Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	23495
Gene name	TNF receptor superfamily member 13B
Gene symbol	TNFRSF13B
Synonyms (NCBI Gene)	CD267CVIDCVID2IGAD2RYZNTACITNFRSF14B
Chromosome	17
Chromosome location	17p11.2
Summary	The protein encoded by this gene is a lymphocyte-specific member of the tumor necrosis factor (TNF) receptor superfamily. It interacts with calcium-modulator and cyclophilin ligand (CAML). The protein induces activation of the transcription factors NFAT,

Show/Hide all (18)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34557412	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign, pathogenic, likely-pathogenic, risk-factor	Missense variant, coding sequence variant
rs72553875	->T	Pathogenic-likely-pathogenic, pathogenic, uncertain-significance	Frameshift variant, coding sequence variant
rs72553876	T>C	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs72553877	A>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs72553879	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs72553882	G>C,T	Pathogenic	Stop gained, coding sequence variant
rs72553883	G>A,T	Likely-pathogenic, conflicting-interpretations-of-pathogenicity, likely-benign, pathogenic	Missense variant, coding sequence variant
rs72553885	G>A,C,T	Pathogenic, uncertain-significance	Synonymous variant, stop gained, missense variant, coding sequence variant
rs104894649	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign, pathogenic	Missense variant, coding sequence variant
rs104894650	G>A,C,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs121908379	GG>CC,TT	Pathogenic	Coding sequence variant, stop gained, missense variant
rs143027621	A>C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs150101848	C>A,G,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs769165409	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1016142312	C>A,T	Pathogenic	Splice donor variant
rs1265262160	CTTGC>-	Pathogenic	Coding sequence variant, frameshift variant
rs1303637368	->TC	Pathogenic	Coding sequence variant, frameshift variant
rs1555550717	G>-	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (81)

