ICAM4
Basic information
Region (hg38): 19:10286955-10288522
Previous symbols: [ "LW" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
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
- not_specified (43 variants)
- Landsteiner-Wiener_phenotype (3 variants)
- not_provided (1 variants)
- ICAM4-related_disorder (1 variants)
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. These statistics are base on transcript: NM_000001544.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 8 | |||||
missense | 35 | 39 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 37 | 11 | 0 |
GnomAD
Source:
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:
- 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