VTN
vitronectin, the group of Receptor ligands|Complement system regulators and receptors
Basic information
Region (hg38): 17:28367284-28373091
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (73 variants)
- not_provided (10 variants)
- VTN-related_disorder (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000638.4. 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 | 9 | |||||
| missense | 68 | 76 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 68 | 12 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VTN | protein_coding | protein_coding | ENST00000226218 | 8 | 8821 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.50e-10 | 0.579 | 125686 | 0 | 61 | 125747 | 0.000243 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.678 | 270 | 303 | 0.891 | 0.0000189 | 3109 |
| Missense in Polyphen | 104 | 127.75 | 0.81408 | 1277 | ||
| Synonymous | 0.342 | 114 | 119 | 0.960 | 0.00000750 | 918 |
| Loss of Function | 1.32 | 19 | 26.3 | 0.722 | 0.00000156 | 256 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000525 | 0.000525 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000167 | 0.000163 |
| Finnish | 0.0000466 | 0.0000462 |
| European (Non-Finnish) | 0.000288 | 0.000281 |
| Middle Eastern | 0.000167 | 0.000163 |
| South Asian | 0.000267 | 0.000261 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Vitronectin is a cell adhesion and spreading factor found in serum and tissues. Vitronectin interact with glycosaminoglycans and proteoglycans. Is recognized by certain members of the integrin family and serves as a cell-to-substrate adhesion molecule. Inhibitor of the membrane-damaging effect of the terminal cytolytic complement pathway.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Complement and coagulation cascades - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Primary Focal Segmental Glomerulosclerosis FSGS;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;EMT transition in Colorectal Cancer;Inflammatory Response Pathway;Senescence and Autophagy in Cancer;Integrin cell surface interactions;Extracellular matrix organization;Innate Immune System;Immune System;Molecules associated with elastic fibres;Elastic fibre formation;Beta3 integrin cell surface interactions;FOXA1 transcription factor network;Regulation of Complement cascade;Syndecan interactions;Non-integrin membrane-ECM interactions;Complement cascade;ECM proteoglycans;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;Beta1 integrin cell surface interactions;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Signaling events mediated by VEGFR1 and VEGFR2;Integrins in angiogenesis
(Consensus)
Recessive Scores
- pRec
- 0.482
Intolerance Scores
- loftool
- 0.932
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.65
Haploinsufficiency Scores
- pHI
- 0.451
- hipred
- N
- hipred_score
- 0.393
- ghis
- 0.537
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.967
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vtn
- Phenotype
- homeostasis/metabolism phenotype; normal phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- receptor-mediated endocytosis;immune response;cell adhesion;cell-matrix adhesion;cell population proliferation;positive regulation of cell-substrate adhesion;negative regulation of endopeptidase activity;positive regulation of smooth muscle cell migration;cell migration;negative regulation of blood coagulation;extracellular matrix organization;regulation of complement activation;positive regulation of vascular endothelial growth factor receptor signaling pathway;positive regulation of protein binding;cell adhesion mediated by integrin;endodermal cell differentiation;positive regulation of receptor-mediated endocytosis;oligodendrocyte differentiation;positive regulation of peptidyl-tyrosine phosphorylation;protein polymerization;smooth muscle cell-matrix adhesion;positive regulation of wound healing;liver regeneration
- Cellular component
- extracellular region;basement membrane;extracellular space;endoplasmic reticulum;Golgi lumen;intracellular membrane-bounded organelle;rough endoplasmic reticulum lumen;collagen-containing extracellular matrix;extracellular exosome;alphav-beta3 integrin-vitronectin complex;blood microparticle
- Molecular function
- scavenger receptor activity;integrin binding;extracellular matrix structural constituent;protein binding;collagen binding;heparin binding;polysaccharide binding;identical protein binding;extracellular matrix binding