TNFSF13 TNF superfamily member 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TNFSF13provided by HGNC
Official Full Name: TNF superfamily member 13provided by HGNC
Primary source: HGNC:HGNC:11928
See related: Ensembl:ENSG00000161955 MIM:604472; AllianceGenome:HGNC:11928
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: APRIL; CD256; TALL2; ZTNF2; TALL-2; TNLG7B; TRDL-1; UNQ383/PRO715
Summary: The protein encoded by this gene is a member of the tumor necrosis factor (TNF) ligand family. This protein is a ligand for TNFRSF17/BCMA, a member of the TNF receptor family. This protein and its receptor are both found to be important for B cell development. In vitro experiments suggested that this protein may be able to induce apoptosis through its interaction with other TNF receptor family proteins such as TNFRSF6/FAS and TNFRSF14/HVEM. Alternative splicing results in multiple transcript variants. Some transcripts that skip the last exon of the upstream gene (TNFSF12) and continue into the second exon of this gene have been identified; such read-through transcripts are contained in GeneID 407977, TNFSF12-TNFSF13. [provided by RefSeq, Oct 2010]
Expression: Ubiquitous expression in lung (RPKM 37.5), gall bladder (RPKM 25.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (7558282..7561601)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (7462543..7465862)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (7461599..7464918)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

APRIL and BAFF play a key role in differentiating vitreoretinal lymphoma from uveitis.
Title: APRIL and BAFF play a key role in differentiating vitreoretinal lymphoma from uveitis.
Mononuclear cells from patients with rhupus are influenced by TNF in their production of gp130/sIL-6Rb and APRIL.
Title: Mononuclear cells from patients with rhupus are influenced by TNF in their production of gp130/sIL-6Rb and APRIL.
Spatial heterogeneity for APRIL production by eosinophils in the small intestine.
Title: Spatial heterogeneity for APRIL production by eosinophils in the small intestine.
B-cell activating factor and A proliferation-inducing ligand in relation to intima-media thickness as biomarkers of premature atherosclerosis in systemic lupus erythematosus patients.
Title: B-cell activating factor and A proliferation-inducing ligand in relation to intima-media thickness as biomarkers of premature atherosclerosis in systemic lupus erythematosus patients.
APRIL Drives a Coordinated but Diverse Response as a Foundation for Plasma Cell Longevity.
Title: APRIL Drives a Coordinated but Diverse Response as a Foundation for Plasma Cell Longevity.
Protein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus.
Title: Protein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus.
BRAK and APRIL as novel biomarkers for ovarian tumors.
Title: BRAK and APRIL as novel biomarkers for ovarian tumors.
The relationship between serum A proliferation-inducing ligand and B-cell activating factor levels with disease activity and organ involvement in systemic lupus erythematosus.
Title: The relationship between serum A proliferation-inducing ligand and B-cell activating factor levels with disease activity and organ involvement in systemic lupus erythematosus.
The number 13 of the family: a proliferation inducing ligand.
Title: The number 13 of the family: a proliferation inducing ligand.
Keeping up with the stress of antibody production: BAFF and APRIL maintain memory plasma cells.
Title: Keeping up with the stress of antibody production: BAFF and APRIL maintain memory plasma cells.

Submit: New GeneRIF Correction See all GeneRIFs (187)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Association of common variants in TNFRSF13B, TNFSF13, and ANXA3 with serum levels of non-albumin protein and immunoglobulin isotypes in Japanese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies TNFSF13 as a susceptibility gene for IgA in a South Chinese population in smokers. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide scan identifies variant in TNFSF13 associated with serum IgM in a healthy Chinese male population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

TNFSF12_268.2 (e-PCR)
- UniSTS:277833

RH98958 (e-PCR)
- UniSTS:85338

RH16009 (e-PCR)
- UniSTS:33639

D1S3688 (e-PCR)
- UniSTS:474266

SHGC-56910 (e-PCR)
- UniSTS:7380

Readthrough TNFSF12-TNFSF13

Readthrough gene: TNFSF12-TNFSF13, Included gene: TNFSF12

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytokine activity	IEA Inferred from Electronic Annotation more info
enables receptor ligand activity	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	TAS Traceable Author Statement more info	PubMed
enables tumor necrosis factor receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of isotype switching to IgA isotypes	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of isotype switching to IgA isotypes	IDA Inferred from Direct Assay more info	PubMed
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tumor necrosis factor ligand superfamily member 13

Names: TNF- and APOL-related leukocyte expressed ligand 2; a proliferation-inducing ligand; tumor necrosis factor (ligand) superfamily, member 13; tumor necrosis factor ligand 7B; tumor necrosis factor superfamily member 13; tumor necrosis factor-like protein ZTNF2; tumor necrosis factor-related death ligand-1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029949.2 RefSeqGene

Range

5470..8321

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001198622.2 → NP_001185551.1 tumor necrosis factor ligand superfamily member 13 isoform delta

See identical proteins and their annotated locations for NP_001185551.1

Status: REVIEWED

Description

Transcript Variant: This variant (delta) lacks an alternate in-frame segment in the 5' coding region, compared to variant alpha, resulting in an isoform (delta) that is shorter than isoform alpha. It is not known whether this isoform (delta) is proteolytically processed in the same manner as isoforms alpha and beta.

Source sequence(s)

AK225556, BI764562, DQ149579

Consensus CDS

CCDS73957.1

UniProtKB/TrEMBL

B3KR02, Q2QBA2

Related

ENSP00000369908.5, ENST00000380535.8

Conserved Domains (1) summary

cd00184
Location:90 → 221

TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
NM_001198623.2 → NP_001185552.1 tumor necrosis factor ligand superfamily member 13 isoform zeta

See identical proteins and their annotated locations for NP_001185552.1

Status: REVIEWED

Description

Transcript Variant: This variant (zeta) lacks an alternate in-frame segment in the 5' coding region, compared to variant alpha, resulting in an isoform (zeta) that is shorter than isoform alpha. It is not known whether this isoform (zeta) is proteolytically processed in the same manner as isoforms alpha and beta.

Source sequence(s)

AK225556, AK301221, BI764562

Consensus CDS

CCDS56018.1

UniProtKB/TrEMBL

B3KR02

Related

ENSP00000486052.1, ENST00000625791.2

Conserved Domains (1) summary

cd00184
Location:89 → 220

TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
NM_001198624.2 → NP_001185553.1 tumor necrosis factor ligand superfamily member 13 isoform eta

Status: REVIEWED

Description

Transcript Variant: This variant (eta) differs in the 5' UTR, uses a downstream start codon, and lacks an alternate in-frame segment in the 5' coding region, compared to variant alpha, resulting in an isoform (eta) that is shorter than isoform alpha. It is not known whether this isoform (eta) is proteolytically processed in the same manner as isoforms alpha and beta.

Source sequence(s)

AC016876, AK225556, BF793371, BI764562

Consensus CDS

CCDS56019.1

UniProtKB/TrEMBL

B3KR02

Related

ENSP00000379792.1, ENST00000396542.5

Conserved Domains (1) summary

cd00184
Location:72 → 203

TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
NM_003808.4 → NP_003799.1 tumor necrosis factor ligand superfamily member 13 isoform alpha precursor

See identical proteins and their annotated locations for NP_003799.1

Status: REVIEWED

Description

Transcript Variant: This variant (alpha) represents the longest transcript and encodes the longest isoform (alpha).

Source sequence(s)

AF046888, AI828515, AK225556, BI764562

Consensus CDS

CCDS11111.1

UniProtKB/Swiss-Prot

A8MYD5, B4DVT2, O75888, Q541E1, Q5U0G8, Q96HV6, Q9P1M8, Q9P1M9

UniProtKB/TrEMBL

Q6FGN4

Related

ENSP00000343505.4, ENST00000338784.9

Conserved Domains (1) summary

cd00184
Location:117 → 248

TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
NM_172087.3 → NP_742084.1 tumor necrosis factor ligand superfamily member 13 isoform beta precursor

See identical proteins and their annotated locations for NP_742084.1

Status: REVIEWED

Description

Transcript Variant: This variant (beta) lacks an alternate in-frame exon in the central coding region, compared to variant alpha, resulting in an isoform (beta) that is shorter than isoform alpha.

Source sequence(s)

AF114012, AI828515, AK090698

Consensus CDS

CCDS11112.1

UniProtKB/TrEMBL

B3KR02

Related

ENSP00000314455.6, ENST00000349228.8

Conserved Domains (1) summary

cd00184
Location:115 → 232

TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
NM_172088.4 → NP_742085.1 tumor necrosis factor ligand superfamily member 13 isoform gamma

See identical proteins and their annotated locations for NP_742085.1

Status: REVIEWED

Description

Transcript Variant: This variant (gamma) lacks an alternate segment in the 3' coding region and 3' UTR, compared to variant alpha, resulting in an isoform (gamma) that has a distinct and shorter C-terminus, compared to isoform alpha. It is not known whether this isoform (gamma) is proteolytically processed in the same manner as isoforms alpha and beta.

Source sequence(s)

AC016876

Consensus CDS

CCDS42256.1

UniProtKB/TrEMBL

A0A0U5EM56

Related

ENSP00000379794.4, ENST00000396545.4

Conserved Domains (1) summary

cd00184
Location:117 → 247

TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

RNA

NR_073490.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (episilon) lacks two internal exons in the 5' region, compared to variant alpha. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant alpha, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI828515, AK090698, EF211088