ICAM4

intercellular adhesion molecule 4 (Landsteiner-Wiener blood group), the group of CD molecules|Ig-like cell adhesion molecule family|Immunoglobulin like domain containing|Blood group antigens

Basic information

Region (hg38): 19:10286955-10288522

Previous symbols: [ "LW" ]

Links

ENSG00000105371 ∙ NCBI:3386 ∙ OMIM:614088 ∙ HGNC:5347 ∙ Uniprot:Q14773 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Landsteiner-Wiener	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	7632968; 8639917

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ICAM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICAM4 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			17	2		19
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in ICAM4

This is a list of pathogenic ClinVar variants found in the ICAM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10287064-C-T		not specified	Uncertain significance (Jan 17, 2023)
19-10287066-G-A			Uncertain significance (-)
19-10287139-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-10287157-T-C		not specified	Uncertain significance (Aug 21, 2023)
19-10287171-C-A		not specified	Uncertain significance (Jan 04, 2022)
19-10287194-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-10287311-A-G		Landsteiner-Wiener phenotype	Affects (Aug 15, 1995)
19-10287321-C-A		Landsteiner-Wiener phenotype	Uncertain significance (-)
19-10287356-TGACCTGCGCA-T		Landsteiner-Wiener phenotype	Affects (Apr 01, 1996)
19-10287386-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-10287563-C-T		not specified	Uncertain significance (May 03, 2023)
19-10287578-G-A		not specified	Uncertain significance (Mar 29, 2024)
19-10287586-T-C		not specified	Uncertain significance (Apr 01, 2024)
19-10287605-T-C		not specified	Uncertain significance (Oct 13, 2023)
19-10287620-C-G		not specified	Uncertain significance (Feb 10, 2022)
19-10287631-T-A		not specified	Uncertain significance (Nov 09, 2023)
19-10287649-C-T		not specified	Uncertain significance (Mar 13, 2023)
19-10287685-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-10287727-G-A		not specified	Uncertain significance (Mar 23, 2022)
19-10287757-C-A		not specified	Uncertain significance (Feb 14, 2023)
19-10287763-G-C		ICAM4-related disorder	Likely benign (Feb 08, 2021)
19-10287789-C-T		not specified	Likely benign (Jan 04, 2024)
19-10287815-C-G		not specified	Uncertain significance (Aug 02, 2022)
19-10287819-A-C		not specified	Likely benign (Dec 11, 2023)
19-10287832-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICAM4	protein_coding	protein_coding	ENST00000340992	3	1556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000121	0.213	125692	0	50	125742	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.405	151	166	0.912	0.00000927	1715
Missense in Polyphen		23	35.334	0.65093		337
Synonymous	1.11	58	69.8	0.831	0.00000382	609
Loss of Function	-0.0197	9	8.94	1.01	4.89e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000654	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.00105	0.00105
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). ICAM4 is also a ligand for alpha-4/beta-1 and alpha-V integrins. {ECO:0000269|PubMed:11435317}.
• Pathway: Integrin cell surface interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Beta2 integrin cell surface interactions (Consensus)

Intolerance Scores

• loftool: 0.823
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.0744
• hipred: N
• hipred_score: 0.285
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Icam4
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: cell adhesion;extracellular matrix organization;regulation of immune response;cell-cell adhesion
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: integrin binding