TNFSF15

TNF superfamily member 15, the group of Tumor necrosis factor superfamily

Basic information

Region (hg38): 9:114784651-114806039

Links

ENSG00000181634 ∙ NCBI:9966 ∙ OMIM:604052 ∙ HGNC:11931 ∙ Uniprot:O95150 ∙ 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 TNFSF15 gene.

• Inborn genetic diseases (7 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF15 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				2	1	3
missense			7		2	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	3

Variants in TNFSF15

This is a list of pathogenic ClinVar variants found in the TNFSF15 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-114785492-T-C		Leprosy, susceptibility to, 1	Uncertain risk allele (Jun 10, 2022)
9-114790645-T-C		not specified	Uncertain significance (Feb 28, 2024)
9-114790663-G-A		not specified	Uncertain significance (Jan 04, 2024)
9-114790777-G-A		not specified	Uncertain significance (Dec 15, 2022)
9-114790814-T-C		not specified	Uncertain significance (Jan 26, 2022)
9-114790867-A-T		not specified	Uncertain significance (Aug 02, 2021)
9-114790878-A-T			Benign (Apr 27, 2018)
9-114792432-T-G			Benign (Apr 10, 2018)
9-114792435-G-A			Likely benign (May 29, 2018)
9-114793562-T-C		not specified	Uncertain significance (May 23, 2023)
9-114796423-C-G		Leprosy, susceptibility to, 1	confers sensitivity (Jun 10, 2022)
9-114805835-G-A		not specified	Uncertain significance (Mar 31, 2023)
9-114805864-A-T		not specified	Uncertain significance (Apr 10, 2023)
9-114805893-G-A			Likely benign (Jun 08, 2018)
9-114805912-C-T		not specified	Uncertain significance (Mar 16, 2022)
9-114805931-C-A		not specified	Uncertain significance (Jan 03, 2024)
9-114805939-C-T			Benign (May 21, 2018)
9-114805950-G-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF15	protein_coding	protein_coding	ENST00000374045	4	21492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00282	0.945	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.540	121	139	0.871	0.00000699	1644
Missense in Polyphen		24	46.52	0.5159		574
Synonymous	0.790	47	54.4	0.864	0.00000292	497
Loss of Function	1.70	6	12.5	0.482	7.03e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for TNFRSF25 and TNFRSF6B. Mediates activation of NF-kappa-B. Inhibits vascular endothelial growth and angiogenesis (in vitro). Promotes activation of caspases and apoptosis. {ECO:0000269|PubMed:10597252, ECO:0000269|PubMed:11911831, ECO:0000269|PubMed:11923219, ECO:0000269|PubMed:9872942}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Senescence and Autophagy in Cancer;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.324
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.198
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.473

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf15
• Phenotype: hematopoietic system phenotype; skeleton phenotype; cellular phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;immune response;signal transduction;activation of NF-kappaB-inducing kinase activity;regulation of signaling receptor activity;tumor necrosis factor-mediated signaling pathway;cytokine metabolic process
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding