ICAM5

intercellular adhesion molecule 5, the group of Ig-like cell adhesion molecule family|Immunoglobulin like domain containing

Basic information

Region (hg38): 19:10289952-10296778

Previous symbols: [ "TLCN" ]

Links

ENSG00000105376 ∙ NCBI:7087 ∙ OMIM:601852 ∙ HGNC:5348 ∙ Uniprot:Q9UMF0 ∙ 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 ICAM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ICAM5 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	31	1	0

Variants in ICAM5

This is a list of pathogenic ClinVar variants found in the ICAM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10290081-T-G		not specified	Uncertain significance (Mar 18, 2024)
19-10291500-C-T		not specified	Uncertain significance (Oct 30, 2023)
19-10291534-C-A		not specified	Uncertain significance (May 26, 2024)
19-10291584-C-A		not specified	Uncertain significance (Sep 17, 2021)
19-10291585-G-A		not specified	Uncertain significance (Nov 06, 2023)
19-10291614-G-C		not specified	Uncertain significance (Mar 18, 2024)
19-10291710-C-T		not specified	Uncertain significance (Mar 16, 2022)
19-10292062-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-10292083-T-C		not specified	Uncertain significance (Sep 22, 2023)
19-10292101-T-C		not specified	Uncertain significance (Mar 20, 2023)
19-10292131-C-T		not specified	Uncertain significance (Mar 29, 2023)
19-10292241-C-G		not specified	Uncertain significance (Nov 08, 2022)
19-10292242-A-T		not specified	Uncertain significance (Nov 09, 2021)
19-10292627-T-G		not specified	Uncertain significance (Jun 01, 2023)
19-10292719-G-A		not specified	Likely benign (May 26, 2024)
19-10292770-G-A		not specified	Uncertain significance (Nov 22, 2022)
19-10293136-T-C		not specified	Uncertain significance (Oct 03, 2022)
19-10293150-C-G		not specified	Uncertain significance (Oct 06, 2021)
19-10293168-G-A		not specified	Uncertain significance (May 15, 2024)
19-10293854-G-C		not specified	Uncertain significance (Dec 11, 2023)
19-10294056-G-T		not specified	Uncertain significance (Sep 27, 2022)
19-10294093-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-10294169-C-A		not specified	Uncertain significance (Dec 21, 2022)
19-10294198-C-T		not specified	Likely benign (Jan 18, 2023)
19-10294201-C-T		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ICAM5	protein_coding	protein_coding	ENST00000221980	11	6798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00214	0.998	125710	0	20	125730	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	366	530	0.691	0.0000274	5732
Missense in Polyphen		87	163	0.53375		1820
Synonymous	1.69	204	237	0.860	0.0000132	2128
Loss of Function	3.62	11	33.6	0.327	0.00000151	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000141	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000218
Finnish	0.0000994	0.0000924
European (Non-Finnish)	0.0000628	0.0000615
Middle Eastern	0.000219	0.000218
South Asian	0.0000654	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ICAM proteins are ligands for the leukocyte adhesion protein LFA-1 (integrin alpha-L/beta-2).
• Pathway: Integrin cell surface interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.533
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• pHI: 0.256
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Icam5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

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