TNFRSF10C

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

Basic information

Region (hg38): 8:23102920-23117445

Links

ENSG00000173535 ∙ NCBI:8794 ∙ OMIM:603613 ∙ HGNC:11906 ∙ Uniprot:O14798 ∙ 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 TNFRSF10C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF10C 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			6	5		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	6	2

Variants in TNFRSF10C

This is a list of pathogenic ClinVar variants found in the TNFRSF10C region.

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

Position	Type	Phenotype	Significance	ClinVar
8-23103164-G-T			Likely benign (May 04, 2018)
8-23111721-T-A		not specified	Uncertain significance (May 07, 2024)
8-23111736-C-A		not specified	Uncertain significance (Nov 10, 2023)
8-23111747-C-T		not specified	Uncertain significance (Dec 19, 2022)
8-23111769-A-C		not specified	Uncertain significance (Sep 01, 2021)
8-23111803-C-A		not specified	Likely benign (Mar 07, 2023)
8-23111807-G-A		not specified	Uncertain significance (Mar 19, 2024)
8-23114662-C-G		not specified	Uncertain significance (Jul 19, 2023)
8-23114694-G-A			Benign (Mar 05, 2018)
8-23114707-G-T		not specified	Uncertain significance (Jul 17, 2023)
8-23114715-C-T			Benign (Jul 06, 2018)
8-23114722-G-A		not specified	Likely benign (Nov 03, 2022)
8-23115599-G-A		not specified	Uncertain significance (Jul 20, 2021)
8-23116718-A-G		not specified	Likely benign (May 24, 2023)
8-23116765-C-T			Likely benign (Jul 01, 2022)
8-23116857-G-C			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF10C	protein_coding	protein_coding	ENST00000356864	5	33083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000316	0.196	125014	4	730	125748	0.00292

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.819	121	149	0.811	0.00000778	1677
Missense in Polyphen		41	35.854	1.1435		427
Synonymous	1.88	35	52.3	0.669	0.00000265	521
Loss of Function	-0.235	8	7.31	1.09	3.08e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00287	0.00287
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000832	0.000832
European (Non-Finnish)	0.00546	0.00544
Middle Eastern	0.00	0.00
South Asian	0.0000342	0.0000327
Other	0.00310	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the cytotoxic ligand TRAIL. Lacks a cytoplasmic death domain and hence is not capable of inducing apoptosis. May protect cells against TRAIL mediated apoptosis by competing with TRAIL-R1 and R2 for binding to the ligand.
• 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;TP53 Regulates Transcription of Cell Death Genes;VEGFA-VEGFR2 Signaling Pathway;Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;Transcriptional Regulation by TP53;Direct p53 effectors;TRAIL signaling pathway;TP53 Regulates Transcription of Death Receptors and Ligands (Consensus)

Intolerance Scores

• loftool: 0.605
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• pHI: 0.0857
• hipred: N
• hipred_score: 0.112
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

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: TRAIL-activated apoptotic signaling pathway;regulation of apoptotic process;positive regulation of apoptotic process
• Cellular component: plasma membrane;cell surface;anchored component of membrane
• Molecular function: transmembrane signaling receptor activity;TRAIL binding