N4BP2L1

NEDD4 binding protein 2 like 1

Basic information

Region (hg38): 13:32400723-32428311

Links

ENSG00000139597 ∙ NCBI:90634 ∙ ∙ HGNC:25037 ∙ Uniprot:Q5TBK1 ∙ 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 N4BP2L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the N4BP2L1 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in N4BP2L1

This is a list of pathogenic ClinVar variants found in the N4BP2L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-32402989-T-C		not specified	Uncertain significance (Jan 02, 2024)
13-32403003-T-C		not specified	Uncertain significance (Oct 06, 2023)
13-32403012-C-T		not specified	Uncertain significance (Aug 09, 2021)
13-32403027-G-A		not specified	Uncertain significance (Dec 27, 2022)
13-32403040-A-G		not specified	Uncertain significance (Apr 09, 2022)
13-32403095-T-G		not specified	Uncertain significance (Mar 01, 2024)
13-32403188-A-G		not specified	Likely benign (Jan 04, 2024)
13-32403200-T-G		not specified	Uncertain significance (May 31, 2023)
13-32404372-A-G		not specified	Uncertain significance (Dec 20, 2021)
13-32407279-C-T		not specified	Uncertain significance (Dec 27, 2023)
13-32407334-T-G		not specified	Uncertain significance (Jul 06, 2021)
13-32427991-C-A		not specified	Uncertain significance (May 26, 2022)
13-32428006-G-A		not specified	Uncertain significance (Mar 29, 2023)
13-32428006-G-T		not specified	Uncertain significance (Mar 19, 2024)
13-32428024-T-C		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
N4BP2L1	protein_coding	protein_coding	ENST00000380130	5	27455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.845	0.155	125733	0	9	125742	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	86	128	0.670	0.00000662	1619
Missense in Polyphen		10	29.975	0.33361		399
Synonymous	0.468	44	48.1	0.914	0.00000267	432
Loss of Function	2.72	1	10.5	0.0953	6.17e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000295	0.0000295
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000164	0.000163
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000164	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.446
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.0812
• hipred: N
• hipred_score: 0.485
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: N4bp2l1