TNFRSF17

TNF receptor superfamily member 17, the group of CD molecules|Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 16:11965210-11968068

Previous symbols: [ "BCMA" ]

Links

ENSG00000048462

∙ NCBI:608 ∙ OMIM:109545 ∙ HGNC:11913 ∙ Uniprot:Q02223 ∙ 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 TNFRSF17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF17 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						0
missense			11 clinvar		1 clinvar	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in TNFRSF17

This is a list of pathogenic ClinVar variants found in the TNFRSF17 region.

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

Position	Phenotype	Significance	ClinVar
16-11965340-G-C		Uncertain significance (Mar 30, 2021)	992503
16-11965388-A-C	not specified	Uncertain significance (Jan 23, 2024)	3180252
16-11965389-T-C	not specified	Uncertain significance (Oct 03, 2024)	3459144
16-11965407-G-A	not specified	Uncertain significance (Sep 06, 2022)	2310235
16-11965427-C-A	not specified	Uncertain significance (Dec 13, 2022)	2224965
16-11966206-T-G	not specified	Uncertain significance (Mar 20, 2023)	2513227
16-11966287-T-G		Uncertain significance (Mar 30, 2021)	626032
16-11966336-A-G	not specified	Uncertain significance (Nov 06, 2023)	3180248
16-11967623-G-A	not specified	Uncertain significance (Oct 06, 2024)	3459146
16-11967672-C-T	not specified	Uncertain significance (Sep 13, 2023)	2602106
16-11967755-A-G	not specified	Uncertain significance (Nov 28, 2023)	3180249
16-11967785-T-C	not specified	Uncertain significance (Nov 12, 2024)	3459147
16-11967786-G-T	not specified	Uncertain significance (Sep 23, 2023)	3180251
16-11967816-C-T	Desmoplastic small round cell tumor	other (May 01, 2016)	438792
16-11967820-G-C		Benign (Feb 26, 2018)	779009
16-11967839-G-T	not specified	Uncertain significance (Oct 26, 2021)	2374590

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF17	protein_coding	protein_coding	ENST00000053243	3	2962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000137	0.124	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	143	107	1.34	0.00000591	1206
Missense in Polyphen		34	31.693	1.0728		362
Synonymous	-1.12	51	41.8	1.22	0.00000261	353
Loss of Function	-0.626	8	6.30	1.27	3.28e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000179
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000979	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000979	0.000979
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Receptor for TNFSF13B/BLyS/BAFF and TNFSF13/APRIL. Promotes B-cell survival and plays a role in the regulation of humoral immunity. Activates NF-kappa-B and JNK. {ECO:0000269|PubMed:10801128, ECO:0000269|PubMed:10903733, ECO:0000269|PubMed:10973284}.;
Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);yaci and bcma stimulation of b cell immune responses;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors (Consensus)

Recessive Scores

pRec: 0.284

Intolerance Scores

loftool: 0.689
rvis_EVS: 0.22
rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

pHI: 0.106
hipred: N
hipred_score: 0.213
ghis: 0.525

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.833

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tnfrsf17
Phenotype: normal phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: adaptive immune response;lymphocyte homeostasis;signal transduction;multicellular organism development;cell population proliferation;tumor necrosis factor-mediated signaling pathway
Cellular component: plasma membrane;endomembrane system;integral component of membrane
Molecular function: signaling receptor activity