has material basis in homozygous mutation in the ITK gene on chromosome 5q32.

UniProtKB/Swiss-Prot : 75 Lymphoproliferative syndrome 1: A rare immunodeficiency characterized by extreme susceptibility to infection with Epstein-Barr virus (EBV). Inadequate immune response to EBV can have a fatal outcome. Clinical features include splenomegaly, lymphadenopathy, anemia, thrombocytopenia, pancytopenia, recurrent infections. There is an increased risk for lymphoma.

Related Diseases for Lymphoproliferative Syndrome 1

Graphical network of the top 20 diseases related to Lymphoproliferative Syndrome 1:



Diseases related to Lymphoproliferative Syndrome 1

Symptoms & Phenotypes for Lymphoproliferative Syndrome 1

Symptoms via clinical synopsis from OMIM:

57
AbdomenSpleen:
splenomegaly

Hematology:
anemia
pancytopenia
thrombocytopenia

Laboratory Abnormalities:
elevated erythrocyte sedimentation rate (esr)
increased c-reactive protein
high ebv viral load

Abdomen Liver:
hepatomegaly
impaired liver function

Immunology:
recurrent infections
lymphadenopathy
autoimmune disorders
hypogammaglobulinemia
mononucleosis
more
Neoplasia:
increased risk for lymphoma hodgkin disease


Clinical features from OMIM:

613011

Human phenotypes related to Lymphoproliferative Syndrome 1:

32 (show all 13)
# Description HPO Frequency HPO Source Accession
1 splenomegaly 32 HP:0001744
2 hepatomegaly 32 HP:0002240
3 anemia 32 HP:0001903
4 pancytopenia 32 HP:0001876
5 autoimmunity 32 HP:0002960
6 thrombocytopenia 32 HP:0001873
7 recurrent infections 32 HP:0002719
8 lymphoma 32 HP:0002665
9 lymphadenopathy 32 HP:0002716
10 igg deficiency 32 HP:0004315
11 recurrent aphthous stomatitis 32 HP:0011107
12 elevated erythrocyte sedimentation rate 32 HP:0003565
13 stomatitis 32 HP:0010280

Drugs & Therapeutics for Lymphoproliferative Syndrome 1

Search Clinical Trials , NIH Clinical Center for Lymphoproliferative Syndrome 1

Genetic Tests for Lymphoproliferative Syndrome 1

Genetic tests related to Lymphoproliferative Syndrome 1:

# Genetic test Affiliating Genes
1 Lymphoproliferative Syndrome 1 29 ITK

Anatomical Context for Lymphoproliferative Syndrome 1

MalaCards organs/tissues related to Lymphoproliferative Syndrome 1:

41
T Cells, Liver, Bone, Bone Marrow, B Cells

Publications for Lymphoproliferative Syndrome 1

Variations for Lymphoproliferative Syndrome 1

UniProtKB/Swiss-Prot genetic disease variations for Lymphoproliferative Syndrome 1:

75
# Symbol AA change Variation ID SNP ID
1 ITK p.Arg335Trp VAR_063424 rs121908191

ClinVar genetic disease variations for Lymphoproliferative Syndrome 1:

