TNIP1

TNFAIP3 interacting protein 1

Basic information

Region (hg38): 5:151029944-151093577

Links

ENSG00000145901 ∙ NCBI:10318 ∙ OMIM:607714 ∙ HGNC:16903 ∙ Uniprot:Q15025 ∙ 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 TNIP1 gene.

• Inborn genetic diseases (22 variants)
• not provided (7 variants)
• Amyotrophic lateral sclerosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNIP1 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	2
missense			22	3	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	22	4	3

Variants in TNIP1

This is a list of pathogenic ClinVar variants found in the TNIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151030721-G-T		not specified	Uncertain significance (Oct 12, 2021)
5-151032353-C-A		not specified	Uncertain significance (Jun 14, 2023)
5-151033630-G-C		not specified	Uncertain significance (Jan 30, 2024)
5-151033641-C-T			Benign (Dec 31, 2019)
5-151033676-G-A		not specified	Uncertain significance (Dec 14, 2021)
5-151033729-G-A			Likely benign (Dec 31, 2019)
5-151033780-T-C		not specified	Uncertain significance (Mar 01, 2023)
5-151033786-C-T		not specified	Uncertain significance (Mar 07, 2024)
5-151035658-C-T		not specified	Uncertain significance (Dec 20, 2023)
5-151035670-C-T		not specified	Uncertain significance (Aug 22, 2023)
5-151036824-T-C		not specified	Uncertain significance (Jan 20, 2023)
5-151036890-G-A		not specified	Uncertain significance (Jan 27, 2022)
5-151039107-C-T		not specified	Uncertain significance (Mar 02, 2023)
5-151039141-G-C		not specified	Uncertain significance (Jan 03, 2022)
5-151039190-C-A		not specified	Uncertain significance (Feb 23, 2023)
5-151042596-G-C		not specified	Uncertain significance (Jun 24, 2022)
5-151042607-C-T		not specified	Uncertain significance (Jul 13, 2022)
5-151042667-G-A		not specified	Uncertain significance (Oct 06, 2023)
5-151042924-C-T		not specified	Uncertain significance (Jan 17, 2024)
5-151045913-G-A		not specified	Uncertain significance (Jun 07, 2023)
5-151045920-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-151049846-T-G		not specified	Uncertain significance (Oct 04, 2022)
5-151049873-G-A		not specified	Uncertain significance (Jan 05, 2022)
5-151049891-G-A			Benign (Dec 31, 2019)
5-151052238-T-C			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNIP1	protein_coding	protein_coding	ENST00000389378	17	63633

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.476	0.524	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.757	325	366	0.889	0.0000227	4116
Missense in Polyphen		153	189.33	0.80813		2094
Synonymous	0.454	135	142	0.952	0.00000821	1220
Loss of Function	4.38	8	36.6	0.219	0.00000179	434

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)	0.0000882	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits NF-kappa-B activation and TNF-induced NF-kappa- B-dependent gene expression by regulating A20/TNFAIP3-mediated deubiquitination of IKBKG; proposed to link A20/TNFAIP3 to ubiquitinated IKBKG. Involved in regulation of EGF-induced ERK1/ERK2 signaling pathway; blocks MAPK3/MAPK1 nuclear translocation and MAPK1-dependent transcription. Increases cell surface CD4(T4) antigen expression. Involved in the anti- inflammatory response of macrophages and positively regulates TLR- induced activation of CEBPB. Involved in the prevention of autoimmunity; this function implicates binding to polyubiquitin. Involved in leukocyte integrin activation during inflammation; this function is mediated by association with SELPLG and dependent on phosphorylation by SRC-family kinases. Interacts with HIV-1 matrix protein and is packaged into virions and overexpression can inhibit viral replication. May regulate matrix nuclear localization, both nuclear import of PIC (Preintegration complex) and export of GAG polyprotein and viral genomic RNA during virion production. In case of infection, promotes association of IKBKG with Shigella flexneri E3 ubiquitin-protein ligase ipah9.8 p which in turn promotes polyubiquitination of IKBKG leading to its proteasome-dependent degradation and thus is perturbing NF-kappa-B activation during bacterial infection. {ECO:0000269|PubMed:12220502, ECO:0000269|PubMed:16684768, ECO:0000269|PubMed:17016622, ECO:0000269|PubMed:17632516, ECO:0000269|PubMed:20010814}.
• Pathway: Rac1-Pak1-p38-MMP-2 pathway;Post-translational protein modification;Metabolism of proteins;EGFR1;Ovarian tumor domain proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.68

Haploinsufficiency Scores

• pHI: 0.137
• hipred: Y
• hipred_score: 0.736
• ghis: 0.468

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.491

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnip1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; liver/biliary 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: MyD88-dependent toll-like receptor signaling pathway;translation;defense response;inflammatory response;leukocyte cell-cell adhesion;glycoprotein biosynthetic process;protein deubiquitination;negative regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of viral genome replication;positive regulation of transcription by RNA polymerase II;positive regulation of inflammatory response;negative regulation of ERK1 and ERK2 cascade;modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade;positive regulation of protein deubiquitination
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding;identical protein binding;mitogen-activated protein kinase binding