N4BP3

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

Basic information

Region (hg38): 5:178113532-178126081

Links

ENSG00000145911 ∙ NCBI:23138 ∙ OMIM:619140 ∙ HGNC:29852 ∙ Uniprot:O15049 ∙ 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 N4BP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the N4BP3 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			78	3		81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	78	3	0

Variants in N4BP3

This is a list of pathogenic ClinVar variants found in the N4BP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178119588-C-T		not specified	Uncertain significance (Dec 01, 2022)
5-178119644-C-T		not specified	Uncertain significance (Dec 03, 2021)
5-178119657-C-A		not specified	Uncertain significance (Sep 30, 2024)
5-178119686-G-A		not specified	Uncertain significance (Feb 17, 2023)
5-178119692-C-T		not specified	Uncertain significance (Dec 13, 2022)
5-178119693-G-A		not specified	Likely benign (Aug 27, 2024)
5-178119711-A-T		not specified	Uncertain significance (Jul 25, 2024)
5-178119722-C-T		not specified	Uncertain significance (Feb 11, 2022)
5-178119740-C-T		not specified	Uncertain significance (May 10, 2023)
5-178119776-G-T		not specified	Uncertain significance (Jul 19, 2022)
5-178119806-G-A		not specified	Uncertain significance (Nov 09, 2023)
5-178119812-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-178119849-G-T		not specified	Uncertain significance (Nov 15, 2024)
5-178119864-C-T		not specified	Uncertain significance (Dec 26, 2023)
5-178119896-C-G		not specified	Uncertain significance (Jun 12, 2023)
5-178119897-G-A		not specified	Uncertain significance (Jun 02, 2024)
5-178120181-C-T		not specified	Uncertain significance (Jun 16, 2023)
5-178120182-G-T		not specified	Uncertain significance (Sep 01, 2024)
5-178120190-C-T		not specified	Uncertain significance (Mar 28, 2024)
5-178120208-A-G		not specified	Likely benign (Apr 11, 2023)
5-178120277-C-T		not specified	Uncertain significance (May 18, 2022)
5-178120328-G-A		not specified	Uncertain significance (Dec 15, 2023)
5-178120341-G-C		not specified	Uncertain significance (Nov 07, 2023)
5-178120350-G-A		not specified	Uncertain significance (Dec 07, 2024)
5-178120375-C-G		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
N4BP3	protein_coding	protein_coding	ENST00000274605	4	12645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000570	0.974	125694	0	17	125711	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.130	375	368	1.02	0.0000261	3451
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000547	0.0000462
European (Non-Finnish)	0.0000654	0.0000616
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000172	0.000163

dbNSFP

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

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.583
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: N4bp3

Gene ontology

• Biological process: nervous system development
• Cellular component: axon;dendrite;cytoplasmic vesicle
• Molecular function: protein binding