TNFSF13

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

Basic information

Region (hg38): 17:7558291-7561608

Links

ENSG00000161955 ∙ NCBI:8741 ∙ OMIM:604472 ∙ HGNC:11928 ∙ Uniprot:O75888 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• common variable immunodeficiency (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNFSF13 gene.

• Inborn genetic diseases (7 variants)
• not provided (5 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF13 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			7		2	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	8	0	3

Variants in TNFSF13

This is a list of pathogenic ClinVar variants found in the TNFSF13 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7559064-C-G		not specified	Uncertain significance (Jun 11, 2021)
17-7559077-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-7559152-C-T		not specified	Uncertain significance (Jul 17, 2023)
17-7559180-T-C			Uncertain significance (Mar 30, 2021)
17-7559229-C-T		not specified	Uncertain significance (May 01, 2023)
17-7559230-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-7559238-G-A		not specified	Benign (Jan 24, 2024)
17-7559617-T-C			Benign (Dec 31, 2019)
17-7559652-A-G		not specified	Benign (Jan 24, 2024)
17-7559695-A-C		not specified	Uncertain significance (Dec 03, 2021)
17-7560057-G-T		not specified	Uncertain significance (Aug 10, 2021)
17-7561096-C-T		not specified	Benign (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF13	protein_coding	protein_coding	ENST00000338784	6	3317

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.817	0.183	125729	0	12	125741	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.526	121	138	0.874	0.00000722	1596
Missense in Polyphen		29	51.536	0.56272		603
Synonymous	-0.200	59	57.1	1.03	0.00000311	530
Loss of Function	3.02	2	14.4	0.139	7.97e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000490	0.000489
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cytokine that binds to TNFRSF13B/TACI and to TNFRSF17/BCMA. Plays a role in the regulation of tumor cell growth. May be involved in monocyte/macrophage-mediated immunological processes. {ECO:0000269|PubMed:10973284}.
• Pathway: Rheumatoid arthritis - 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;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Metabolism of RNA;Immune System;TNFs bind their physiological receptors;HuR (ELAVL1) binds and stabilizes mRNA;Regulation of mRNA stability by proteins that bind AU-rich elements (Consensus)

Recessive Scores

• pRec: 0.504

Intolerance Scores

• loftool: 0.200
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.350
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfsf13
• Phenotype: hematopoietic system phenotype; normal phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: immune response;signal transduction;positive regulation of cell population proliferation;regulation of signaling receptor activity;tumor necrosis factor-mediated signaling pathway;regulation of mRNA stability;positive regulation of isotype switching to IgA isotypes
• Cellular component: extracellular region;nucleoplasm;cytoplasm;cytosol;membrane;extracellular exosome
• Molecular function: signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding