TNFRSF12A

TNF receptor superfamily member 12A, the group of CD molecules|Tumor necrosis factor receptor superfamily

Basic information

Region (hg38): 16:3018445-3022383

Links

ENSG00000006327 ∙ ∙ OMIM:605914 ∙ HGNC:18152 ∙ Uniprot:Q9NP84 ∙ 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 TNFRSF12A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFRSF12A 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					1	1
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in TNFRSF12A

This is a list of pathogenic ClinVar variants found in the TNFRSF12A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3020405-G-A		not specified	Uncertain significance (Mar 04, 2024)
16-3020419-C-G		not specified	Uncertain significance (Jul 20, 2022)
16-3020455-G-A		not specified	Uncertain significance (Nov 10, 2022)
16-3021269-T-C		not specified	Uncertain significance (Aug 08, 2022)
16-3021277-G-A		not specified	Uncertain significance (Jul 27, 2024)
16-3021317-G-C		not specified	Uncertain significance (Mar 24, 2023)
16-3021566-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-3021627-T-C		not specified	Uncertain significance (Dec 28, 2023)
16-3021633-G-C		not specified	Uncertain significance (Aug 05, 2024)
16-3021653-G-A		not specified	Uncertain significance (Oct 10, 2023)
16-3021820-C-A			Benign (Dec 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFRSF12A	protein_coding	protein_coding	ENST00000326577	4	3939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0180	0.739	106224	0	3	106227	0.0000141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.141	60	57.0	1.05	0.00000253	792
Missense in Polyphen		26	30.485	0.85288		369
Synonymous	-1.40	33	24.2	1.36	0.00000109	290
Loss of Function	0.776	3	4.84	0.619	2.15e-7	62

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)	0.0000312	0.0000312
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for TNFSF12/TWEAK. Weak inducer of apoptosis in some cell types. Promotes angiogenesis and the proliferation of endothelial cells. May modulate cellular adhesion to matrix proteins. {ECO:0000269|PubMed:11728344}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human);TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway;TWEAK;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)

Intolerance Scores

• loftool: 0.275
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.665
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.541

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfrsf12a
• Phenotype: liver/biliary system phenotype; immune system phenotype

Gene ontology

• Biological process: angiogenesis;substrate-dependent cell migration, cell attachment to substrate;tumor necrosis factor-mediated signaling pathway;positive regulation of apoptotic process;regulation of angiogenesis;positive regulation of axon extension;regulation of wound healing;extrinsic apoptotic signaling pathway;positive regulation of extrinsic apoptotic signaling pathway
• Cellular component: ruffle;plasma membrane;cell surface;integral component of membrane
• Molecular function: protein binding