TNIP3

TNFAIP3 interacting protein 3

Basic information

Region (hg38): 4:121131408-121227466

Links

ENSG00000050730

∙ NCBI:79931 ∙ OMIM:608019 ∙ HGNC:19315 ∙ Uniprot:Q96KP6 ∙ 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 TNIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNIP3 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in TNIP3

This is a list of pathogenic ClinVar variants found in the TNIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-121142759-C-T		not specified	Uncertain significance (Jan 10, 2023)	2457338
4-121216430-G-A		not specified	Uncertain significance (Oct 12, 2021)	2345390

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNIP3	protein_coding	protein_coding	ENST00000509841	13	96059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0154	0.984	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.549	176	198	0.890	0.0000102	2501
Missense in Polyphen		44	55.316	0.79543		797
Synonymous	0.713	65	72.7	0.894	0.00000420	610
Loss of Function	3.24	8	25.7	0.311	0.00000125	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000913	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to zinc finger protein TNFAIP3 and inhibits NF- kappa-B activation induced by tumor necrosis factor, Toll-like receptor 4 (TLR4), interleukin-1 and 12-O-tetradecanoylphorbol-13- acetate. Overexpression inhibits NF-kappa-B-dependent gene expression in response to lipopolysaccharide at a level downstream of TRAF6 and upstream of IKBKB. NF-kappa-B inhibition is independent of TNFAIP3 binding. {ECO:0000269|PubMed:17088249}.;
Pathway: Rac1-Pak1-p38-MMP-2 pathway;Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination (Consensus)

Recessive Scores

pRec: 0.150

Intolerance Scores

loftool: 0.477
rvis_EVS: 0.44
rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

pHI: 0.0703
hipred: N
hipred_score: 0.233
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.817

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tnip3
Phenotype

Gene ontology

Biological process: MyD88-independent toll-like receptor signaling pathway;inflammatory response;protein deubiquitination;toll-like receptor 4 signaling pathway;negative regulation of I-kappaB kinase/NF-kappaB signaling;cellular response to lipopolysaccharide
Cellular component: cytosol
Molecular function: protein binding;polyubiquitin modification-dependent protein binding