miRTarBase ID	miRNA	Experiments	Reference
MIRT037200	hsa-miR-877-3p	CLASH	23622248
MIRT625335	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT625334	hsa-miR-181a-2-3p	HITS-CLIP	23824327
MIRT625333	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT661879	hsa-miR-6742-3p	HITS-CLIP	23824327
MIRT625332	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT625331	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT625330	hsa-miR-1254	HITS-CLIP	23824327
MIRT625329	hsa-miR-3116	HITS-CLIP	23824327
MIRT625328	hsa-miR-661	HITS-CLIP	23824327
MIRT625327	hsa-miR-4284	HITS-CLIP	23824327
MIRT625326	hsa-miR-24-3p	HITS-CLIP	23824327
MIRT625325	hsa-miR-6509-3p	HITS-CLIP	23824327
MIRT625324	hsa-miR-8057	HITS-CLIP	23824327
MIRT625335	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT625334	hsa-miR-181a-2-3p	HITS-CLIP	23824327
MIRT625333	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT625332	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT625331	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT625330	hsa-miR-1254	HITS-CLIP	23824327
MIRT625329	hsa-miR-3116	HITS-CLIP	23824327
MIRT625328	hsa-miR-661	HITS-CLIP	23824327
MIRT625327	hsa-miR-4284	HITS-CLIP	23824327
MIRT625326	hsa-miR-24-3p	HITS-CLIP	23824327
MIRT625325	hsa-miR-6509-3p	HITS-CLIP	23824327
MIRT625324	hsa-miR-8057	HITS-CLIP	23824327
MIRT625335	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT625334	hsa-miR-181a-2-3p	HITS-CLIP	23824327
MIRT625333	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT661879	hsa-miR-6742-3p	HITS-CLIP	23824327
MIRT625332	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT625331	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT625330	hsa-miR-1254	HITS-CLIP	23824327
MIRT625329	hsa-miR-3116	HITS-CLIP	23824327
MIRT625328	hsa-miR-661	HITS-CLIP	23824327
MIRT625327	hsa-miR-4284	HITS-CLIP	23824327
MIRT625326	hsa-miR-24-3p	HITS-CLIP	23824327
MIRT625325	hsa-miR-6509-3p	HITS-CLIP	23824327
MIRT625324	hsa-miR-8057	HITS-CLIP	23824327
MIRT625335	hsa-miR-6890-3p	HITS-CLIP	23824327
MIRT625334	hsa-miR-181a-2-3p	HITS-CLIP	23824327
MIRT625333	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT625332	hsa-miR-1304-3p	HITS-CLIP	23824327
MIRT625331	hsa-miR-4772-3p	HITS-CLIP	23824327
MIRT625330	hsa-miR-1254	HITS-CLIP	23824327
MIRT625329	hsa-miR-3116	HITS-CLIP	23824327
MIRT625328	hsa-miR-661	HITS-CLIP	23824327
MIRT625327	hsa-miR-4284	HITS-CLIP	23824327
MIRT625326	hsa-miR-24-3p	HITS-CLIP	23824327
MIRT625325	hsa-miR-6509-3p	HITS-CLIP	23824327
MIRT625324	hsa-miR-8057	HITS-CLIP	23824327
MIRT1442960	hsa-miR-125a-5p	CLIP-seq
MIRT1442961	hsa-miR-125b	CLIP-seq
MIRT1442962	hsa-miR-1470	CLIP-seq
MIRT1442963	hsa-miR-3183	CLIP-seq
MIRT1442964	hsa-miR-3675-3p	CLIP-seq
MIRT1442965	hsa-miR-4287	CLIP-seq
MIRT1442966	hsa-miR-4319	CLIP-seq
MIRT1442967	hsa-miR-4446-5p	CLIP-seq
MIRT1442968	hsa-miR-4469	CLIP-seq
MIRT1442969	hsa-miR-4667-3p	CLIP-seq
MIRT1442970	hsa-miR-4685-3p	CLIP-seq
MIRT1442971	hsa-miR-4723-3p	CLIP-seq
MIRT1442972	hsa-miR-4732-3p	CLIP-seq
MIRT1442973	hsa-miR-4755-5p	CLIP-seq
MIRT1442974	hsa-miR-642a	CLIP-seq
MIRT1442975	hsa-miR-670	CLIP-seq
MIRT2132561	hsa-miR-3120-5p	CLIP-seq
MIRT1442963	hsa-miR-3183	CLIP-seq
MIRT1442968	hsa-miR-4469	CLIP-seq
MIRT1442971	hsa-miR-4723-3p	CLIP-seq
MIRT2132562	hsa-miR-593	CLIP-seq
MIRT1442974	hsa-miR-642a	CLIP-seq
MIRT2132561	hsa-miR-3120-5p	CLIP-seq
MIRT1442963	hsa-miR-3183	CLIP-seq
MIRT1442965	hsa-miR-4287	CLIP-seq
MIRT1442968	hsa-miR-4469	CLIP-seq
MIRT1442970	hsa-miR-4685-3p	CLIP-seq
MIRT1442971	hsa-miR-4723-3p	CLIP-seq
MIRT2132562	hsa-miR-593	CLIP-seq
MIRT1442974	hsa-miR-642a	CLIP-seq

Show/Hide all (11)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001782	Process	B cell homeostasis	IBA
GO:0002244	Process	Hematopoietic progenitor cell differentiation	IBA
GO:0002250	Process	Adaptive immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	10801128, 10880535, 10956646, 20676093, 25416956, 25910212, 32296183
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	9311921
GO:0007166	Process	Cell surface receptor signaling pathway	TAS	9311921
GO:0016020	Component	Membrane	IEA
GO:0030889	Process	Negative regulation of B cell proliferation	IBA
GO:0038023	Function	Signaling receptor activity	TAS	9311921

MIM	HGNC	e!Ensembl
604907	18153	ENSG00000240505

O14836

Protein name

Tumor necrosis factor receptor superfamily member 13B (Transmembrane activator and CAML interactor) (CD antigen CD267)

Protein function

Receptor for TNFSF13/APRIL and TNFSF13B/TALL1/BAFF/BLYS that binds both ligands with similar high affinity. Mediates calcineurin-dependent activation of NF-AT, as well as activation of NF-kappa-B and AP-1. Involved in the stimulation of B- and T

PDB

1XU1 , 1XUT

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF09305	TACI-CRD2	32 → 68	TACI, cysteine-rich domain	Domain
PF09305	TACI-CRD2	69 → 107	TACI, cysteine-rich domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in spleen, thymus, small intestine and peripheral blood leukocytes. Expressed in resting B-cells and activated T-cells, but not in resting T-cells.

Sequence

MSGLGRSRRGGRSRVDQEERFPQGLWTGVAMRSCPEEQYWDPLLGTCMSCKTICNHQSQR
TCAAFCRSLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLRSPVNLPPELRR
QRSGEVENNSDNSGRYQGLEHRGSEASPALPGLKLSADQVALVYSTLGLCLCAVLCCFLV
AVACFLKKRGDPCSCQPRSRPRQSPAKSSQDHAMEAGSPVSTSPEPVETCSFCFPECRAP
TQESAVTPGTPDPTCAGRWGCHTRTTVLQPCPHIPDSGLGIVCVPAQEGGPGA

Sequence length

293

Interactions

View interactions

	KEGG		Reactome
	Cytokine-cytokine receptor interaction Intestinal immune network for IgA production Primary immunodeficiency		TNFs bind their physiological receptors

396

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Common variable immunodeficiency	Likely pathogenic; Pathogenic	rs72553883, rs760885614	RCV001199863 RCV003493823
Immunodeficiency, common variable, 1	Pathogenic	rs104894650	RCV002283472
Immunodeficiency, common variable, 2	Pathogenic; Likely pathogenic	rs1286642936, rs756955033, rs1383649750, rs2087501902, rs72553878, rs1016142312, rs1286673507, rs760885614, rs72553882, rs774955611, rs72553883, rs121908379, rs104894650, rs1406728306, rs1179744489 View all (7 more)	RCV001384166 RCV001809180 RCV001945527 RCV001935071 RCV001946976 RCV001958606 RCV001886081 RCV002002029 RCV000185537 RCV002765802 RCV000005625 RCV000005630 RCV000005631 RCV000702330 RCV003614269 RCV003614277 RCV000648133 RCV000813899 RCV000814655 RCV000801536 RCV000801740 RCV001043041 RCV001057949 RCV001212531 RCV001267804
Immunoglobulin A deficiency 2	Likely pathogenic; Pathogenic	rs1016142312, rs72553882, rs72553883, rs144718007	RCV002492126 RCV000185538 RCV000005626 RCV001254048
See cases	Likely pathogenic; Pathogenic	rs72553883	RCV002251881
TNFRSF13B-related disorder	Pathogenic; Likely pathogenic	rs72553878, rs1434385525, rs2508206711, rs1265262160	RCV003941225 RCV003404696 RCV003391570 RCV003908104

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Common Variable Immune Deficiency, Dominant	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	rs104894649, rs74811083, rs11078355, rs35062843, rs140781824, rs55916807, rs72553875, rs886052653, rs148297590, rs546986339, rs34562254, rs56059714, rs56153623, rs886052652, rs752825527 View all (5 more)	RCV000397011 RCV000355524 RCV000347652 RCV000359099 RCV000298350 RCV000266832 RCV000380683 RCV000323777 RCV000384290 RCV000344312 RCV000312789 RCV000292496 RCV000287110 RCV000382635 RCV000290410 RCV000406669 RCV000322279 RCV000379188 RCV000269924 RCV000352164 RCV000327385
Hyper-IgM syndrome type 2	Conflicting classifications of pathogenicity	rs72553875	RCV003995848
IgAD1	Conflicting classifications of pathogenicity	rs72553877	RCV002508946
Immune deficiency, familial variable	Conflicting classifications of pathogenicity; risk factor	rs34557412	RCV003448244
Malignant lymphoma, large B-cell, diffuse	Benign	rs3818716	RCV005920287
Sarcoma	Uncertain significance	rs374249932	RCV005912529
Severe SARS-CoV-2 infection, susceptibility to	Conflicting classifications of pathogenicity; risk factor	rs34557412	RCV001374734

