TNFAIP6

TNF alpha induced protein 6, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 2:151357592-151380046

Links

ENSG00000123610 ∙ NCBI:7130 ∙ OMIM:600410 ∙ HGNC:11898 ∙ Uniprot:P98066 ∙ 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 TNFAIP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFAIP6 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in TNFAIP6

This is a list of pathogenic ClinVar variants found in the TNFAIP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-151357697-C-G		not specified	Uncertain significance (Apr 12, 2022)
2-151363946-G-T		not specified	Uncertain significance (Apr 07, 2023)
2-151363972-G-C		not specified	Uncertain significance (Dec 19, 2023)
2-151363976-G-T		not specified	Uncertain significance (Jan 06, 2023)
2-151363992-G-T		not specified	Uncertain significance (Nov 09, 2023)
2-151364041-C-G		not specified	Uncertain significance (Dec 20, 2023)
2-151366092-G-A		not specified	Uncertain significance (Sep 13, 2023)
2-151370027-G-C		not specified	Uncertain significance (Mar 07, 2024)
2-151370037-G-A		not specified	Uncertain significance (Oct 20, 2021)
2-151370130-T-C		not specified	Uncertain significance (Jul 06, 2022)
2-151370140-G-A		not specified	Likely benign (Oct 17, 2023)
2-151370184-G-A		not specified	Uncertain significance (Jun 10, 2024)
2-151373559-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-151379438-A-G		not specified	Likely benign (Jun 12, 2023)
2-151379477-A-T		not specified	Uncertain significance (Jun 21, 2022)
2-151379517-G-T		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFAIP6	protein_coding	protein_coding	ENST00000243347	6	22455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000109	0.577	125626	0	121	125747	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.567	131	151	0.870	0.00000765	1818
Missense in Polyphen		36	55.381	0.65004		629
Synonymous	1.45	41	54.6	0.751	0.00000305	494
Loss of Function	0.920	11	14.8	0.742	6.93e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000669	0.000669
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000544
Finnish	0.00148	0.00148
European (Non-Finnish)	0.000506	0.000492
Middle Eastern	0.0000559	0.0000544
South Asian	0.000261	0.000261
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possibly involved in cell-cell and cell-matrix interactions during inflammation and tumorigenesis.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.826
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.21

Haploinsufficiency Scores

• pHI: 0.764
• hipred: N
• hipred_score: 0.251
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.270

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfaip6
• Phenotype: immune system phenotype; reproductive system phenotype; respiratory system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: inflammatory response;cell adhesion;signal transduction;cell-cell signaling;positive regulation of cell migration;ovulation;neutrophil degranulation;negative regulation of inflammatory response
• Cellular component: extracellular region;extracellular space;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: protein binding;hyaluronic acid binding