TNFSF10

TNF superfamily member 10, the group of CD molecules|Tumor necrosis factor superfamily

Basic information

Region (hg38): 3:172505508-172523475

Links

ENSG00000121858 ∙ ∙ OMIM:603598 ∙ HGNC:11925 ∙ Uniprot:P50591 ∙ 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 TNFSF10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF10 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	2	3
missense			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	12	1	7

Variants in TNFSF10

This is a list of pathogenic ClinVar variants found in the TNFSF10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-172506285-C-T			Benign (Nov 12, 2018)
3-172506513-A-G			Benign (Nov 12, 2018)
3-172506580-T-C		not specified	Uncertain significance (Jan 23, 2024)
3-172506612-G-C		not specified	Uncertain significance (Dec 14, 2023)
3-172506729-G-T		not specified	Uncertain significance (Nov 03, 2023)
3-172506773-A-C		not specified	Uncertain significance (Jun 28, 2023)
3-172506805-T-C		not specified	Uncertain significance (Sep 22, 2023)
3-172506882-G-C		not specified	Uncertain significance (May 02, 2024)
3-172506904-T-G		not specified	Uncertain significance (Dec 01, 2022)
3-172509291-C-G		not specified	Uncertain significance (May 24, 2023)
3-172509409-C-T			Benign (Nov 12, 2018)
3-172511623-C-T		not specified	Uncertain significance (Apr 18, 2023)
3-172514870-G-A			Likely benign (Jul 20, 2018)
3-172514982-G-A		not specified	Uncertain significance (Dec 30, 2023)
3-172518650-T-G			Benign (Nov 12, 2018)
3-172523209-T-G			Benign (Nov 12, 2018)
3-172523280-G-A			Benign (Jul 31, 2018)
3-172523288-C-T			Benign (Jul 13, 2018)
3-172523303-A-T		not specified	Uncertain significance (Dec 19, 2022)
3-172523359-C-G		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF10	protein_coding	protein_coding	ENST00000241261	5	18000

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.135	0.861	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.166	142	148	0.962	0.00000715	1871
Missense in Polyphen		39	45.131	0.86414		622
Synonymous	0.154	51	52.4	0.973	0.00000268	496
Loss of Function	2.51	4	14.2	0.281	6.67e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.0000552	0.0000544
South Asian	0.0000983	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that binds to TNFRSF10A/TRAILR1, TNFRSF10B/TRAILR2, TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and possibly also to TNFRSF11B/OPG (PubMed:26457518, PubMed:10549288). Induces apoptosis. Its activity may be modulated by binding to the decoy receptors TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4 and TNFRSF11B/OPG that cannot induce apoptosis. {ECO:0000269|PubMed:10549288, ECO:0000269|PubMed:26457518}.
• Pathway: Influenza A - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Measles - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);TP53 Network;Apoptosis Modulation and Signaling;Apoptosis;Photodynamic therapy-induced AP-1 survival signaling.;Apoptotic Signaling Pathway;Protein alkylation leading to liver fibrosis;Signal Transduction;induction of apoptosis through dr3 and dr4/5 death receptors;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;Regulation of necroptotic cell death;GPCR signaling-cholera toxin;Dimerization of procaspase-8;GPCR signaling-pertussis toxin;Regulation by c-FLIP;Ligand-dependent caspase activation;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;CASP8 activity is inhibited;Regulated Necrosis;Programmed Cell Death;RIPK1-mediated regulated necrosis;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;TRAIL signaling;JAK STAT pathway and regulation;Death Receptor Signalling;GPCR signaling-G alpha i;Caspase Cascade in Apoptosis;TRAIL signaling pathway (Consensus)

Recessive Scores

• pRec: 0.671

Intolerance Scores

• loftool: 0.331
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.0960
• hipred: Y
• hipred_score: 0.598
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.516

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf10
• Phenotype: skeleton phenotype; immune system phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); liver/biliary system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: tnfsf10
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;immune response;signal transduction;cell surface receptor signaling pathway;cell-cell signaling;male gonad development;regulation of signaling receptor activity;response to insulin;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of release of cytochrome c from mitochondria;regulation of extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of extrinsic apoptotic signaling pathway
• Cellular component: extracellular region;integral component of plasma membrane;extracellular exosome
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;protein binding;zinc ion binding;identical protein binding;TRAIL binding