Show/Hide Text Mining Associations (67)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Agammaglobulinemia	Associate	18981294, 22697072, 23225259
Anemia Hemolytic Autoimmune	Associate	33838017
Anti N Methyl D Aspartate Receptor Encephalitis	Stimulate	38063052
Arthritis Rheumatoid	Associate	33483588
Autoimmune Diseases	Associate	17556024, 22697072, 23956760, 24051372, 34441032, 34686572
Autoimmune Diseases of the Nervous System	Associate	18981294, 24051380
Carcinoma Ovarian Epithelial	Associate	24740199
Chronic Pain	Associate	28221285
Combined Cellular And Humoral Immune Defects With Granulomas	Associate	21514638
Common Variable Immunodeficiency	Associate	17556024, 17983875, 18254984, 18981294, 19210517, 19775471, 20652909, 21514638, 21815909, 21905497, 22697072, 23237420, 23956760, 24051372, 24051380 View all (11 more)
Diabetes Mellitus	Associate	34822764
Diabetes Mellitus Type 1	Associate	28951327
Dysgammaglobulinemia	Associate	19210517, 19903677
Genetic Diseases Inborn	Associate	34441032
Glomerulonephritis IGA	Associate	31088610
Granulomatous Disease Chronic	Inhibit	23773925
Graves Disease	Inhibit	33926416
Hematologic Neoplasms	Associate	23955597
Hereditary leiomyomatosis and renal cell cancer	Associate	16960154
HIV Infections	Associate	26707220
Hodgkin Disease	Associate	16960154, 19291294
Humoral Hypercalcemia Of Malignancy	Associate	19775471
Hyper IgM Immunodeficiency Syndrome	Associate	20652909
Hypertrophy	Associate	23956760
Idiopathic Pulmonary Fibrosis	Associate	34073225
IgG Deficiency	Associate	19903677, 23956760
Immune Dysregulation Polyendocrinopathy Enteropathy X Linked Syndrome	Associate	33864888
Immune System Diseases	Associate	17983875, 28834165, 33710309, 33726816, 33838017, 38547930
Immunologic Deficiency Syndromes	Associate	17983875, 18981294, 19210517, 20652909, 21419480, 23237420, 25569260, 26100089, 27016798, 27123465, 34686572, 34975878
Inflammation	Associate	17556024
Kotzot Richter syndrome	Associate	39596634
Leukemia	Associate	14504101, 21687682
Leukemia Lymphocytic Chronic B Cell	Associate	22593611, 25950010
Lupus Erythematosus Discoid	Associate	24315762
Lupus Erythematosus Systemic	Associate	35053379, 37675114
Lymphangiectasia pulmonary congenital	Associate	32991402
Lymphoma	Associate	19291294, 38547930
Lymphoma B Cell	Associate	19291294
Lymphoma B Cell Marginal Zone	Associate	22110251
Lymphoma Large B Cell Diffuse	Associate	17190854
Lymphoma Non Hodgkin	Associate	14978135, 28028945
Metabolic Syndrome	Associate	23418049
Monoclonal Gammopathy of Undetermined Significance	Associate	24449210
Multiple Myeloma	Associate	14512299, 15827134, 16825497, 17550853, 17692805, 23955597, 24449210, 30135465, 33751038, 37980341, 38035078
Multiple Myeloma	Stimulate	19291294
Neoplasm Metastasis	Associate	34159752
Neoplasms	Associate	27422711, 32840410
Neoplasms	Inhibit	34159752
Neoplastic Syndromes Hereditary	Associate	28834165
Neutropenia	Associate	33838017
Paraproteinemias	Associate	25950010
pediatric multisystem inflammatory disease COVID 19 related	Associate	37588055
Pleural Effusion Malignant	Associate	18064389
Primary Immunodeficiency Diseases	Associate	18981294, 27123465, 31572362, 34441032, 34786962
Pseudolymphoma	Associate	17983875
Purpura Thrombocytopenic Idiopathic	Associate	17983875, 26749059, 28834165, 34786962
Sarcoidosis	Associate	23956760
Sjogren's Syndrome	Associate	32201227
Skin Manifestations	Associate	24051380
Smith Magenis Syndrome	Associate	21514638, 26100089
Splenomegaly	Associate	17556024, 17983875, 34441032
Squamous Cell Carcinoma of Head and Neck	Associate	33134377
Thrombocytopenia	Associate	32991402
Thyroid Neoplasms	Stimulate	19291294
Uveal melanoma	Associate	33665679
Waldenstrom Macroglobulinemia	Associate	19291294
Young Syndrome	Associate	19775471

TNFRSF13B (TNF receptor superfamily member 13B)