TNFSF9

TNF superfamily member 9, the group of Tumor necrosis factor superfamily

Basic information

Region (hg38): 19:6531026-6535924

Links

ENSG00000125657 ∙ NCBI:8744 ∙ OMIM:606182 ∙ HGNC:11939 ∙ Uniprot:P41273 ∙ 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 TNFSF9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF9 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			17	2	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	1

Variants in TNFSF9

This is a list of pathogenic ClinVar variants found in the TNFSF9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6531046-G-A		not specified	Uncertain significance (Sep 25, 2023)
19-6531052-G-A		not specified	Uncertain significance (Dec 21, 2022)
19-6531062-T-C		not specified	Uncertain significance (Oct 17, 2024)
19-6531112-G-C		not specified	Likely benign (Mar 16, 2022)
19-6531116-T-A		not specified	Uncertain significance (Jan 18, 2025)
19-6531160-G-A			Benign (Feb 01, 2023)
19-6531160-G-C		not specified	Uncertain significance (Mar 15, 2024)
19-6531190-C-T		not specified	Uncertain significance (Mar 31, 2023)
19-6531205-G-C		not specified	Uncertain significance (Nov 14, 2024)
19-6531230-C-G		not specified	Uncertain significance (Dec 20, 2023)
19-6534632-A-G		not specified	Uncertain significance (Oct 05, 2021)
19-6534663-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-6534711-A-G		not specified	Uncertain significance (Nov 10, 2024)
19-6534717-G-C			Likely benign (Aug 28, 2018)
19-6534720-T-G			Uncertain significance (Apr 12, 2024)
19-6534845-A-G		not specified	Uncertain significance (Jul 17, 2024)
19-6534905-C-G		not specified	Uncertain significance (Sep 25, 2023)
19-6534926-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-6534952-C-A		not specified	Uncertain significance (Mar 03, 2025)
19-6534953-A-C		not specified	Uncertain significance (Mar 03, 2025)
19-6534965-G-A		not specified	Uncertain significance (Jul 14, 2024)
19-6534974-G-A		not specified	Uncertain significance (May 31, 2023)
19-6534987-C-T		not specified	Uncertain significance (Jun 26, 2024)
19-6534993-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-6535052-C-G		not specified	Uncertain significance (Feb 13, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF9	protein_coding	protein_coding	ENST00000245817	3	4922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.318	0.620	125638	0	1	125639	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.480	169	152	1.11	0.00000892	1527
Missense in Polyphen		33	35.96	0.91769		359
Synonymous	0.130	79	80.5	0.982	0.00000497	619
Loss of Function	1.44	1	4.18	0.239	1.80e-7	43

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that binds to TNFRSF9. Induces the proliferation of activated peripheral blood T-cells. May have a role in activation-induced cell death (AICD). May play a role in cognate interactions between T-cells and B-cells/macrophages. {ECO:0000269|PubMed:20032458}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;the 41bb-dependent immune response;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.0631
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.87

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.257
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf9
• Phenotype: immune system phenotype; hematopoietic 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;positive regulation of activated T cell proliferation;positive regulation of cytotoxic T cell differentiation
• Cellular component: extracellular space;plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;tumor necrosis factor receptor superfamily binding