TNFRSF14

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

Basic information

Region (hg38): 1:2555638-2565382

Links

ENSG00000157873 ∙ NCBI:8764 ∙ OMIM:602746 ∙ HGNC:11912 ∙ Uniprot:Q92956 ∙ 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 TNFRSF14 gene.

• not specified (33 variants)
• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF14 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	1

Variants in TNFRSF14

This is a list of pathogenic ClinVar variants found in the TNFRSF14 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-2556673-T-C			Benign (Mar 29, 2018)
1-2556695-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-2556701-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-2556714-A-G		not specified	not provided (Sep 19, 2013)
1-2557726-G-A		not specified	Uncertain significance (Apr 08, 2022)
1-2557788-G-C		not specified	Uncertain significance (Jan 17, 2024)
1-2557828-A-C		not specified	Uncertain significance (Sep 13, 2023)
1-2559013-C-T		not specified	not provided (Sep 19, 2013)
1-2559074-C-G		not specified	not provided (Sep 19, 2013)
1-2559092-C-T		not specified	not provided (Sep 19, 2013)
1-2559110-C-T		not specified	not provided (Sep 19, 2013)
1-2559169-A-G		not specified	not provided (Sep 19, 2013)
1-2559170-T-C		not specified	not provided (Sep 19, 2013)
1-2559347-C-T		not specified	not provided (Sep 19, 2013)
1-2559361-G-T		not specified	not provided (Sep 19, 2013)
1-2559422-G-T		not specified	not provided (Sep 19, 2013)
1-2559426-T-A		not specified	not provided (Sep 19, 2013)
1-2559459-C-A		not specified	not provided (Sep 19, 2013)
1-2559495-C-A		not specified	not provided (Sep 19, 2013)
1-2559503-C-A		not specified	not provided (Sep 19, 2013)
1-2559515-C-T		not specified	not provided (Sep 19, 2013)
1-2559574-C-T		not specified	not provided (Sep 19, 2013)
1-2559622-G-A		not specified	not provided (Sep 19, 2013)
1-2559632-C-G		not specified	not provided (Sep 19, 2013)
1-2559632-C-T		not specified	not provided (Sep 19, 2013)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF14	protein_coding	protein_coding	ENST00000355716	8	9744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.808	0.192	125098	0	3	125101	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	151	174	0.869	0.0000106	1800
Missense in Polyphen		22	40.59	0.54201		459
Synonymous	-1.23	90	76.3	1.18	0.00000576	546
Loss of Function	3.00	2	14.2	0.141	6.05e-7	164

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)	0.0000185	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000177	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for BTLA. Receptor for TNFSF14/LIGHT and homotrimeric TNFSF1/lymphotoxin-alpha. Involved in lymphocyte activation. Plays an important role in HSV pathogenesis because it enhanced the entry of several wild-type HSV strains of both serotypes into CHO cells, and mediated HSV entry into activated human T-cells. {ECO:0000269|PubMed:8898196}.; FUNCTION: (Microbial infection) Acts as a receptor for Herpes simplex virus 2/HHV-2. {ECO:0000269|PubMed:11511370, ECO:0000269|PubMed:9696799}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Costimulation by the CD28 family;Immune System;Adaptive Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.186
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.0835
• hipred: Y
• hipred_score: 0.546
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf14
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of cytokine secretion involved in immune response;immune response;cell surface receptor signaling pathway;T cell costimulation;tumor necrosis factor-mediated signaling pathway;negative regulation of alpha-beta T cell proliferation;viral entry into host cell;positive regulation of peptidyl-tyrosine phosphorylation;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;positive regulation of T cell migration
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: virus receptor activity;tumor necrosis factor-activated receptor activity;protein binding;ubiquitin protein ligase binding