TNFSF13

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

Basic information

Region (hg38): 17:7558292-7561608

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.

not_specified (11 variants)
not_provided (2 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. These statistics are base on transcript: NM_000003808.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	11	1	0

Loading clinvar variants...

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

pHI
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