N4BP3

protein-coding

NEDD4 binding protein 3, the group of Leucine zipper tumor suppressor family

Gene summary

Predicted to be involved in innate immune response and nervous system development. Predicted to be located in axon and dendrite. Predicted to be active in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015111.2

Inheritance

—

ClinVar variants

U:131B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr5:178,113,532-178,126,081

External References & Databases

Ensembl (ENSG00000145911)

Transcript & Mutation Effects

hg38 • Region Span ~12.5 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 N4BP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 133

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015111.2. 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			130 clinvar	4 clinvar		134
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	131	5	0	136

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015111.2	RefSeq	NP_055926.1	4	MANE Select
ENST00000274605.6	Ensembl	ENSP00000274605.4	4	MANE Select
ENST00000850869.1	Ensembl	ENSP00000520954.1	4	Standard
ENST00000850869.2	Ensembl	ENSP00000520954.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nervous system development

Molecular Function

protein binding

Cellular Component

axon
dendrite
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000274605
Coding exons: 4
Length: 12645
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125711
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.130	375	368	1.02	0.0000261	3451
Missense (PolyPhen)		147	157.17	0.93527		1517
Synonymous	-0.758	169	157	1.08	0.0000102	1194
Loss of Function	2.01	10	19.6	0.511	0.00000105	199

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000071	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000055	0.000046	rare
European (Non-Finnish)	0.000065	0.000062	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in axon and dendrite arborization during cranial nerve development. May also be important for neural crest migration and early development of other anterior structures including eye, brain and cranial cartilage. {ECO:0000250|UniProtKB:A0A1L8GXY6}.;

Intolerance Scores

LoFtool: 0.328
RVIS EVS: -0.47
RVIS percentile EVS: 23.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

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