TNFRSF10D

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

Basic information

Region (hg38): 8:23135587-23164027

Links

ENSG00000173530 ∙ NCBI:8793 ∙ OMIM:603614 ∙ HGNC:11907 ∙ Uniprot:Q9UBN6 ∙ 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 TNFRSF10D gene.

• Inborn genetic diseases (14 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF10D 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			13	1	3	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	4

Variants in TNFRSF10D

This is a list of pathogenic ClinVar variants found in the TNFRSF10D region.

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

Position	Type	Phenotype	Significance	ClinVar
8-23137925-G-A		not specified	Uncertain significance (Aug 22, 2023)
8-23137993-C-A		not specified	Uncertain significance (Sep 01, 2021)
8-23137998-T-G			Benign (Jun 19, 2018)
8-23144464-G-A		not specified	Uncertain significance (Sep 17, 2021)
8-23144475-A-G			Benign (Feb 26, 2021)
8-23144532-G-C			Benign (Jun 19, 2018)
8-23144572-C-T		not specified	Uncertain significance (Jan 30, 2024)
8-23144583-T-C		not specified	Uncertain significance (May 10, 2022)
8-23144592-G-A		not specified	Uncertain significance (Jan 31, 2023)
8-23144604-C-T		not specified	Likely benign (Jun 06, 2023)
8-23144619-C-T		not specified	Uncertain significance (Feb 16, 2023)
8-23145722-C-A		not specified	Uncertain significance (Jun 11, 2021)
8-23145745-A-C		not specified	Uncertain significance (Feb 02, 2024)
8-23145803-T-A		not specified	Uncertain significance (May 03, 2023)
8-23145886-G-A		not specified	Uncertain significance (Aug 30, 2022)
8-23147026-A-G			Benign (Jun 19, 2018)
8-23147031-C-T		not specified	Uncertain significance (Dec 20, 2023)
8-23147057-C-T		not specified	Uncertain significance (Nov 07, 2023)
8-23148486-C-T		not specified	Uncertain significance (Dec 19, 2023)
8-23154918-G-A		not specified	Uncertain significance (Oct 13, 2023)
8-23154956-G-C		not specified	Uncertain significance (Jan 03, 2024)
8-23154967-A-G		not specified	Uncertain significance (Jan 30, 2024)
8-23154975-C-T		not specified	Likely benign (Oct 13, 2023)
8-23163790-A-C		not specified	Uncertain significance (Apr 26, 2023)
8-23163791-G-T		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF10D	protein_coding	protein_coding	ENST00000312584	9	28443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-8	0.522	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00939	218	218	1.00	0.0000122	2409
Missense in Polyphen		36	46.404	0.77579		587
Synonymous	0.401	82	86.8	0.945	0.00000494	792
Loss of Function	1.01	14	18.7	0.748	8.93e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000762	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.000762	0.000761
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the cytotoxic ligand TRAIL. Contains a truncated death domain and hence is not capable of inducing apoptosis but protects against TRAIL-mediated apoptosis. Reports are contradictory with regards to its ability to induce the NF- kappa-B pathway. According to PubMed:9382840, it cannot but according to PubMed:9430226, it can induce the NF-kappa-B pathway.
• 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;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;TRAIL signaling;Cell surface interactions at the vascular wall;Hemostasis;Death Receptor Signalling;Transcriptional Regulation by TP53;Direct p53 effectors;TRAIL signaling pathway;TP53 Regulates Transcription of Death Receptors and Ligands (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.206
• rvis_EVS: 3.11
• rvis_percentile_EVS: 99.26

Haploinsufficiency Scores

• pHI: 0.0435
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00884

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;signal transduction;cell surface receptor signaling pathway;regulation of apoptotic process;negative regulation of apoptotic process;leukocyte migration
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: transmembrane signaling receptor activity;TRAIL binding