TNFRSF19

TNF receptor superfamily member 19, the group of Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 13:23570370-23676104

Links

ENSG00000127863 ∙ NCBI:55504 ∙ OMIM:606122 ∙ HGNC:11915 ∙ Uniprot:Q9NS68 ∙ 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 TNFRSF19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF19 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	21	3	0

Variants in TNFRSF19

This is a list of pathogenic ClinVar variants found in the TNFRSF19 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-23590218-C-T		not specified	Uncertain significance (Apr 19, 2023)
13-23593341-T-C			Benign (Aug 09, 2018)
13-23593384-C-A		not specified	Uncertain significance (Nov 17, 2022)
13-23615888-G-A		not specified	Uncertain significance (Apr 09, 2024)
13-23615913-G-A		not specified	Uncertain significance (Sep 26, 2023)
13-23615920-C-G		not specified	Uncertain significance (Nov 12, 2021)
13-23615946-A-G		not specified	Uncertain significance (Apr 30, 2024)
13-23615973-C-T		not specified	Uncertain significance (May 08, 2024)
13-23626718-A-C		not specified	Uncertain significance (Feb 06, 2023)
13-23626787-C-T		not specified	Uncertain significance (Apr 17, 2023)
13-23659110-C-T		not specified	Uncertain significance (Sep 01, 2021)
13-23659125-T-C		not specified	Uncertain significance (Feb 16, 2023)
13-23659170-G-A		not specified	Uncertain significance (Mar 25, 2024)
13-23660394-A-G		not specified	Uncertain significance (Jun 07, 2023)
13-23660401-C-T		not specified	Uncertain significance (May 08, 2024)
13-23660470-G-A		not specified	Uncertain significance (Nov 18, 2022)
13-23660478-G-T		not specified	Uncertain significance (Nov 09, 2022)
13-23660489-C-T			Likely benign (Apr 01, 2023)
13-23667980-G-A		not specified	Uncertain significance (Aug 08, 2022)
13-23667988-C-T		not specified	Uncertain significance (Apr 26, 2024)
13-23668019-C-A		not specified	Uncertain significance (Sep 17, 2021)
13-23668028-C-T		not specified	Uncertain significance (Dec 21, 2022)
13-23668034-C-T		not specified	Uncertain significance (May 30, 2024)
13-23668052-G-A		not specified	Uncertain significance (Aug 02, 2021)
13-23668707-C-T			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF19	protein_coding	protein_coding	ENST00000382258	8	105724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0329	0.959	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.231	237	247	0.959	0.0000145	2729
Missense in Polyphen		68	88.286	0.77022		960
Synonymous	-0.304	109	105	1.04	0.00000725	836
Loss of Function	2.33	5	14.6	0.343	6.14e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000546	0.0000527
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000349	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can mediate activation of JNK and NF-kappa-B. May promote caspase-independent cell death.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.532
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.0833
• hipred: N
• hipred_score: 0.253
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.419

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf19
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype

Zebrafish Information Network

• Gene name: tnfrsf19
• Affected structure: central artery
• Phenotype tag: abnormal
• Phenotype quality: decreased branchiness

Gene ontology

• Biological process: hair follicle development;apoptotic process;JNK cascade;tumor necrosis factor-mediated signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of JNK cascade
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: tumor necrosis factor-activated receptor activity;signaling receptor activity