F11R

F11 receptor, the group of V-set domain containing|CD molecules|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 1:160995210-161021343

Previous symbols: [ "JAM1" ]

Links

ENSG00000158769 ∙ NCBI:50848 ∙ OMIM:605721 ∙ HGNC:14685 ∙ Uniprot:Q9Y624 ∙ 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 F11R gene.

• Inborn genetic diseases (10 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.

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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in F11R

This is a list of pathogenic ClinVar variants found in the F11R region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160998887-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-160999700-T-A		not specified	Uncertain significance (Dec 30, 2023)
1-160999715-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-160999741-C-T		not specified	Uncertain significance (Jun 09, 2022)
1-160999888-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-160999915-C-G		not specified	Uncertain significance (Jul 08, 2022)
1-160999927-G-A		not specified	Uncertain significance (Mar 11, 2022)
1-161000159-G-A		not specified	Uncertain significance (Oct 25, 2023)
1-161000195-C-A		not specified	Uncertain significance (Mar 14, 2024)
1-161000203-T-G		not specified	Uncertain significance (Jul 25, 2023)
1-161000299-C-T			Benign (May 29, 2018)
1-161000703-T-C		not specified	Uncertain significance (May 04, 2022)
1-161000762-C-T		not specified	Uncertain significance (May 09, 2022)
1-161001071-A-T		not specified	Uncertain significance (Mar 06, 2023)
1-161001112-C-T		not specified	Uncertain significance (Nov 03, 2022)
1-161001297-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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