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.

• not_provided (416 variants)
• not_specified (81 variants)
• TNFRSF6B-related_disorder (20 variants)
• Dyskeratosis_congenita,_autosomal_recessive_5 (16 variants)
• Long_QT_syndrome (1 variants)

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. These statistics are base on transcript: NM_000003823.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	107	6	115
missense			243	14	1	258
nonsense			8			8
start loss			1			1
frameshift			8			8
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	263	121	7

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