TNFRSF25

TNF receptor superfamily member 25, the group of Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 1:6460786-6466175

Previous symbols: [ "TNFRSF12" ]

Links

ENSG00000215788 ∙ NCBI:8718 ∙ OMIM:603366 ∙ HGNC:11910 ∙ Uniprot:Q93038 ∙ 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 TNFRSF25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF25 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				6	4	10
missense			22	2	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1	2	4
Total	0	0	23	9	7

Variants in TNFRSF25

This is a list of pathogenic ClinVar variants found in the TNFRSF25 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-6461457-T-C		not specified	Uncertain significance (Oct 27, 2023)
1-6461487-C-G		not specified	Uncertain significance (Mar 30, 2024)
1-6461493-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-6461504-G-T		not specified	Uncertain significance (May 13, 2024)
1-6461549-T-G		not specified	Uncertain significance (Jan 24, 2024)
1-6461613-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-6461622-G-C		not specified	Uncertain significance (May 22, 2023)
1-6461641-C-T		TNFRSF25-related disorder	Likely benign (Nov 12, 2019)
1-6461651-C-G		not specified	Uncertain significance (Dec 20, 2021)
1-6461733-C-G		not specified	Uncertain significance (Dec 03, 2021)
1-6462033-C-A		not specified	Uncertain significance (Sep 07, 2022)
1-6462033-C-T		not specified	Likely benign (Jan 03, 2024)
1-6462065-T-C		not specified	Uncertain significance (Oct 03, 2022)
1-6462103-G-A		TNFRSF25-related disorder	Likely benign (Jan 08, 2020)
1-6462140-G-T		not specified	Uncertain significance (Jun 16, 2023)
1-6462148-G-A			Benign (Aug 20, 2018)
1-6462184-A-G		TNFRSF25-related disorder	Likely benign (Apr 07, 2018)
1-6462630-G-A		not specified	Uncertain significance (May 18, 2023)
1-6462873-G-A		TNFRSF25-related disorder	Likely benign (Jul 31, 2019)
1-6462901-G-A		not specified	Uncertain significance (Feb 14, 2024)
1-6462905-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-6462945-A-T			Likely benign (Jul 01, 2022)
1-6462970-A-G		not specified	Uncertain significance (Sep 01, 2021)
1-6463086-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-6463101-C-T		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF25	protein_coding	protein_coding	ENST00000377782	10	5045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00865	0.991	125724	0	9	125733	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	205	279	0.736	0.0000183	2676
Missense in Polyphen		39	72.353	0.53902		748
Synonymous	1.01	107	121	0.883	0.00000886	876
Loss of Function	3.05	8	24.1	0.331	0.00000122	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000634	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for TNFSF12/APO3L/TWEAK. Interacts directly with the adapter TRADD. Mediates activation of NF-kappa-B and induces apoptosis. May play a role in regulating lymphocyte homeostasis.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Apoptosis Modulation and Signaling;Apoptosis;Apoptotic Signaling Pathway;TWEAK;induction of apoptosis through dr3 and dr4/5 death receptors;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.0895

Intolerance Scores

• loftool: 0.0238
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.0764
• hipred: Y
• hipred_score: 0.643
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf25
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; 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); immune system phenotype

Gene ontology

• Biological process: apoptotic process;signal transduction;cell surface receptor signaling pathway;tumor necrosis factor-mediated signaling pathway;regulation of apoptotic process;apoptotic signaling pathway
• Cellular component: extracellular region;cytosol;plasma membrane;integral component of plasma membrane
• Molecular function: tumor necrosis factor-activated receptor activity;signaling receptor activity