ICAM1
intercellular adhesion molecule 1, the group of Receptor ligands|Immunoglobulin like domain containing|CD molecules|Ig-like cell adhesion molecule family
Basic information
Region (hg38): 19:10271093-10286615
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (63 variants)
- not_provided (16 variants)
- ICAM1-related_disorder (8 variants)
- Malaria,_susceptibility_to (5 variants)
- Malaria,_cerebral,_susceptibility_to (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICAM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000201.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 12 | |||||
| missense | 62 | 71 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 64 | 14 | 6 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ICAM1 | protein_coding | protein_coding | ENST00000264832 | 7 | 15781 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0353 | 0.963 | 125633 | 0 | 115 | 125748 | 0.000457 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0190 | 322 | 323 | 0.997 | 0.0000201 | 3346 |
| Missense in Polyphen | 83 | 99.352 | 0.83542 | 1085 | ||
| Synonymous | -0.0937 | 150 | 149 | 1.01 | 0.00000944 | 1200 |
| Loss of Function | 2.79 | 6 | 19.2 | 0.313 | 9.75e-7 | 214 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00470 | 0.00463 |
| European (Non-Finnish) | 0.0000892 | 0.0000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000329 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: ICAM proteins are ligands for the leukocyte adhesion protein LFA-1 (integrin alpha-L/beta-2). During leukocyte trans- endothelial migration, ICAM1 engagement promotes the assembly of endothelial apical cups through ARHGEF26/SGEF and RHOG activation. {ECO:0000269|PubMed:11173916, ECO:0000269|PubMed:17875742}.; FUNCTION: (Microbial infection) Acts as a receptor for Coxsackievirus A21 capsid proteins. {ECO:0000269|PubMed:11160747, ECO:0000269|PubMed:16004874, ECO:0000269|PubMed:9539703}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Influenza A - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Malaria - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;Interleukin-11 Signaling Pathway;Spinal Cord Injury;Human Complement System;IL1 and megakaryocytes in obesity;Photodynamic therapy-induced NF-kB survival signaling;VEGFA-VEGFR2 Signaling Pathway;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Type II interferon signaling (IFNG);Cytokine Signaling in Immune system;Integrin cell surface interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Glucocorticoid receptor regulatory network;Thromboxane A2 receptor signaling;Interferon gamma signaling;Interferon Signaling;amb2 Integrin signaling;Beta2 integrin cell surface interactions
(Consensus)
Intolerance Scores
- loftool
- 0.605
- rvis_EVS
- 0.25
- rvis_percentile_EVS
- 69.66
Haploinsufficiency Scores
- pHI
- 0.0585
- hipred
- N
- hipred_score
- 0.493
- ghis
- 0.396
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.439
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Icam1
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype;
Gene ontology
- Biological process
- ovarian follicle development;regulation of leukocyte mediated cytotoxicity;response to amphetamine;T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;acute inflammatory response to antigenic stimulus;T cell antigen processing and presentation;positive regulation of cellular extravasation;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;leukocyte cell-cell adhesion;cell aging;sensory perception of sound;regulation of cell shape;response to ionizing radiation;response to sulfur dioxide;cytokine-mediated signaling pathway;membrane to membrane docking;extracellular matrix organization;positive regulation of actin filament polymerization;cellular response to nutrient levels;response to insulin;cell adhesion mediated by integrin;response to gonadotropin;response to amino acid;positive regulation of GTPase activity;adhesion of symbiont to host;positive regulation of nitric oxide biosynthetic process;response to ethanol;positive regulation of vasoconstriction;response to copper ion;viral entry into host cell;receptor-mediated virion attachment to host cell;positive regulation of peptidyl-tyrosine phosphorylation;regulation of immune response;leukocyte migration;positive regulation of NF-kappaB transcription factor activity;negative regulation of calcium ion transport;interferon-gamma-mediated signaling pathway;establishment of endothelial barrier;positive regulation of ERK1 and ERK2 cascade;cellular response to lipopolysaccharide;cellular response to alkaloid;cellular response to glucose stimulus;cellular response to interleukin-1;cellular response to interleukin-6;cellular response to tumor necrosis factor;cellular response to hypoxia;cellular response to dexamethasone stimulus;T cell extravasation;establishment of endothelial intestinal barrier;establishment of Sertoli cell barrier;regulation of ruffle assembly;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of leukocyte adhesion to vascular endothelial cell;cellular response to leukemia inhibitory factor;negative regulation of endothelial cell apoptotic process
- Cellular component
- immunological synapse;extracellular space;plasma membrane;integral component of plasma membrane;focal adhesion;external side of plasma membrane;cell surface;membrane;membrane raft;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- virus receptor activity;transmembrane signaling receptor activity;integrin binding;protein binding;signaling receptor activity