TNFAIP1

protein-coding

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

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. Studies of a similar gene in mouse suggest that the expression of this gene is developmentally regulated in a tissue-specific manner. [provided by RefSeq, Jul 2008]

Previous symbols:

EDP1

MANE transcript

NM_021137.5

Inheritance

—

ClinVar variants

U:47B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr17:28,335,602-28,347,009

External References & Databases

Ensembl (ENSG00000109079)

Transcript & Mutation Effects

hg38 • Region Span ~11.4 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 TNFAIP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021137.5. 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		1 clinvar	2
missense			43 clinvar			43
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	0	1	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021137.5	RefSeq	NP_066960.1	6	MANE Select
ENST00000226225.7	Ensembl	ENSP00000226225.2	6	MANE Select
ENST00000544907.6	Ensembl	ENSP00000440749.2	5	Standard
ENST00000544907.7	Ensembl	ENSP00000440749.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA replication
apoptotic process
immune response
cell migration
protein ubiquitination

Molecular Function

ubiquitin-protein transferase activity
protein binding
GTP-Rho binding
protein domain specific binding
identical protein binding

Cellular Component

nucleolus
cytoplasm
endosome
Cul3-RING ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000226225
Coding exons: 6
Length: 11408
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	143	205	0.698	0.0000140	2067
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.977

Gene Damage Prediction

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