TNFSF8

TNF superfamily member 8, the group of CD molecules|Tumor necrosis factor superfamily

Basic information

Region (hg38): 9:114893342-114930595

Previous symbols: [ "CD30LG" ]

Links

ENSG00000106952 ∙ NCBI:944 ∙ OMIM:603875 ∙ HGNC:11938 ∙ Uniprot:P32971 ∙ 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 TNFSF8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF8 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						0
missense			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in TNFSF8

This is a list of pathogenic ClinVar variants found in the TNFSF8 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-114904001-T-C		not specified	Uncertain significance (May 20, 2024)
9-114904080-C-T		not specified	Likely benign (Feb 10, 2022)
9-114904136-T-C		not specified	Uncertain significance (Mar 21, 2023)
9-114904137-G-C		not specified	Likely benign (Aug 02, 2023)
9-114904179-T-C		not specified	Uncertain significance (Oct 25, 2023)
9-114918105-G-A		not specified	Uncertain significance (Sep 25, 2023)
9-114930180-T-C		not specified	Uncertain significance (Aug 08, 2023)
9-114930210-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-114930219-T-C		not specified	Uncertain significance (Dec 27, 2023)
9-114930279-G-C		not specified	Uncertain significance (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF8	protein_coding	protein_coding	ENST00000223795	4	36695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.758	0.240	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.834	99	125	0.790	0.00000643	1518
Missense in Polyphen		24	33.414	0.71827		438
Synonymous	0.674	48	54.3	0.884	0.00000322	464
Loss of Function	2.48	1	9.03	0.111	3.82e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000353	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that binds to TNFRSF8/CD30. Induces proliferation of T-cells.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.0787
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.314
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf8
• Phenotype: immune system phenotype

Gene ontology

• Biological process: apoptotic process;immune response;signal transduction;cell-cell signaling;cell population proliferation;regulation of signaling receptor activity;tumor necrosis factor-mediated signaling pathway;CD8-positive, alpha-beta T cell differentiation;positive regulation of transcription by RNA polymerase II;defense response to Gram-positive bacterium
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding