N4BP2

NEDD4 binding protein 2

Basic information

Region (hg38): 4:40056797-40158252

Links

ENSG00000078177 ∙ NCBI:55728 ∙ OMIM:619139 ∙ HGNC:29851 ∙ Uniprot:Q86UW6 ∙ 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 N4BP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the N4BP2 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				1		1
missense			83	9	2	94
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	83	10	2

Variants in N4BP2

This is a list of pathogenic ClinVar variants found in the N4BP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-40097369-G-T		not specified	Uncertain significance (Sep 27, 2021)
4-40097389-G-A		not specified	Uncertain significance (Mar 11, 2022)
4-40097428-C-T		not specified	Uncertain significance (Jun 26, 2023)
4-40097429-G-T		not specified	Uncertain significance (Jan 11, 2023)
4-40097431-G-C		not specified	Uncertain significance (Sep 12, 2023)
4-40097498-G-A		not specified	Uncertain significance (Sep 14, 2023)
4-40102127-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-40102156-C-T		not specified	Uncertain significance (Aug 02, 2023)
4-40102203-C-T		not specified	Likely benign (Mar 28, 2024)
4-40102306-A-T		not specified	Uncertain significance (Mar 07, 2023)
4-40102307-C-G		not specified	Uncertain significance (Mar 20, 2023)
4-40102431-A-G			Benign (Aug 08, 2017)
4-40102462-C-A		not specified	Uncertain significance (Feb 15, 2023)
4-40102516-C-T		not specified	Uncertain significance (Oct 16, 2023)
4-40102614-G-A		not specified	Uncertain significance (Apr 12, 2022)
4-40102710-A-G		not specified	Uncertain significance (Jun 22, 2023)
4-40102812-G-A		not specified	Uncertain significance (Dec 08, 2023)
4-40102813-G-A		not specified	Likely benign (Nov 08, 2022)
4-40102901-G-C		not specified	Uncertain significance (Dec 20, 2023)
4-40102915-C-T		not specified	Uncertain significance (Mar 29, 2023)
4-40102923-C-T		not specified	Uncertain significance (Mar 01, 2023)
4-40102931-G-A		not specified	Uncertain significance (Dec 07, 2023)
4-40103064-C-T		not specified	Uncertain significance (Jun 16, 2023)
4-40103085-A-G		not specified	Uncertain significance (Dec 19, 2022)
4-40103103-T-C		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
N4BP2	protein_coding	protein_coding	ENST00000261435	16	101427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.75e-11	1.00	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.803	825	893	0.924	0.0000435	11783
Missense in Polyphen		233	275.59	0.84547		3708
Synonymous	0.0250	320	321	0.998	0.0000170	3235
Loss of Function	4.16	29	65.2	0.445	0.00000295	957

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000821	0.000799
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000154	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000237	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has 5'-polynucleotide kinase and nicking endonuclease activity. May play a role in DNA repair or recombination. {ECO:0000269|PubMed:12730195}.

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• loftool: 0.918
• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.92

Haploinsufficiency Scores

• pHI: 0.354
• hipred: N
• hipred_score: 0.270
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: N4bp2

Gene ontology

• Biological process: phosphorylation;nucleic acid phosphodiester bond hydrolysis
• Cellular component: cytosol
• Molecular function: endonuclease activity;protein binding;ATP binding;ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity