TNFRSF10A

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

Basic information

Region (hg38): 8:23190451-23225102

Links

ENSG00000104689 ∙ NCBI:8797 ∙ OMIM:603611 ∙ HGNC:11904 ∙ Uniprot:O00220 ∙ 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 TNFRSF10A gene.

• Inborn genetic diseases (27 variants)
• not provided (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF10A 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				4	4	8
missense			26	1	3	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					2	2
Total	0	0	26	5	9

Variants in TNFRSF10A

This is a list of pathogenic ClinVar variants found in the TNFRSF10A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-23191695-C-A			Benign (Jun 16, 2018)
8-23191760-G-C			Benign (Dec 31, 2019)
8-23191788-C-T		not specified	Uncertain significance (Sep 29, 2023)
8-23191800-C-G		not specified	Uncertain significance (Dec 01, 2022)
8-23191839-C-T		not specified	Uncertain significance (Jan 03, 2022)
8-23191888-C-T		not specified	Uncertain significance (Jan 30, 2024)
8-23191904-A-G			Likely benign (Jul 04, 2018)
8-23191905-G-C		not specified	Uncertain significance (Apr 07, 2023)
8-23191906-C-T		not specified	Uncertain significance (Mar 08, 2024)
8-23191958-G-T		not specified	Uncertain significance (Aug 09, 2021)
8-23191966-A-G		not specified	Uncertain significance (Nov 09, 2022)
8-23191978-C-T		not specified	Uncertain significance (Nov 17, 2023)
8-23197122-A-C			Benign (Aug 15, 2018)
8-23197125-C-T			Benign (Jul 18, 2017)
8-23197133-C-G		not specified	Uncertain significance (Mar 08, 2024)
8-23197149-C-T		not specified	Uncertain significance (Jun 18, 2021)
8-23197200-G-A		not specified	Uncertain significance (May 22, 2023)
8-23199347-A-G			Benign (Jun 21, 2018)
8-23199352-C-A		not specified	Uncertain significance (Mar 20, 2023)
8-23199352-C-T		not specified	Likely benign (Jun 23, 2023)
8-23199374-G-A			Benign (Jul 18, 2017)
8-23199389-G-A			Benign (Dec 31, 2019)
8-23199391-T-G			Benign (Aug 15, 2018)
8-23199417-C-A		not specified	Uncertain significance (Apr 05, 2023)
8-23199427-G-C		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF10A	protein_coding	protein_coding	ENST00000221132	10	34675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.07e-15	0.00708	125580	0	168	125748	0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.645	291	262	1.11	0.0000139	2984
Missense in Polyphen		51	44.885	1.1362		560
Synonymous	-1.06	120	106	1.13	0.00000606	954
Loss of Function	-0.342	21	19.4	1.08	9.32e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000326	0.000326
Finnish	0.000601	0.000601
European (Non-Finnish)	0.00125	0.00125
Middle Eastern	0.000326	0.000326
South Asian	0.00	0.00
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the cytotoxic ligand TNFSF10/TRAIL (PubMed:26457518). The adapter molecule FADD recruits caspase-8 to the activated receptor. The resulting death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation which initiates the subsequent cascade of caspases (aspartate-specific cysteine proteases) mediating apoptosis. Promotes the activation of NF-kappa-B. {ECO:0000269|PubMed:26457518, ECO:0000269|PubMed:9430227}.
• Pathway: Influenza A - 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);Apoptosis Modulation and Signaling;miR-targeted genes in lymphocytes - TarBase;TP53 Regulates Transcription of Cell Death Genes;Signal Transduction;Gene expression (Transcription);induction of apoptosis through dr3 and dr4/5 death receptors;Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;Regulation of necroptotic cell death;Dimerization of procaspase-8;Regulation by c-FLIP;Ligand-dependent caspase activation;RNA Polymerase II Transcription;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;CASP8 activity is inhibited;Regulated Necrosis;Programmed Cell Death;RIPK1-mediated regulated necrosis;TRAIL signaling;Cell surface interactions at the vascular wall;Hemostasis;Death Receptor Signalling;Transcriptional Regulation by TP53;Direct p53 effectors;Caspase Cascade in Apoptosis;TRAIL signaling pathway;TP53 Regulates Transcription of Death Receptors and Ligands (Consensus)

Recessive Scores

• pRec: 0.0662

Intolerance Scores

• loftool: 0.280
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.402
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf10b
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; immune 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); hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;signal transduction;cell surface receptor signaling pathway;activation of NF-kappaB-inducing kinase activity;extrinsic apoptotic signaling pathway via death domain receptors;TRAIL-activated apoptotic signaling pathway;regulation of apoptotic process;positive regulation of apoptotic process;leukocyte migration;cellular response to mechanical stimulus;extrinsic apoptotic signaling pathway;regulation of extrinsic apoptotic signaling pathway via death domain receptors;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: protease binding;death receptor activity;protein binding;transcription factor binding;signaling receptor activity;TRAIL binding