F11R
Basic information
Region (hg38): 1:160995211-161021175
Previous symbols: [ "JAM1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (29 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the F11R gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016946.6. 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 | 1 | |||||
missense | 27 | 29 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 27 | 2 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
F11R | protein_coding | protein_coding | ENST00000368026 | 10 | 26138 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000185 | 0.895 | 125730 | 0 | 18 | 125748 | 0.0000716 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.951 | 141 | 177 | 0.799 | 0.0000101 | 1923 |
Missense in Polyphen | 53 | 64.43 | 0.82259 | 665 | ||
Synonymous | 0.572 | 63 | 69.1 | 0.912 | 0.00000377 | 610 |
Loss of Function | 1.54 | 10 | 16.8 | 0.595 | 8.94e-7 | 197 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000152 | 0.000152 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000217 | 0.000217 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000880 | 0.0000879 |
Middle Eastern | 0.000217 | 0.000217 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to play a role in epithelial tight junction formation. Appears early in primordial forms of cell junctions and recruits PARD3 (PubMed:11489913). The association of the PARD6- PARD3 complex may prevent the interaction of PARD3 with JAM1, thereby preventing tight junction assembly (By similarity). Plays a role in regulating monocyte transmigration involved in integrity of epithelial barrier (By similarity). Ligand for integrin alpha- L/beta-2 involved in memory T-cell and neutrophil transmigration (PubMed:11812992). Involved in platelet activation (PubMed:10753840). {ECO:0000250|UniProtKB:O88792, ECO:0000269|PubMed:10753840, ECO:0000269|PubMed:11489913, ECO:0000269|PubMed:11812992}.; FUNCTION: (Microbial infection) Acts as a receptor for Human Rotavirus strain Wa. {ECO:0000269|PubMed:25481868}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Tight junction - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Signal Transduction;Integrin cell surface interactions;Extracellular matrix organization;Beta3 integrin cell surface interactions;Cell surface interactions at the vascular wall;Hemostasis;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Cell-Cell communication;Nectin adhesion pathway;TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition);Integrins in angiogenesis;Beta2 integrin cell surface interactions
(Consensus)
Recessive Scores
- pRec
- 0.0689
Intolerance Scores
- loftool
- 0.635
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.57
Haploinsufficiency Scores
- pHI
- 0.102
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.474
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.834
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- F11r
- Phenotype
- immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- f11r.1
- Affected structure
- endothelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- regulation of cytokine production;inflammatory response;cell adhesion;transforming growth factor beta receptor signaling pathway;response to radiation;extracellular matrix organization;actomyosin structure organization;negative regulation of GTPase activity;positive regulation of GTPase activity;positive regulation of blood pressure;viral entry into host cell;intestinal absorption;leukocyte migration;bicellular tight junction assembly;protein localization to plasma membrane;establishment of endothelial intestinal barrier;regulation of membrane permeability;regulation of actin cytoskeleton reorganization
- Cellular component
- plasma membrane;cell-cell junction;bicellular tight junction;integral component of membrane;cell junction;cytoplasmic vesicle;slit diaphragm;extracellular exosome
- Molecular function
- virus receptor activity;protein binding;PDZ domain binding;cadherin binding