TNFRSF6B

TNF receptor superfamily member 6b, the group of Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 20:63696652-63698684

Links

ENSG00000243509 ∙ NCBI:8771 ∙ OMIM:603361 ∙ HGNC:11921 ∙ Uniprot:O95407 ∙ 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 TNFRSF6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF6B 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	95	11	109
missense			208	5	1	214
nonsense			6			6
start loss						0
frameshift			6			6
inframe indel			8			8
splice donor/acceptor (+/-2bp)			1			1
splice region			2	5		7
non coding			6	24	1	31
Total	0	0	238	124	13

Variants in TNFRSF6B

This is a list of pathogenic ClinVar variants found in the TNFRSF6B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63696774-G-T			Uncertain significance (May 18, 2022)
20-63696775-C-T			Uncertain significance (Jul 30, 2023)
20-63696776-G-C			Likely benign (Oct 30, 2023)
20-63696780-G-A			Uncertain significance (Jul 25, 2023)
20-63696783-G-A			Likely benign (Jan 05, 2024)
20-63696786-C-A			Uncertain significance (Oct 08, 2023)
20-63696792-C-G			Uncertain significance (Oct 04, 2022)
20-63696796-C-T			Uncertain significance (Aug 04, 2023)
20-63696797-G-A			Likely benign (Nov 24, 2023)
20-63696797-G-T			Likely benign (Dec 01, 2022)
20-63696799-T-G		not specified	Uncertain significance (Apr 18, 2023)
20-63696800-G-C			Likely benign (Sep 29, 2023)
20-63696801-C-G		TNFRSF6B-related disorder	Uncertain significance (Nov 08, 2023)
20-63696807-C-T			Likely benign (Aug 24, 2023)
20-63696809-G-A			Likely benign (Jun 13, 2022)
20-63696817-C-T			Uncertain significance (Aug 02, 2023)
20-63696819-C-T			Likely benign (Jan 04, 2024)
20-63696822-C-T			Uncertain significance (Nov 28, 2023)
20-63696823-C-T			Uncertain significance (Nov 02, 2022)
20-63696827-C-G			Likely benign (Jun 03, 2023)
20-63696828-C-T			Likely benign (Jan 20, 2021)
20-63696829-T-C			Uncertain significance (Nov 17, 2023)
20-63696831-CTGCCGG-C			Uncertain significance (Sep 30, 2023)
20-63696832-T-C		TNFRSF6B-related disorder	Uncertain significance (Dec 15, 2022)
20-63696835-C-T			Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF6B	protein_coding	protein_coding	ENST00000369996	3	2017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000387	0.219	123602	0	212	123814	0.000856

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.30	250	199	1.26	0.0000138	1845
Missense in Polyphen		50	51.187	0.9768		540
Synonymous	-4.41	145	91.4	1.59	0.00000650	669
Loss of Function	-0.145	8	7.57	1.06	3.75e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00206	0.00200
Ashkenazi Jewish	0.000410	0.000403
East Asian	0.00106	0.00104
Finnish	0.00144	0.00140
European (Non-Finnish)	0.000852	0.000813
Middle Eastern	0.00106	0.00104
South Asian	0.000526	0.000523
Other	0.000694	0.000662

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Decoy receptor that can neutralize the cytotoxic ligands TNFS14/LIGHT, TNFSF15 and TNFSF6/FASL. Protects against apoptosis. {ECO:0000269|PubMed:21300286}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Apoptosis Modulation and Signaling;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Homology Directed Repair;Immune System;TNFs bind their physiological receptors;Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA);Resolution of D-Loop Structures;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.370
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.258
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Gene ontology

• Biological process: apoptotic process;tumor necrosis factor-mediated signaling pathway;negative regulation of apoptotic process
• Cellular component: extracellular region;extracellular space
• Molecular function: protein binding;signaling receptor activity