TNFRSF18

TNF receptor superfamily member 18, the group of CD molecules|Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 1:1203508-1206592

Links

ENSG00000186891 ∙ NCBI:8784 ∙ OMIM:603905 ∙ HGNC:11914 ∙ Uniprot:Q9Y5U5 ∙ 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 TNFRSF18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF18 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			28	9		37
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	11	0

Variants in TNFRSF18

This is a list of pathogenic ClinVar variants found in the TNFRSF18 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1203598-C-G		not specified	Uncertain significance (May 03, 2023)
1-1203622-G-C		not specified	Uncertain significance (Oct 17, 2023)
1-1203662-A-C		not specified	Uncertain significance (Oct 12, 2021)
1-1203689-A-G		not specified	Uncertain significance (Mar 19, 2024)
1-1203694-C-G		not specified	Uncertain significance (Jan 04, 2022)
1-1203701-G-A		not specified	Uncertain significance (Aug 08, 2023)
1-1203755-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-1203770-G-A		not specified	Likely benign (Oct 27, 2022)
1-1203781-G-A		not specified	Uncertain significance (Apr 19, 2023)
1-1203802-G-T		not specified	Uncertain significance (Dec 20, 2021)
1-1203820-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-1203836-G-A			Likely benign (May 01, 2023)
1-1203884-G-T		not specified	Likely benign (Jan 08, 2024)
1-1203891-C-T		not specified	Likely benign (Nov 27, 2023)
1-1203897-G-A		not specified	Likely benign (Dec 20, 2023)
1-1203906-C-T		not specified	Likely benign (Jun 30, 2023)
1-1203928-G-A		not specified	Likely benign (Apr 21, 2022)
1-1203934-G-A		not specified	Likely benign (Oct 12, 2021)
1-1203940-C-T		not specified	Likely benign (Jan 26, 2022)
1-1203941-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-1204417-T-G		not specified	Uncertain significance (May 20, 2024)
1-1204439-A-G		not specified	Uncertain significance (Jan 10, 2023)
1-1205411-C-T		not specified	Likely benign (Apr 25, 2023)
1-1205420-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-1205424-A-G		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF18	protein_coding	protein_coding	ENST00000328596	4	3184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000145	0.128	124996	0	32	125028	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.567	175	155	1.13	0.00000940	1596
Missense in Polyphen		42	42.78	0.98178		453
Synonymous	-0.866	77	67.9	1.13	0.00000461	535
Loss of Function	-0.598	8	6.37	1.26	2.72e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000588
Ashkenazi Jewish	0.000104	0.000100
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000984	0.0000976
Middle Eastern	0.0000548	0.0000544
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for TNFSF18. Seems to be involved in interactions between activated T-lymphocytes and endothelial cells and in the regulation of T-cell receptor-mediated cell death. Mediated NF-kappa-B activation via the TRAF2/NIK pathway.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);Gene expression (Transcription);Generic Transcription Pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;RNA Polymerase II Transcription;Immune System;TNFs bind their physiological receptors;RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs);Transcriptional regulation by RUNX1;Downstream signaling in naïve CD8+ T cells (Consensus)

Recessive Scores

• pRec: 0.164

Haploinsufficiency Scores

• pHI: 0.0380
• hipred: N
• hipred_score: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf18
• Phenotype: hematopoietic system phenotype; cellular phenotype; immune system phenotype

Gene ontology

• Biological process: positive regulation of leukocyte migration;apoptotic process;signal transduction;tumor necrosis factor-mediated signaling pathway;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of apoptotic process;regulation of regulatory T cell differentiation;positive regulation of cell adhesion
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane
• Molecular function: tumor necrosis factor-activated receptor activity;protein binding