TNFRSF13C

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

Basic information

Region (hg38): 22:41922031-41926806

Links

ENSG00000159958 ∙ NCBI:115650 ∙ OMIM:606269 ∙ HGNC:17755 ∙ Uniprot:Q96RJ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• common variable immunodeficiency (Supportive), mode of inheritance: AD
• immunodeficiency, common variable, 4 (Limited), mode of inheritance: Unknown
• immunodeficiency, common variable, 4 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency, common variable 4	AR	Allergy/Immunology/Infectious	Individuals may be susceptible to a number of infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	19666484
Although the condition has only been described in adults, interventions may be indicated in the pediatric period

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNFRSF13C gene.

• Immunodeficiency, common variable, 4 (126 variants)
• not provided (10 variants)
• Inborn genetic diseases (2 variants)
• not specified (1 variants)
• Immunodeficiency, common variable, 2 (1 variants)
• Common Variable Immune Deficiency, Recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF13C 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			2	35	1	38
missense		1	49		1	51
nonsense						0
start loss			1			1
frameshift			1			1
inframe indel			8			8
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding			5	7	6	18
Total	0	1	66	42	8

Variants in TNFRSF13C

This is a list of pathogenic ClinVar variants found in the TNFRSF13C region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41925114-G-A		Immunodeficiency, common variable, 4	Uncertain significance (Jan 12, 2018)
22-41925247-A-G		Immunodeficiency, common variable, 4	Benign (Jun 19, 2021)
22-41925254-C-T		Immunodeficiency, common variable, 4	Uncertain significance (Jan 13, 2018)
22-41925260-C-G		Immunodeficiency, common variable, 4	Uncertain significance (Jan 13, 2018)
22-41925357-C-G		TNFRSF13C-related disorder	Likely benign (May 08, 2019)
22-41925379-AGGGCCGGCC-CCTGCTATT		Immunodeficiency, common variable, 4	Uncertain significance (Dec 11, 2023)
22-41925384-C-G		Immunodeficiency, common variable, 4	Uncertain significance (May 22, 2023)
22-41925384-C-T		Immunodeficiency, common variable, 4	Uncertain significance (Dec 22, 2022)
22-41925385-G-A		Immunodeficiency, common variable, 4	Likely benign (Aug 30, 2022)
22-41925385-G-C		Immunodeficiency, common variable, 4	Likely benign (Sep 01, 2022)
22-41925400-C-T		Immunodeficiency, common variable, 4	Likely benign (May 09, 2022)
22-41925410-G-C		Immunodeficiency, common variable, 4 • not specified	Uncertain significance (Jan 24, 2024)
22-41925411-T-A		Immunodeficiency, common variable, 4	Uncertain significance (Feb 27, 2023)
22-41925414-A-G		Immunodeficiency, common variable, 4	Uncertain significance (Dec 19, 2023)
22-41925415-G-A		Immunodeficiency, common variable, 4	Likely benign (Feb 04, 2020)
22-41925418-C-T		Immunodeficiency, common variable, 4	Likely benign (Jun 15, 2023)
22-41925425-G-A		Immunodeficiency, common variable, 4	Uncertain significance (Jun 22, 2021)
22-41925437-G-A		Immunodeficiency, common variable, 4	Uncertain significance (Aug 08, 2018)
22-41925443-C-A		Immunodeficiency, common variable, 4	Uncertain significance (Aug 31, 2021)
22-41925444-T-C		Immunodeficiency, common variable, 4	Uncertain significance (Jun 21, 2019)
22-41925447-G-A		Immunodeficiency, common variable, 4	Conflicting classifications of pathogenicity (Jan 29, 2024)
22-41925470-T-A		Immunodeficiency, common variable, 4	Uncertain significance (Jun 20, 2022)
22-41925475-C-T		Immunodeficiency, common variable, 4	Likely benign (Dec 10, 2023)
22-41925477-C-T		Immunodeficiency, common variable, 4	Uncertain significance (Dec 26, 2023)
22-41925486-G-A		Immunodeficiency, common variable, 4	Conflicting classifications of pathogenicity (Jan 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF13C	protein_coding	protein_coding	ENST00000291232	3	1778

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.270	0.644	125149	0	1	125150	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.645	65	81.4	0.799	0.00000394	1101
Missense in Polyphen		15	23.16	0.64768		316
Synonymous	-2.13	59	41.5	1.42	0.00000215	459
Loss of Function	1.28	1	3.64	0.275	1.56e-7	47

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)	0.00000884	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: B-cell receptor specific for TNFSF13B/TALL1/BAFF/BLyS. Promotes the survival of mature B-cells and the B-cell response. {ECO:0000269|PubMed:11591325, ECO:0000269|PubMed:12387744}.
• Pathway: Primary immunodeficiency - Homo sapiens (human);HTLV-I infection - 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);TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System (Consensus)

Recessive Scores

• pRec: 0.177

Haploinsufficiency Scores

• pHI: 0.0982
• hipred: N
• hipred_score: 0.353

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.777

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf13c
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: B cell homeostasis;adaptive immune response;positive regulation of germinal center formation;positive regulation of B cell proliferation;T cell costimulation;B cell costimulation;tumor necrosis factor-mediated signaling pathway;positive regulation of T cell proliferation;positive regulation of interferon-gamma biosynthetic process
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane