eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| whim syndrome | ||||
| Disease ID | 355 |
|---|---|
| Disease | whim syndrome |
| Definition | WHIM Syndrome (or Warts, Hypogammaglobulinemia, Infections, and Myelokathexis syndrome) is a rare congenital immunodeficiency disorder characterized by chronic noncyclic neutropenia. - NORD Reference: NORD |
| Synonym | warts, hypogammaglobulinaemia, infections, and myelokathexis warts, hypogammaglobulinemia, infections, and myelokathexis warts, hypogammaglobulinemia, infections, and myelokathexis (disorder) warts, hypogammaglobulinemia, infections, and myelokathexis syndrome whim - warts, hypogammaglobulinaemia, infections and myelokathexis whim - warts, hypogammaglobulinemia, infections and myelokathexis whims |
| Orphanet | |
| OMIM | |
| UMLS | C0472817 |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:1) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:24) 204 | AK2 | 2.74 | DISEASES 408 | ARRB1 | 2.725 | DISEASES 1233 | CCR4 | 2.15 | DISEASES 930 | CD19 | 1.02 | DISEASES 959 | CD40LG | 1.057 | DISEASES 1103 | CHAT | 1.009 | DISEASES 6387 | CXCL12 | 5.532 | DISEASES 7852 | CXCR4 | 6.112 | DISEASES 81704 | DOCK8 | 2.091 | DISEASES 2624 | GATA2 | 1.389 | DISEASES 2870 | GRK6 | 4.196 | DISEASES 10456 | HAX1 | 1.993 | DISEASES 8517 | IKBKG | 1.271 | DISEASES 83737 | ITCH | 2.503 | DISEASES 5601 | MAPK9 | 1.294 | DISEASES 4352 | MPL | 1.237 | DISEASES 4734 | NEDD4 | 1.959 | DISEASES 4776 | NFATC4 | 2.553 | DISEASES 5688 | PSMA7 | 1.77 | DISEASES 53637 | S1PR5 | 2.659 | DISEASES 6295 | SAG | 2.791 | DISEASES 100129060 | SEMA3F-AS1 | 3.322 | DISEASES 7454 | WAS | 1.229 | DISEASES 7456 | WIPF1 | 2.642 | DISEASES |
| Locus | Symbol | Locus(Total Locus:1) CXCR4 | 2q22.1 |
| Disease ID | 355 |
|---|---|
| Disease | whim syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:10) HP:0004315 | IgG deficiency HP:0004313 | Decreased immunoglobulin level HP:0000055 | Abnormality of female external genitalia HP:0002718 | Recurrent pyogenic infections HP:0005561 | Abnormality of bone marrow cell morphology HP:0002110 | Bronchiectasis HP:0001875 | Neutropenia HP:0000008 | Abnormality of female internal genitalia HP:0002788 | Recurrent upper respiratory infection HP:0200043 | Verrucae |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:2) |
| Disease ID | 355 |
|---|---|
| Disease | whim syndrome |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:3) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:13) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104893624 | 25355818 | 6387 | CXCL12 | umls:C0472817 | BeFree | CXCL12 stimulation triggered CXCR4(R334X) internalization in FLNA-deficient M2 cells but not in the FLNA-expressing M2 subclone A7; this suggests a role for FLNA in stabilization of WHIM-like CXCR4 at the cell surface. | 0.002442977 | 2015 | CXCR4;LOC105373632 | 2 | 136114928 | G | A |
| rs104893624 | 22596258 | 7852 | CXCR4 | umls:C0472817 | BeFree | Accordingly, like CXCR4(R334X), the most common truncation mutation in WHIM syndrome, CXCR4(E343K) mediated approximately 2-fold increased signaling in calcium flux and chemotaxis assays relative to wild-type CXCR4; however, CXCR4(E343K) had a reduced effect on blocking normal receptor down-regulation from the cell surface. | 0.449771907 | 2012 | CXCR4;LOC105373632 | 2 | 136114928 | G | A |
| rs104893624 | 19476565 | 7852 | CXCR4 | umls:C0472817 | BeFree | A nonsense mutation (C-->T) truncating the CXC chemokine receptor 4 (CXCR4) C-terminal cytoplasmic tail domain occurred at nucleotide position 1000(R334X) of the CXCR4 gene in one allele of the patient was identified, and the person was diagnosed as having WHIM syndrome. | 0.449771907 | 2009 | CXCR4;LOC105373632 | 2 | 136114928 | G | A |
| rs104893624 | NA | 7852 | CXCR4 | umls:C0472817 | CLINVAR | NA | 0.449771907 | NA | CXCR4;LOC105373632 | 2 | 136114928 | G | A |
| rs104893624 | 21070597 | 7852 | CXCR4 | umls:C0472817 | BeFree | AMD3100 is a potent antagonist at CXCR4(R334X) , a hyperfunctional mutant chemokine receptor and cause of WHIM syndrome. | 0.449771907 | 2011 | CXCR4;LOC105373632 | 2 | 136114928 | G | A |
| rs104893625 | 22596258 | 7852 | CXCR4 | umls:C0472817 | BeFree | Accordingly, like CXCR4(R334X), the most common truncation mutation in WHIM syndrome, CXCR4(E343K) mediated approximately 2-fold increased signaling in calcium flux and chemotaxis assays relative to wild-type CXCR4; however, CXCR4(E343K) had a reduced effect on blocking normal receptor down-regulation from the cell surface. | 0.449771907 | 2012 | CXCR4;LOC105373632 | 2 | 136114901 | C | A |
| rs104893625 | 23734232 | 6387 | CXCL12 | umls:C0472817 | BeFree | WHIM syndrome-associated CXCR4 truncation mutants lacking the S346/347 phosphosite and the recently identified E343K WHIM mutant displayed strongly impaired phosphorylation at S324/325 and S338/339 as well as reduced CXCL12-induced receptor internalization. | 0.002442977 | 2013 | CXCR4;LOC105373632 | 2 | 136114901 | C | A |
