TNFSF14

TNF superfamily member 14, the group of CD molecules|Tumor necrosis factor superfamily

Basic information

Region (hg38): 19:6658085-6670588

Links

ENSG00000125735 ∙ NCBI:8740 ∙ OMIM:604520 ∙ HGNC:11930 ∙ Uniprot:O43557 ∙ 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 TNFSF14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF14 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					3	3
missense			9	2		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	9	2	3

Variants in TNFSF14

This is a list of pathogenic ClinVar variants found in the TNFSF14 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6664944-G-A			Benign (Jul 10, 2018)
19-6664996-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-6665046-G-A			Benign (Jul 23, 2018)
19-6665066-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-6665084-G-A		not specified	Uncertain significance (Aug 09, 2021)
19-6665143-C-T		not specified	Uncertain significance (Mar 20, 2024)
19-6665156-C-T		not specified	Uncertain significance (May 23, 2024)
19-6665299-T-C		not specified	Uncertain significance (Oct 13, 2023)
19-6665330-C-T		not specified	Uncertain significance (Jan 31, 2022)
19-6665332-G-A		not specified	Uncertain significance (Jul 15, 2021)
19-6665350-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-6667119-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-6667440-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-6667446-C-T		not specified	Likely benign (Mar 18, 2024)
19-6669936-A-G		not specified	Uncertain significance (Oct 12, 2021)
19-6669978-T-C		not specified	Likely benign (Mar 24, 2023)
19-6670013-G-A			Benign (Dec 31, 2019)
19-6670026-C-A		not specified	Uncertain significance (Oct 20, 2023)
19-6670054-C-G		not specified	Uncertain significance (Jun 07, 2024)
19-6670059-C-A			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF14	protein_coding	protein_coding	ENST00000599359	4	7452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0517	0.929	125740	0	4	125744	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.638	135	158	0.857	0.0000107	1500
Missense in Polyphen		33	52.689	0.62631		555
Synonymous	0.845	57	65.7	0.867	0.00000402	543
Loss of Function	2.04	4	11.5	0.349	6.66e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that binds to TNFRSF3/LTBR. Binding to the decoy receptor TNFRSF6B modulates its effects. Activates NFKB, stimulates the proliferation of T-cells, and inhibits growth of the adenocarcinoma HT-29. Acts as a receptor for Herpes simplex virus.
• Pathway: NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.264

Intolerance Scores

• loftool: 0.185
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.107
• hipred: Y
• hipred_score: 0.643
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf14
• Phenotype: immune system phenotype; renal/urinary system phenotype; hematopoietic system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: apoptotic process;immune response;signal transduction;regulation of signaling receptor activity;positive regulation of T cell chemotaxis;T cell costimulation;tumor necrosis factor-mediated signaling pathway;T cell proliferation;T cell activation;T cell homeostasis;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of myoblast differentiation;cellular response to mechanical stimulus;positive regulation of NIK/NF-kappaB signaling;positive regulation of myoblast fusion
• Cellular component: extracellular space;cytoplasm;plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;protein binding;cysteine-type endopeptidase inhibitor activity involved in apoptotic process