VTCN1

V-set domain containing T cell activation inhibitor 1, the group of B7 family|V-set domain containing

Basic information

Region (hg38): 1:117143587-117210960

Links

ENSG00000134258

∙ NCBI:79679 ∙ OMIM:608162 ∙ HGNC:28873 ∙ Uniprot:Q7Z7D3 ∙ 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 VTCN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTCN1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VTCN1	protein_coding	protein_coding	ENST00000369458	5	67348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-12	0.00722	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.861	125	155	0.805	0.00000791	1841
Missense in Polyphen		37	54.435	0.67971		626
Synonymous	0.180	60	61.8	0.971	0.00000330	566
Loss of Function	-0.996	16	12.2	1.31	6.03e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000874	0.000870
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000134	0.000123
Middle Eastern	0.000874	0.000870
South Asian	0.000751	0.000752
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Negatively regulates T-cell-mediated immune response by inhibiting T-cell activation, proliferation, cytokine production and development of cytotoxicity. When expressed on the cell surface of tumor macrophages, plays an important role, together with regulatory T-cells (Treg), in the suppression of tumor- associated antigen-specific T-cell immunity. Involved in promoting epithelial cell transformation. {ECO:0000250|UniProtKB:Q7TSP5, ECO:0000269|PubMed:15878339, ECO:0000269|PubMed:16606666, ECO:0000269|PubMed:17509674, ECO:0000269|PubMed:17875732}.;
Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.0858

Intolerance Scores

loftool: 0.754
rvis_EVS: 0.24
rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

pHI: 0.152
hipred: N
hipred_score: 0.170
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0365

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Vtcn1
Phenotype: cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; normal phenotype; 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); hematopoietic system phenotype;

Gene ontology

Biological process: response to protozoan;adaptive immune response;positive regulation of T cell proliferation;negative regulation of T cell proliferation;negative regulation of apoptotic process;regulation of immune response;T cell receptor signaling pathway;negative regulation of T cell activation;interleukin-4 secretion;interferon-gamma secretion;positive regulation of interleukin-2 secretion
Cellular component: external side of plasma membrane;integral component of membrane
Molecular function: molecular_function;signaling receptor binding