TNFSF18

TNF superfamily member 18, the group of Tumor necrosis factor superfamily

Basic information

Region (hg38): 1:173039201-173050941

Links

ENSG00000120337

∙ NCBI:8995 ∙ OMIM:603898 ∙ HGNC:11932 ∙ Uniprot:Q9UNG2 ∙ 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 TNFSF18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF18 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			6 clinvar	1 clinvar		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1 clinvar	1 clinvar		2
Total	0	0	7	2	0

Variants in TNFSF18

This is a list of pathogenic ClinVar variants found in the TNFSF18 region.

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

Position	Phenotype	Significance	ClinVar
1-173041411-A-G	not specified	Uncertain significance (Mar 14, 2023)	2495917
1-173041534-T-G	not specified	Uncertain significance (Oct 02, 2023)	3180334
1-173041654-A-T	not specified	Uncertain significance (Jul 28, 2021)	3180333
1-173041671-G-A	not specified	Uncertain significance (Jun 19, 2024)	3327548
1-173041701-G-A	not specified	Uncertain significance (Jun 05, 2023)	2556426
1-173043957-G-A	not specified	Uncertain significance (Mar 31, 2023)	2517850
1-173050799-A-G	not specified	Likely benign (Sep 19, 2023)	3180332
1-173050869-G-T	not specified	Uncertain significance (Oct 12, 2022)	2318419
1-173050917-T-C	not specified	Uncertain significance (Feb 28, 2024)	3180335
1-173050933-A-T		Likely benign (Oct 06, 2023)	1645718

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF18	protein_coding	protein_coding	ENST00000404377	3	11004

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000192	0.492	125421	0	21	125442	0.0000837

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.555	115	99.4	1.16	0.00000447	1302
Missense in Polyphen		30	24.495	1.2247		348
Synonymous	0.302	34	36.3	0.936	0.00000165	370
Loss of Function	0.354	6	7.01	0.856	2.95e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000654	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.00000965	0.00000882
Middle Eastern	0.000654	0.000653
South Asian	0.000219	0.000196
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cytokine that binds to TNFRSF18/AITR/GITR. Regulates T- cell responses. Can function as costimulator and lower the threshold for T-cell activation and T-cell proliferation. Important for interactions between activated T-lymphocytes and endothelial cells. Mediates activation of NF-kappa-B. Triggers increased phosphorylation of STAT1 and up-regulates expression of VCAM1 and ICAM1 (PubMed:23892569). Promotes leukocyte adhesion to endothelial cells (PubMed:23892569). Regulates migration of monocytes from the splenic reservoir to sites of inflammation (By similarity). {ECO:0000250|UniProtKB:Q7TS55, ECO:0000269|PubMed:17449724, ECO:0000269|PubMed:18040044, ECO:0000269|PubMed:23892569}.;
Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

pRec: 0.174

Intolerance Scores

loftool: 0.533
rvis_EVS: -0.05
rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

pHI: 0.172
hipred: N
hipred_score: 0.123
ghis: 0.430

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tnfsf18
Phenotype: growth/size/body region phenotype;

Zebrafish Information Network

Gene name: tnfsf18
Affected structure: somite border
Phenotype tag: abnormal
Phenotype quality: irregular spatial pattern

Gene ontology

Biological process: adaptive immune response;T cell proliferation involved in immune response;positive regulation of leukocyte migration;signal transduction;cell-cell signaling;regulation of signaling receptor activity;tumor necrosis factor-mediated signaling pathway;regulation of T cell proliferation;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of apoptotic process;positive regulation of cell adhesion;positive regulation of NF-kappaB transcription factor activity
Cellular component: extracellular space;plasma membrane;cell surface;integral component of membrane
Molecular function: signaling receptor binding;cytokine activity;protein binding;tumor necrosis factor receptor superfamily binding;identical protein binding