TNFAIP8L3

TNF alpha induced protein 8 like 3

Basic information

Region (hg38): 15:51056597-51105276

Links

ENSG00000183578 ∙ NCBI:388121 ∙ OMIM:616438 ∙ HGNC:20620 ∙ Uniprot:Q5GJ75 ∙ 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 TNFAIP8L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFAIP8L3 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	21	2	1

Variants in TNFAIP8L3

This is a list of pathogenic ClinVar variants found in the TNFAIP8L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-51057893-C-G		not specified	Uncertain significance (Jan 19, 2022)
15-51057918-T-C		not specified	Uncertain significance (Oct 03, 2022)
15-51057951-C-G		not specified	Uncertain significance (Dec 14, 2023)
15-51057954-T-C		not specified	Uncertain significance (Feb 16, 2023)
15-51057969-G-C		not specified	Uncertain significance (Dec 28, 2022)
15-51058015-T-C		not specified	Uncertain significance (Nov 17, 2022)
15-51058021-C-T		not specified	Uncertain significance (Apr 04, 2024)
15-51058035-G-A		not specified	Uncertain significance (May 05, 2023)
15-51058044-C-T		not specified	Uncertain significance (Jun 24, 2022)
15-51058128-T-C		not specified	Uncertain significance (Dec 19, 2023)
15-51058147-T-G		not specified	Uncertain significance (Jan 27, 2022)
15-51058178-C-G		not specified	Uncertain significance (Jun 07, 2023)
15-51058204-T-C		not specified	Uncertain significance (Aug 17, 2022)
15-51058357-T-C		not specified	Uncertain significance (Dec 04, 2021)
15-51094562-C-T		not specified	Uncertain significance (May 09, 2024)
15-51094649-C-T		not specified	Uncertain significance (Jan 23, 2023)
15-51094681-G-C		not specified	Uncertain significance (May 11, 2022)
15-51094685-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-51094695-CCGGGCGGCG-C			Benign (Dec 31, 2019)
15-51105005-C-G			Likely benign (Apr 10, 2018)
15-51105034-G-C		not specified	Uncertain significance (Jan 31, 2022)
15-51105052-G-A		not specified	Uncertain significance (Feb 28, 2024)
15-51105097-T-C		not specified	Likely benign (Dec 27, 2023)
15-51105143-C-A		not specified	Uncertain significance (Jan 30, 2024)
15-51105143-C-G		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFAIP8L3	protein_coding	protein_coding	ENST00000327536	3	48679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000187	0.278	125721	0	9	125730	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.584	135	155	0.868	0.00000871	1912
Missense in Polyphen		56	69.107	0.81034		804
Synonymous	0.298	63	66.1	0.953	0.00000405	572
Loss of Function	-0.0969	7	6.73	1.04	2.84e-7	107

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)	0.0000716	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a lipid transfer protein. Preferentially captures and shuttles two lipid second messengers, i.e., phosphatidylinositol 4,5- bisphosphate and phosphatidylinositol 3,4,5-trisphosphate and increases their levels in the plasma membrane. Additionally, may also function as a lipid-presenting protein to enhance the activity of the PI3K-AKT and MEK-ERK pathways. May act as a regulator of tumorigenesis through its activation of phospholipid signaling. {ECO:0000250|UniProtKB:Q3TBL6}.
• Pathway: Metabolism of lipids;Metabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.343

Intolerance Scores

• loftool: 0.766
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.364
• hipred: N
• hipred_score: 0.264
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfaip8l3

Gene ontology

• Biological process: phospholipid metabolic process;phospholipid transport;regulation of lipid metabolic process;regulation of apoptotic process;positive regulation of phosphatidylinositol 3-kinase activity;inositol lipid-mediated signaling;positive regulation of protein kinase B signaling;positive regulation of ERK1 and ERK2 cascade
• Cellular component: nucleoplasm;cytoplasm;cytosol;plasma membrane
• Molecular function: phosphatidylinositol transporter activity;phosphatidylinositol binding