6
(show all 36)
# Gene Variation Type Significance SNP ID Assembly Location
1 ITK NM_005546.3(ITK): c.1003C> T (p.Arg335Trp) single nucleotide variant Pathogenic rs121908191 GRCh37 Chromosome 5, 156668673: 156668673
2 ITK NM_005546.3(ITK): c.1003C> T (p.Arg335Trp) single nucleotide variant Pathogenic rs121908191 GRCh38 Chromosome 5, 157241663: 157241663
3 ITK NM_005546.3(ITK): c.1764C> G (p.Tyr588Ter) single nucleotide variant Pathogenic rs397514260 GRCh37 Chromosome 5, 156675990: 156675990
4 ITK NM_005546.3(ITK): c.1764C> G (p.Tyr588Ter) single nucleotide variant Pathogenic rs397514260 GRCh38 Chromosome 5, 157248980: 157248980
5 ITK NM_005546.3(ITK): c.86G> A (p.Arg29His) single nucleotide variant Pathogenic rs397514261 GRCh37 Chromosome 5, 156608074: 156608074
6 ITK NM_005546.3(ITK): c.86G> A (p.Arg29His) single nucleotide variant Pathogenic rs397514261 GRCh38 Chromosome 5, 157181063: 157181063
7 ITK NM_005546.3(ITK): c.237G> A (p.Pro79=) single nucleotide variant Conflicting interpretations of pathogenicity rs201403794 GRCh37 Chromosome 5, 156635998: 156635998
8 ITK NM_005546.3(ITK): c.237G> A (p.Pro79=) single nucleotide variant Conflicting interpretations of pathogenicity rs201403794 GRCh38 Chromosome 5, 157208987: 157208987
9 ITK NM_005546.3(ITK): c.769-13C> T single nucleotide variant Benign/Likely benign rs56100638 GRCh37 Chromosome 5, 156665106: 156665106
10 ITK NM_005546.3(ITK): c.769-13C> T single nucleotide variant Benign/Likely benign rs56100638 GRCh38 Chromosome 5, 157238096: 157238096
11 ITK NM_005546.3(ITK): c.1741C> T (p.Arg581Trp) single nucleotide variant Conflicting interpretations of pathogenicity rs34482255 GRCh38 Chromosome 5, 157248957: 157248957
12 ITK NM_005546.3(ITK): c.1741C> T (p.Arg581Trp) single nucleotide variant Conflicting interpretations of pathogenicity rs34482255 GRCh37 Chromosome 5, 156675967: 156675967
13 ITK NM_005546.3(ITK): c.578G> A (p.Arg193Gln) single nucleotide variant Conflicting interpretations of pathogenicity rs17054374 GRCh37 Chromosome 5, 156649955: 156649955
14 ITK NM_005546.3(ITK): c.578G> A (p.Arg193Gln) single nucleotide variant Conflicting interpretations of pathogenicity rs17054374 GRCh38 Chromosome 5, 157222945: 157222945
15 ITK NM_005546.3(ITK): c.769-10A> T single nucleotide variant Benign/Likely benign rs55646940 GRCh38 Chromosome 5, 157238099: 157238099
16 ITK NM_005546.3(ITK): c.769-10A> T single nucleotide variant Benign/Likely benign rs55646940 GRCh37 Chromosome 5, 156665109: 156665109
17 ITK NM_005546.3(ITK): c.1455C> T (p.Ala485=) single nucleotide variant Conflicting interpretations of pathogenicity rs201568204 GRCh38 Chromosome 5, 157245731: 157245731
18 ITK NM_005546.3(ITK): c.1455C> T (p.Ala485=) single nucleotide variant Conflicting interpretations of pathogenicity rs201568204 GRCh37 Chromosome 5, 156672741: 156672741
19 ITK NM_005546.3(ITK): c.1492G> T (p.Val498Leu) single nucleotide variant Uncertain significance rs758820629 GRCh38 Chromosome 5, 157245768: 157245768
20 ITK NM_005546.3(ITK): c.1492G> T (p.Val498Leu) single nucleotide variant Uncertain significance rs758820629 GRCh37 Chromosome 5, 156672778: 156672778
21 ITK NM_005546.3(ITK): c.1715G> A (p.Ser572Asn) single nucleotide variant Uncertain significance rs140542010 GRCh37 Chromosome 5, 156675941: 156675941
22 ITK NM_005546.3(ITK): c.1715G> A (p.Ser572Asn) single nucleotide variant Uncertain significance rs140542010 GRCh38 Chromosome 5, 157248931: 157248931
23 ITK NM_005546.3(ITK): c.1759G> A (p.Val587Ile) single nucleotide variant Benign/Likely benign rs56005928 GRCh38 Chromosome 5, 157248975: 157248975
24 ITK NM_005546.3(ITK): c.1759G> A (p.Val587Ile) single nucleotide variant Benign/Likely benign rs56005928 GRCh37 Chromosome 5, 156675985: 156675985
25 ITK NM_005546.3(ITK): c.767C> T (p.Thr256Ile) single nucleotide variant Uncertain significance rs115751349 GRCh37 Chromosome 5, 156659403: 156659403
26 ITK NM_005546.3(ITK): c.767C> T (p.Thr256Ile) single nucleotide variant Uncertain significance rs115751349 GRCh38 Chromosome 5, 157232393: 157232393
27 ITK NM_005546.3(ITK): c.1829G> A (p.Arg610His) single nucleotide variant Uncertain significance rs138438785 GRCh38 Chromosome 5, 157252644: 157252644
28 ITK NM_005546.3(ITK): c.1829G> A (p.Arg610His) single nucleotide variant Uncertain significance rs138438785 GRCh37 Chromosome 5, 156679654: 156679654
29 ITK NM_005546.3(ITK): c.1398G> T (p.Val466=) single nucleotide variant Benign rs17595896 GRCh37 Chromosome 5, 156671437: 156671437
30 ITK NM_005546.3(ITK): c.1398G> T (p.Val466=) single nucleotide variant Benign rs17595896 GRCh38 Chromosome 5, 157244427: 157244427
31 ITK NM_005546.3(ITK): c.631G> C (p.Val211Leu) single nucleotide variant Uncertain significance rs142038079 GRCh37 Chromosome 5, 156650008: 156650008
32 ITK NM_005546.3(ITK): c.631G> C (p.Val211Leu) single nucleotide variant Uncertain significance rs142038079 GRCh38 Chromosome 5, 157222998: 157222998
33 ITK NM_005546.3(ITK): c.725A> G (p.Lys242Arg) single nucleotide variant Uncertain significance rs761513530 GRCh37 Chromosome 5, 156659361: 156659361
34 ITK NM_005546.3(ITK): c.725A> G (p.Lys242Arg) single nucleotide variant Uncertain significance rs761513530 GRCh38 Chromosome 5, 157232351: 157232351
35 ITK NM_005546.3(ITK): c.1510A> T (p.Thr504Ser) single nucleotide variant Uncertain significance rs151046132 GRCh37 Chromosome 5, 156672796: 156672796
36 ITK NM_005546.3(ITK): c.1510A> T (p.Thr504Ser) single nucleotide variant Uncertain significance rs151046132 GRCh38 Chromosome 5, 157245786: 157245786

Expression for Lymphoproliferative Syndrome 1

Search GEO for disease gene expression data for Lymphoproliferative Syndrome 1.

Pathways for Lymphoproliferative Syndrome 1

Pathways related to Lymphoproliferative Syndrome 1 according to KEGG:

37
# Name Kegg Source Accession
1 T cell receptor signaling pathway hsa04660

Pathways related to Lymphoproliferative Syndrome 1 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 11.47 ITK SH2D1A
2 10.79 ITK SH2D1A

GO Terms for Lymphoproliferative Syndrome 1

Biological processes related to Lymphoproliferative Syndrome 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 immune system process GO:0002376 9.26 ITK SH2D1A
2 innate immune response GO:0045087 9.16 ITK SH2D1A
3 adaptive immune response GO:0002250 8.96 ITK SH2D1A
4 cellular defense response GO:0006968 8.62 ITK SH2D1A

Sources for Lymphoproliferative Syndrome 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
Content
Loading form....