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): 19:10271092-10286615

Links

ENSG00000090339 ∙ NCBI:3383 ∙ OMIM:147840 ∙ HGNC:5344 ∙ Uniprot:P05362 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ICAM1 gene.

• Inborn genetic diseases (21 variants)
• not provided (15 variants)
• Malaria, susceptibility to (4 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	5	4	10
missense			23	3	1	27
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	25	8	5

Variants in ICAM1

This is a list of pathogenic ClinVar variants found in the ICAM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-10271151-A-C		ICAM1-related disorder	Benign (Dec 05, 2019)
19-10274815-C-T		Malaria, susceptibility to	Uncertain significance (Jul 12, 2022)
19-10274827-G-A		not specified	Uncertain significance (May 15, 2023)
19-10274844-C-T			Likely benign (Jul 12, 2018)
19-10274859-G-A		ICAM1-related disorder	Likely benign (Nov 16, 2019)
19-10274864-A-T		Malaria, cerebral, susceptibility to • ICAM1-related disorder	Benign (Dec 05, 2019)
19-10274921-A-G		not specified	Uncertain significance (Apr 12, 2023)
19-10274989-G-C		not specified	Uncertain significance (Oct 20, 2023)
19-10283477-G-A			Likely benign (Mar 01, 2022)
19-10283515-C-G			Likely benign (Jun 13, 2018)
19-10283549-C-A		not specified	Uncertain significance (Dec 13, 2023)
19-10283549-C-T		not specified	Uncertain significance (Mar 27, 2023)
19-10283565-G-A		not specified	Uncertain significance (Dec 06, 2021)
19-10283591-G-A		not specified	Uncertain significance (Oct 22, 2021)
19-10283603-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-10283648-G-T		not specified	Uncertain significance (May 31, 2023)
19-10283652-A-C		not specified	Uncertain significance (Feb 02, 2022)
19-10283664-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-10283688-A-G		not specified	Uncertain significance (Jul 19, 2022)
19-10283708-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-10283720-G-C			Uncertain significance (May 04, 2022)
19-10283762-G-A		not specified	Uncertain significance (Jun 02, 2023)
19-10283763-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-10284088-G-A		ICAM1-related disorder	Likely benign (Mar 04, 2019)
19-10284091-G-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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