TNIP2

TNFAIP3 interacting protein 2

Basic information

Region (hg38): 4:2741648-2756342

Links

ENSG00000168884 ∙ NCBI:79155 ∙ OMIM:610669 ∙ HGNC:19118 ∙ Uniprot:Q8NFZ5 ∙ 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 TNIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNIP2 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			32	4		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	4	0

Variants in TNIP2

This is a list of pathogenic ClinVar variants found in the TNIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-2742364-C-T		not specified	Likely benign (Mar 20, 2023)
4-2742366-C-T		not specified	Uncertain significance (Jan 24, 2024)
4-2742405-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-2742502-C-G		not specified	Uncertain significance (Feb 10, 2023)
4-2742513-C-T		not specified	Likely benign (Jun 28, 2023)
4-2744407-G-A		not specified	Uncertain significance (May 10, 2022)
4-2744419-C-T		not specified	Likely benign (May 09, 2022)
4-2744423-C-A		not specified	Uncertain significance (Jun 07, 2024)
4-2744721-C-G		not specified	Uncertain significance (Jul 06, 2022)
4-2744731-G-A		not specified	Uncertain significance (Aug 16, 2021)
4-2744738-G-A		not specified	Uncertain significance (May 01, 2022)
4-2744827-T-G		not specified	Uncertain significance (May 02, 2024)
4-2744886-C-G		not specified	Uncertain significance (Jan 23, 2024)
4-2744887-C-G		not specified	Uncertain significance (Nov 09, 2023)
4-2744891-C-A		not specified	Uncertain significance (Nov 19, 2022)
4-2744897-C-T			Uncertain significance (Sep 01, 2023)
4-2744918-G-A		not specified	Uncertain significance (Oct 29, 2021)
4-2744919-C-A		not specified	Uncertain significance (May 23, 2023)
4-2744936-G-A		not specified	Uncertain significance (Apr 26, 2023)
4-2745453-A-G		not specified	Uncertain significance (Jun 29, 2023)
4-2745471-C-T		not specified	Uncertain significance (Aug 10, 2021)
4-2745489-T-C		not specified	Uncertain significance (Feb 12, 2024)
4-2747672-C-G		not specified	Uncertain significance (Nov 10, 2022)
4-2747734-T-C		not specified	Uncertain significance (Apr 24, 2024)
4-2747759-G-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNIP2	protein_coding	protein_coding	ENST00000315423	6	14729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00159	0.993	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.496	219	241	0.910	0.0000155	2741
Missense in Polyphen		57	67.534	0.84402		848
Synonymous	-0.202	110	107	1.02	0.00000737	865
Loss of Function	2.43	8	19.6	0.408	0.00000118	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits NF-kappa-B activation by blocking the interaction of RIPK1 with its downstream effector NEMO/IKBKG. Forms a ternary complex with NFKB1 and MAP3K8 but appears to function upstream of MAP3K8 in the TLR4 signaling pathway that regulates MAP3K8 activation. Involved in activation of the MEK/ERK signaling pathway during innate immune response; this function seems to be stimulus- and cell type specific. Required for stability of MAP3K8. Involved in regulation of apoptosis in endothelial cells; promotes TEK agonist-stimulated endothelial survival. May act as transcriptional coactivator when translocated to the nucleus. Enhances CHUK-mediated NF-kappa-B activation involving NF-kappa-B p50-p65 and p50-c-Rel complexes. {ECO:0000269|PubMed:12595760, ECO:0000269|PubMed:12753905, ECO:0000269|PubMed:12933576, ECO:0000269|PubMed:14653779, ECO:0000269|PubMed:15169888, ECO:0000269|PubMed:21784860}.
• Pathway: Rac1-Pak1-p38-MMP-2 pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Post-translational protein modification;Metabolism of proteins;Interleukin-1 signaling;Innate Immune System;Immune System;MAP3K8 (TPL2)-dependent MAPK1/3 activation;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;Ovarian tumor domain proteases;Deubiquitination;Angiopoietin receptor Tie2-mediated signaling;TNFalpha;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.788
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.532
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnip2
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;inflammatory response;I-kappaB kinase/NF-kappaB signaling;protein deubiquitination;CD40 signaling pathway;toll-like receptor 2 signaling pathway;toll-like receptor 3 signaling pathway;toll-like receptor 9 signaling pathway;positive regulation of macrophage activation;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of transcription by RNA polymerase II;protein stabilization;positive regulation of B cell activation;stress-activated MAPK cascade;interleukin-1-mediated signaling pathway;cellular response to lipopolysaccharide;negative regulation of endothelial cell apoptotic process
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: protein binding;protein kinase binding;polyubiquitin modification-dependent protein binding;metal ion binding;K63-linked polyubiquitin modification-dependent protein binding