ICAM2

intercellular adhesion molecule 2, the group of CD molecules|Ig-like cell adhesion molecule family|Receptor ligands|Immunoglobulin like domain containing

Basic information

Region (hg38): 17:64002594-64020634

Links

ENSG00000108622 ∙ NCBI:3384 ∙ OMIM:146630 ∙ HGNC:5345 ∙ Uniprot:P13598 ∙ 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 ICAM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICAM2 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						0
missense			24	6		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	6	0

Variants in ICAM2

This is a list of pathogenic ClinVar variants found in the ICAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-64002787-C-T		not specified	Likely benign (Dec 19, 2022)
17-64002791-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-64002817-C-T		not specified	Likely benign (Aug 04, 2023)
17-64002860-C-T		not specified	Uncertain significance (Nov 27, 2024)
17-64002861-G-C		not specified	Uncertain significance (Feb 09, 2023)
17-64002868-G-A		not specified	Likely benign (May 06, 2024)
17-64002883-A-G		not specified	Uncertain significance (Aug 22, 2023)
17-64002895-A-T		not specified	Uncertain significance (Jan 08, 2025)
17-64003658-A-G		not specified	Uncertain significance (Apr 22, 2024)
17-64003686-T-A		not specified	Uncertain significance (Aug 11, 2024)
17-64003695-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-64003751-C-T		not specified	Uncertain significance (Mar 20, 2024)
17-64003754-T-C		not specified	Uncertain significance (Apr 09, 2024)
17-64003809-C-T		not specified	Uncertain significance (May 03, 2023)
17-64003862-C-T		not specified	Uncertain significance (Apr 06, 2022)
17-64003872-G-C		not specified	Uncertain significance (Jun 24, 2022)
17-64003898-A-G		not specified	Uncertain significance (Dec 21, 2022)
17-64003920-C-A		not specified	Uncertain significance (Jul 17, 2024)
17-64003947-T-C		not specified	Uncertain significance (Apr 23, 2024)
17-64005119-C-T		not specified	Likely benign (Nov 08, 2022)
17-64005137-C-T		not specified	Likely benign (Jan 03, 2024)
17-64005175-G-A		not specified	Uncertain significance (Jan 17, 2024)
17-64005180-A-T		not specified	Likely benign (Aug 28, 2024)
17-64005224-C-T		not specified	Uncertain significance (May 16, 2022)
17-64005274-T-C		not specified	Uncertain significance (Jul 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICAM2	protein_coding	protein_coding	ENST00000412356	4	18041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000750	0.780	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.406	157	172	0.913	0.0000105	1784
Missense in Polyphen		41	47.378	0.86538		541
Synonymous	0.555	72	78.2	0.920	0.00000521	578
Loss of Function	1.04	6	9.43	0.636	5.84e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000326	0.000326
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ICAM proteins are ligands for the leukocyte adhesion protein LFA-1 (integrin alpha-L/beta-2). ICAM2 may play a role in lymphocyte recirculation by blocking LFA-1-dependent cell adhesion. It mediates adhesive interactions important for antigen- specific immune response, NK-cell mediated clearance, lymphocyte recirculation, and other cellular interactions important for immune response and surveillance.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Human Complement System;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Integrin cell surface interactions;CD209 (DC-SIGN) signaling;C-type lectin receptors (CLRs);Extracellular matrix organization;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Beta2 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.764
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.145
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Icam2
• Phenotype: hematopoietic system phenotype; respiratory system phenotype; immune system phenotype

Gene ontology

• Biological process: stimulatory C-type lectin receptor signaling pathway;cell adhesion;extracellular matrix organization;regulation of immune response;cell-cell adhesion
• Cellular component: uropod;plasma membrane;integral component of plasma membrane;microvillus;membrane;cleavage furrow
• Molecular function: integrin binding