TNFAIP2

TNF alpha induced protein 2

Basic information

Region (hg38): 14:103121475-103137439

Links

ENSG00000185215 ∙ NCBI:7127 ∙ OMIM:603300 ∙ HGNC:11895 ∙ Uniprot:Q03169 ∙ 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 TNFAIP2 gene.

• Inborn genetic diseases (29 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNFAIP2 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					3	3
missense			26	3	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	4

Variants in TNFAIP2

This is a list of pathogenic ClinVar variants found in the TNFAIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-103126515-T-C		not specified	Uncertain significance (Dec 01, 2022)
14-103126524-G-A		not specified	Uncertain significance (Sep 12, 2023)
14-103126556-G-A			Benign (May 14, 2018)
14-103126654-C-A		not specified	Uncertain significance (Aug 09, 2021)
14-103126656-G-A		not specified	Likely benign (Mar 21, 2023)
14-103126678-G-A		not specified	Uncertain significance (Jan 19, 2022)
14-103126681-C-T		not specified	Uncertain significance (Feb 14, 2023)
14-103126683-C-T		not specified	Uncertain significance (Oct 30, 2023)
14-103126688-C-A			Benign (Feb 05, 2018)
14-103127009-G-C		not specified	Uncertain significance (Jun 22, 2021)
14-103127040-C-G		not specified	Uncertain significance (Dec 14, 2021)
14-103127107-T-C		not specified	Likely benign (Apr 07, 2023)
14-103127113-A-C		not specified	Uncertain significance (Apr 07, 2023)
14-103127157-G-C		not specified	Uncertain significance (Apr 07, 2023)
14-103127158-A-T		not specified	Uncertain significance (Apr 07, 2023)
14-103127184-G-C		not specified	Uncertain significance (Apr 07, 2023)
14-103127190-C-T		not specified	Uncertain significance (Mar 06, 2023)
14-103127290-G-A		not specified	Uncertain significance (Sep 06, 2022)
14-103127313-C-T		not specified	Uncertain significance (Jan 20, 2023)
14-103127364-G-C		not specified	Uncertain significance (Sep 20, 2023)
14-103127376-G-T		not specified	Uncertain significance (Jan 03, 2024)
14-103127388-G-A		not specified	Uncertain significance (Feb 21, 2024)
14-103127400-G-A		not specified	Uncertain significance (Jan 10, 2023)
14-103127403-G-A		not specified	Uncertain significance (Jan 03, 2024)
14-103127482-T-G		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNFAIP2	protein_coding	protein_coding	ENST00000560869	11	13998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000825	0.997	125720	0	22	125742	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.04	219	322	0.679	0.0000198	4124
Missense in Polyphen		50	102.81	0.48635		1391
Synonymous	1.31	129	149	0.863	0.0000100	1375
Loss of Function	2.58	11	24.9	0.441	0.00000133	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000729	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000233	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as a mediator of inflammation and angiogenesis.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.419

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.366
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.290

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnfaip2

Gene ontology

• Biological process: angiogenesis;exocytosis;cell differentiation;exocyst localization
• Cellular component: exocyst;extracellular space
• Molecular function: SNARE binding