ICAM3

intercellular adhesion molecule 3, the group of Immunoglobulin like domain containing|CD molecules|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 19:10333776-10339661

Links

ENSG00000076662 ∙ NCBI:3385 ∙ OMIM:146631 ∙ HGNC:5346 ∙ Uniprot:P32942 ∙ 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 ICAM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICAM3 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	1
missense			36	2	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	36	2	2

Variants in ICAM3

This is a list of pathogenic ClinVar variants found in the ICAM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10334036-C-A		not specified	Uncertain significance (Apr 15, 2024)
19-10334054-T-C		not specified	Uncertain significance (Jan 30, 2024)
19-10334198-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-10334211-C-G		not specified	Uncertain significance (Dec 21, 2022)
19-10334246-A-G		not specified	Uncertain significance (Mar 01, 2023)
19-10334250-A-G		not specified	Likely benign (Dec 20, 2021)
19-10334288-T-G		not specified	Uncertain significance (May 29, 2024)
19-10334301-G-A		not specified	Uncertain significance (May 08, 2023)
19-10334357-T-C		not specified	Uncertain significance (Sep 01, 2021)
19-10334384-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-10334542-T-C		not specified	Uncertain significance (Nov 03, 2023)
19-10334632-T-G		not specified	Uncertain significance (Dec 01, 2022)
19-10334692-T-C		not specified	Uncertain significance (Apr 12, 2023)
19-10334708-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-10334710-A-T		not specified	Uncertain significance (Dec 15, 2023)
19-10334719-A-G		not specified	Uncertain significance (May 24, 2024)
19-10335086-C-T		not specified	Uncertain significance (Apr 24, 2024)
19-10335111-G-C		not specified	Uncertain significance (May 07, 2024)
19-10335123-A-T		not specified	Uncertain significance (Jun 12, 2023)
19-10335130-C-T			Benign (Jun 26, 2018)
19-10335137-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-10335201-T-G		not specified	Uncertain significance (Dec 27, 2022)
19-10335275-A-G		not specified	Uncertain significance (Jan 24, 2024)
19-10335339-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-10335341-G-A		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICAM3	protein_coding	protein_coding	ENST00000160262	7	6048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-25	0.00000444	125384	0	363	125747	0.00144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.301	306	321	0.953	0.0000173	3472
Missense in Polyphen		82	92.995	0.88176		1063
Synonymous	-0.747	158	147	1.08	0.00000868	1189
Loss of Function	-2.29	31	20.0	1.55	9.99e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00207	0.00199
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.00853	0.00852
Finnish	0.00162	0.00162
European (Non-Finnish)	0.000499	0.000492
Middle Eastern	0.00853	0.00852
South Asian	0.00173	0.00170
Other	0.000675	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ICAM proteins are ligands for the leukocyte adhesion protein LFA-1 (integrin alpha-L/beta-2) (PubMed:1448173). ICAM3 is also a ligand for integrin alpha-D/beta-2. In association with integrin alpha-L/beta-2, contributes to apoptotic neutrophil phagocytosis by macrophages (PubMed:23775590). {ECO:0000269|PubMed:1448173, ECO:0000269|PubMed:23775590}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);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: 0.187

Intolerance Scores

• loftool: 0.941
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.5

Haploinsufficiency Scores

• pHI: 0.0266
• hipred: N
• hipred_score: 0.398
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.294

Gene Damage Prediction

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

Gene ontology

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