N4BP1

NEDD4 binding protein 1

Basic information

Region (hg38): 16:48538726-48620148

Links

ENSG00000102921 ∙ NCBI:9683 ∙ OMIM:619138 ∙ HGNC:29850 ∙ Uniprot:O75113 ∙ 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 N4BP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the N4BP1 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			46	9		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	9	1

Variants in N4BP1

This is a list of pathogenic ClinVar variants found in the N4BP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-48542956-G-C		not specified	Uncertain significance (Mar 29, 2022)
16-48543034-G-C		not specified	Uncertain significance (Feb 15, 2023)
16-48543038-C-T		not specified	Uncertain significance (Feb 10, 2025)
16-48543059-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-48543154-C-T			Likely benign (Jan 01, 2023)
16-48543160-G-A		not specified	Uncertain significance (Nov 03, 2022)
16-48543172-C-T		not specified	Uncertain significance (Jun 06, 2023)
16-48543182-C-T		not specified	Uncertain significance (Sep 08, 2024)
16-48543213-G-T		not specified	Uncertain significance (Sep 30, 2024)
16-48543251-G-A		not specified	Uncertain significance (May 31, 2023)
16-48546183-C-T		not specified	Uncertain significance (Oct 08, 2024)
16-48548020-T-C		not specified	Uncertain significance (Sep 30, 2024)
16-48548097-G-A		not specified	Uncertain significance (Jan 20, 2025)
16-48560779-T-A		not specified	Uncertain significance (Apr 28, 2023)
16-48560799-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-48560802-C-T		not specified	Uncertain significance (May 02, 2024)
16-48560887-T-C		not specified	Uncertain significance (Dec 17, 2023)
16-48560895-G-C		not specified	Uncertain significance (Aug 02, 2021)
16-48560919-G-C		not specified	Uncertain significance (Apr 23, 2024)
16-48560944-G-C		not specified	Uncertain significance (Nov 20, 2024)
16-48560961-A-G		not specified	Uncertain significance (Jan 24, 2025)
16-48560965-T-C		not specified	Likely benign (Feb 06, 2025)
16-48560985-T-C		not specified	Uncertain significance (Feb 18, 2025)
16-48560989-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-48561005-T-C			Benign (Feb 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
N4BP1	protein_coding	protein_coding	ENST00000262384	7	81423

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.621	0.379	124629	0	13	124642	0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	370	438	0.844	0.0000209	5895
Missense in Polyphen		82	154.04	0.53234		2035
Synonymous	1.45	140	164	0.856	0.00000826	1754
Loss of Function	3.99	6	29.3	0.205	0.00000147	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000908	0.0000885
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of the E3 ubiquitin-protein ligase ITCH. Acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0969

Intolerance Scores

• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.416
• hipred: N
• hipred_score: 0.328
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.498

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: N4bp1

Gene ontology

• Biological process: negative regulation of protein ubiquitination;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;cellular response to UV
• Cellular component: nucleolus;PML body
• Molecular function: protein binding