TNFAIP2

protein-coding

TNF alpha induced protein 2

Gene summary

This gene was identified as a gene whose expression can be induced by the tumor necrosis factor alpha (TNF) in umbilical vein endothelial cells. The expression of this gene was shown to be induced by retinoic acid in a cell line expressing a oncogenic version of the retinoic acid receptor alpha fusion protein, which suggested that this gene may be a retinoic acid target gene in acute promyelocytic leukemia. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006291.4

Inheritance

—

ClinVar variants

U:98B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr14:103,121,476-103,137,439

External References & Databases

Ensembl (ENSG00000185215)

Transcript & Mutation Effects

hg38 • Region Span ~16.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNFAIP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006291.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	3 clinvar	4
missense			95 clinvar	5 clinvar	1 clinvar	101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	98	6	4	108

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006291.4	RefSeq	NP_006282.2	11	MANE Select
ENST00000560869.6	Ensembl	ENSP00000452634.2	11	MANE Select
NM_001371220.1	RefSeq	NP_001358149.1	12	Standard
NM_001371221.1	RefSeq	NP_001358150.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

angiogenesis
exocytosis
cell differentiation
exocyst localization

Molecular Function

SNARE binding

Cellular Component

exocyst
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000560869
Coding exons: 11
Length: 13998
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125742
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.04	219	322	0.679	0.0000198	4124
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000073	0.000070	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role as a mediator of inflammation and angiogenesis.;

Recessive Scores

pRec: 0.419

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.290

Gene Damage Prediction

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