TNFSF13B

TNF superfamily member 13b, the group of CD molecules|Tumor necrosis factor superfamily

Basic information

Region (hg38): 13:108251240-108308484

Previous symbols: [ "TNFSF20" ]

Links

ENSG00000102524 ∙ NCBI:10673 ∙ OMIM:603969 ∙ HGNC:11929 ∙ Uniprot:Q9Y275 ∙ 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 TNFSF13B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF13B 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	2
missense			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	4	1	4

Variants in TNFSF13B

This is a list of pathogenic ClinVar variants found in the TNFSF13B region.

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

Position	Type	Phenotype	Significance	ClinVar
13-108270038-T-A		not specified	Uncertain significance (Dec 08, 2021)
13-108270047-C-G		not specified	Uncertain significance (Feb 28, 2023)
13-108270079-A-G		not specified	Uncertain significance (Apr 09, 2024)
13-108270100-G-A		not specified	Uncertain significance (Apr 25, 2022)
13-108270208-G-A			Benign (May 24, 2018)
13-108286850-A-G		not specified	Uncertain significance (Dec 02, 2022)
13-108303116-C-G			Benign (Jun 19, 2021)
13-108303266-T-C			Likely benign (Apr 19, 2018)
13-108303585-T-C			Benign (Jul 06, 2018)
13-108303821-T-A			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF13B	protein_coding	protein_coding	ENST00000375887	6	57245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0181	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	75	149	0.505	0.00000713	1822
Missense in Polyphen		6	39.645	0.15134		523
Synonymous	0.385	56	59.8	0.937	0.00000303	584
Loss of Function	3.24	0	12.2	0.00	5.81e-7	159

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that binds to TNFRSF13B/TACI and TNFRSF17/BCMA. TNFSF13/APRIL binds to the same 2 receptors. Together, they form a 2 ligands -2 receptors pathway involved in the stimulation of B- and T-cell function and the regulation of humoral immunity. A third B-cell specific BAFF-receptor (BAFFR/BR3) promotes the survival of mature B-cells and the B-cell response. {ECO:0000269|PubMed:10973284}.; FUNCTION: Isoform 3: Acts as a transcription factor for its own parent gene, in association with NF-kappa-B p50 subunit, at least in autoimmune and proliferative B-cell diseases. The presence of Delta4BAFF is essential for soluble BAFF release by IFNG/IFN- gamma-stimulated monocytes and for B-cell survival. It can directly or indirectly regulate the differential expression of a large number of genes involved in the innate immune response and the regulation of apoptosis. {ECO:0000269|PubMed:10973284}.
• Pathway: Rheumatoid arthritis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Spinal Cord Injury;yaci and bcma stimulation of b cell immune responses;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: 0.277

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.0410
• hipred: N
• hipred_score: 0.380
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.433

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf13b
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: B cell homeostasis;positive regulation of germinal center formation;immune response;signal transduction;cell population proliferation;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of B cell proliferation;T cell costimulation;B cell costimulation;tumor necrosis factor-mediated signaling pathway;positive regulation of T cell proliferation;immunoglobulin secretion
• Cellular component: extracellular region;extracellular space;cytoplasm;plasma membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;protein binding