VTN

vitronectin, the group of Receptor ligands|Complement system regulators and receptors

Basic information

Region (hg38): 17:28367283-28373091

Links

ENSG00000109072 ∙ NCBI:7448 ∙ OMIM:193190 ∙ HGNC:12724 ∙ Uniprot:P04004 ∙ 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 VTN gene.

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.

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				5	5	10
missense			38	2	2	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				2	1	3
Total	0	0	38	9	8

Variants in VTN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-28367362-C-CT		VTN-related disorder	Likely benign (Nov 03, 2023)
17-28367411-G-A			Likely benign (Feb 09, 2018)
17-28367413-T-C		not specified	Uncertain significance (May 14, 2024)
17-28367424-T-C		VTN-related disorder	Uncertain significance (Oct 20, 2022)
17-28367431-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-28367440-T-C		not specified	Likely benign (May 23, 2023)
17-28367455-T-A		not specified	Uncertain significance (Sep 06, 2022)
17-28367457-C-A		not specified	Uncertain significance (May 09, 2024)
17-28367462-A-G		VTN-related disorder	Benign (Nov 08, 2019)
17-28367725-G-T		not specified	Uncertain significance (May 23, 2023)
17-28367772-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-28367777-C-T		not specified	Uncertain significance (Nov 17, 2023)
17-28367840-G-A		VTN-related disorder	Benign (Oct 30, 2019)
17-28367843-G-A		not specified	Uncertain significance (Aug 17, 2022)
17-28367844-C-T		not specified	Uncertain significance (Jan 18, 2022)
17-28367856-G-A		not specified	Uncertain significance (Feb 27, 2023)
17-28367869-G-A			Benign (Dec 31, 2019)
17-28367873-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-28367882-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-28367915-T-C		not specified	Likely benign (Jun 10, 2024)
17-28367958-G-C		not specified	Uncertain significance (Mar 07, 2023)
17-28367989-C-A		not specified	Uncertain significance (May 03, 2023)
17-28368017-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-28368019-G-A		VTN-related disorder	Likely benign (Sep 08, 2023)
17-28368023-C-G		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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_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