TNFAIP1

TNF alpha induced protein 1, the group of BTB domain containing

Basic information

Region (hg38): 17:28335601-28347009

Previous symbols: [ "EDP1" ]

Links

ENSG00000109079 ∙ NCBI:7126 ∙ OMIM:191161 ∙ HGNC:11894 ∙ Uniprot:Q13829 ∙ 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 TNFAIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFAIP1 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
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in TNFAIP1

This is a list of pathogenic ClinVar variants found in the TNFAIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28339592-G-T		not specified	Uncertain significance (Oct 26, 2022)
17-28339597-G-C		not specified	Uncertain significance (Oct 03, 2022)
17-28339639-T-C		not specified	Uncertain significance (Jul 20, 2021)
17-28339664-G-A		not specified	Uncertain significance (Mar 07, 2023)
17-28340381-C-A		not specified	Uncertain significance (Feb 05, 2024)
17-28341282-A-T		not specified	Uncertain significance (Mar 15, 2024)
17-28342263-C-G		not specified	Uncertain significance (Jan 22, 2024)
17-28342335-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-28342346-C-T			Benign (Feb 01, 2024)
17-28342361-G-T		not specified	Uncertain significance (Mar 19, 2024)
17-28344430-G-A		not specified	Uncertain significance (Apr 07, 2023)
17-28344503-C-A		not specified	Uncertain significance (Feb 22, 2024)
17-28344503-C-T		not specified	Uncertain significance (May 31, 2023)
17-28344520-C-T		not specified	Uncertain significance (Nov 06, 2023)
17-28344521-G-A		not specified	Uncertain significance (Nov 21, 2023)
17-28344529-C-T		not specified	Uncertain significance (Sep 14, 2022)
17-28344595-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFAIP1	protein_coding	protein_coding	ENST00000226225	6	11408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.135	0.861	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	143	205	0.698	0.0000140	2067
Missense in Polyphen		50	81.48	0.61365		822
Synonymous	-0.110	83	81.7	1.02	0.00000513	616
Loss of Function	2.51	4	14.2	0.281	7.74e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000546	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex involved in regulation of cytoskeleton structure. The BCR(TNFAIP1) E3 ubiquitin ligase complex mediates the ubiquitination of RHOA, leading to its degradation by the proteasome, thereby regulating the actin cytoskeleton and cell migration. Its interaction with RHOB may regulate apoptosis. May enhance the PCNA-dependent DNA polymerase delta activity. {ECO:0000269|PubMed:19637314, ECO:0000269|PubMed:19782033}.

Recessive Scores

• pRec: 0.493

Intolerance Scores

• loftool: 0.489
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.434
• hipred: Y
• hipred_score: 0.703
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfaip1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: DNA replication;apoptotic process;immune response;cell migration;protein ubiquitination;negative regulation of Rho protein signal transduction;stress fiber assembly;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of DNA replication;protein homooligomerization
• Cellular component: nucleolus;cytoplasm;endosome;Cul3-RING ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding;GTP-Rho binding;protein domain specific binding;identical protein binding