TNFAIP8L2

TNF alpha induced protein 8 like 2

Basic information

Region (hg38): 1:151156648-151159749

Links

ENSG00000163154 ∙ NCBI:79626 ∙ OMIM:612112 ∙ HGNC:26277 ∙ Uniprot:Q6P589 ∙ 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 TNFAIP8L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFAIP8L2 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					2	2
missense			9		1	10
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	3

Variants in TNFAIP8L2

This is a list of pathogenic ClinVar variants found in the TNFAIP8L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151158739-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-151158762-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-151158768-G-A			Benign (Jan 02, 2019)
1-151158850-C-A		not specified	Uncertain significance (Dec 13, 2021)
1-151158862-G-C		not specified	Uncertain significance (Jun 18, 2021)
1-151158869-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-151158870-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-151159031-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-151159060-C-G			Benign (Dec 31, 2019)
1-151159105-G-A			Benign (Jul 04, 2018)
1-151159128-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-151159133-G-A		not specified	Uncertain significance (Feb 01, 2023)
1-151159177-T-A		not specified	Uncertain significance (Dec 11, 2023)
1-151159223-A-G		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFAIP8L2	protein_coding	protein_coding	ENST00000368910	1	3121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0384	0.658	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.895	90	117	0.767	0.00000772	1189
Missense in Polyphen		41	54.785	0.74837		515
Synonymous	0.929	41	49.3	0.832	0.00000303	399
Loss of Function	0.430	2	2.77	0.722	1.16e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of innate and adaptive immunity by maintaining immune homeostasis. Negative regulator of Toll-like receptor and T-cell receptor function. Prevents hyperresponsiveness of the immune system and maintains immune homeostasis. Inhibits JUN/AP1 and NF-kappa-B activation. Promotes Fas-induced apoptosis (By similarity). {ECO:0000250}.
• Pathway: Metabolism of lipids;Metabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.369

Intolerance Scores

• loftool: 0.325
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.325
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfaip8l2
• Phenotype: liver/biliary system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; digestive/alimentary phenotype; cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of apoptotic process;innate immune response;negative regulation of inflammatory response;negative regulation of T cell activation
• Cellular component: cytoplasm
• Molecular function: protein binding