TNFSF12-TNFSF13

TNFSF12-TNFSF13 readthrough

Basic information

Region (hg38): 17:7549099-7561601

Links

ENSG00000248871

∙ NCBI:407977 ∙ ∙ HGNC:33537 ∙ ∙ ∙ 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 TNFSF12-TNFSF13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFSF12-TNFSF13 gene is commonly pathogenic or not. These statistics are base on transcript: . 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				41 clinvar	4 clinvar	45
missense			75 clinvar		1 clinvar	76
nonsense			4 clinvar			4
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	81	41	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFSF12-TNFSF13	protein_coding	protein_coding	ENST00000293826	11	12503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.770	0.230	124514	0	15	124529	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.983	137	173	0.790	0.0000101	2068
Missense in Polyphen		31	55.131	0.56229		612
Synonymous	-0.330	74	70.5	1.05	0.00000413	699
Loss of Function	3.60	4	22.4	0.178	0.00000137	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000461	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000607	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000269	0.0000269
Middle Eastern	0.0000607	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to FN14 and possibly also to TNRFSF12/APO3. Weak inducer of apoptosis in some cell types. Mediates NF-kappa-B activation. Promotes angiogenesis and the proliferation of endothelial cells. Also involved in induction of inflammatory cytokines. Promotes IL8 secretion. {ECO:0000269|PubMed:10085077, ECO:0000269|PubMed:23667509}.;

Intolerance Scores

loftool
rvis_EVS: -0.14
rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

pHI
hipred: Y
hipred_score: 0.519
ghis: 0.394

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tnfsfm13
Phenotype

Gene ontology

Biological process: immune response;regulation of signaling receptor activity
Cellular component: extracellular space;membrane
Molecular function: cytokine activity;tumor necrosis factor receptor binding