| rs104893625 | NA | 7852 | CXCR4 | umls:C0472817 | CLINVAR | NA | 0.449771907 | NA | CXCR4;LOC105373632 | 2 | 136114901 | C | A |
| rs104893626 | 24711662 | 7852 | CXCR4 | umls:C0472817 | BeFree | We screened 418 patients with B-cell lymphoproliferative disorders and described the presence of the C1013G/CXCR4 warts, hypogammaglobulinemia, infections, and myelokathexis-associated mutation in 28.2% (37/131) of patients with lymphoplasmacytic lymphoma (Waldenström macroglobulinemia [WM]), being either absent or present in only 7% of other B-cell lymphomas. | 0.449771907 | 2014 | CXCR4;LOC105373632 | 2 | 136114915 | G | C |
| rs104893626 | NA | 7852 | CXCR4 | umls:C0472817 | CLINVAR | NA | 0.449771907 | NA | CXCR4;LOC105373632 | 2 | 136114915 | G | C |
| rs387907272 | 24553177 | 4615 | MYD88 | umls:C0472817 | BeFree | Fewer patients with MYD88(L265P) and CXCR4(WHIM/FS or NS) vs MYD88(L265P)CXCR4(WT) presented with adenopathy (P < .01), further delineating differences in disease tropism based on CXCR4 status. | 0.000271442 | 2014 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 24553177 | 7852 | CXCR4 | umls:C0472817 | BeFree | Fewer patients with MYD88(L265P) and CXCR4(WHIM/FS or NS) vs MYD88(L265P)CXCR4(WT) presented with adenopathy (P < .01), further delineating differences in disease tropism based on CXCR4 status. | 0.449771907 | 2014 | MYD88 | 3 | 38141150 | T | C |
| rs730880320 | NA | 7852 | CXCR4 | umls:C0472817 | CLINVAR | NA | 0.449771907 | NA | CXCR4;LOC105373632 | 2 | 136114911 | AG | - |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:7) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000055 | Abnormality of female external genitalia | MP:0012167 | abnormal epigenetic regulation of gene expression | any anomaly in the process that modulates the frequency, rate or extent of gene expression, in which the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA |
| HP:0002788 | Recurrent upper respiratory tract infections | MP:0010955 | abnormal respiratory electron transport chain | anomaly in the process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient |
| HP:0004315 | IgG deficiency | MP:0002493 | increased IgG level | greater than normal immunoglobulin class G level |
| HP:0005561 | Abnormality of bone marrow cell morphology | MP:0013283 | failure of ventral body wall closure | failure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h |
| HP:0004313 | Decreased antibody level in blood | MP:0011460 | decreased urine chloride ion level | abnormally low amounts of chloride ion in the urine |
| HP:0002718 | Recurrent bacterial infections | MP:0009788 | increased susceptibility to bacterial infection induced morbidity/mortality | increased likelihood that an organism will display the expected moribund state caused by a bacterial invasion or from components of or toxins produced by bacteria |
| HP:0000008 | Abnormality of female internal genitalia | MP:0009403 | increased variability of skeletal muscle fiber size | greater range or dispersion within a distribution of skeletal muscle fiber size within a muscle compared to controls |
Mapped by homologous gene(Total Items:10) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0200043 | Verrucae | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002788 | Recurrent upper respiratory tract infections | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002110 | Bronchiectasis | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0004315 | IgG deficiency | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0001875 | Neutropenia | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0000055 | Abnormality of female external genitalia | MP:0014044 | absent cardiac outflow tract | absence of or complete failure to form the common arterial trunk that normally forms the aorta and pulmonary artery and the ventricular outflow regions |
| HP:0002718 | Recurrent bacterial infections | MP:0020216 | decreased circulating complement protein level | less than normal levels of the serum proteins that act sequentially to allow for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes |
| HP:0000008 | Abnormality of female internal genitalia | MP:0013785 | abnormal mammary gland bud morphology | any structural anomaly of the morphologically distinct bulb of epithelial cells formed once each mammary placode expands and invaginates into the underlying mesenchyme; in mouse embryos at E12.5, each epithelial bud with its contiguous mesenchyme is eleva |
| HP:0004313 | Decreased antibody level in blood | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0005561 | Abnormality of bone marrow cell morphology | MP:0014071 | increased cardiac muscle glycogen level | greater than the normal concentration of a readily converted carbohydrate reserve in heart muscle |
| Disease ID | 355 |
|---|---|
| Disease | whim syndrome |
| Case | (Waiting for update.) |