N4BP2L2

NEDD4 binding protein 2 like 2

Basic information

Region (hg38): 13:32432417-32538885

Links

ENSG00000244754 ∙ NCBI:10443 ∙ OMIM:615788 ∙ HGNC:26916 ∙ Uniprot:Q92802 ∙ 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 N4BP2L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the N4BP2L2 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			3	2		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	2	0

Variants in N4BP2L2

This is a list of pathogenic ClinVar variants found in the N4BP2L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-32442391-T-C		not specified	Likely benign (Jun 11, 2021)
13-32442619-T-C		not specified	Uncertain significance (Jun 21, 2021)
13-32442971-A-T		not specified	Uncertain significance (Sep 16, 2021)
13-32442975-T-A		not specified	Uncertain significance (Aug 12, 2021)
13-32443085-A-AT		Short stature	Pathogenic (Nov 18, 2001)
13-32443611-G-A		not specified	Likely benign (Aug 09, 2021)
13-32443989-G-A		not specified	Uncertain significance (Jul 20, 2021)
13-32522256-C-G		not specified	Uncertain significance (Feb 28, 2024)
13-32522256-C-T		not specified	Likely benign (Jul 12, 2023)
13-32527482-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
N4BP2L2	protein_coding	protein_coding	ENST00000399396	8	106417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-9	0.941	125730	0	10	125740	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.400	343	365	0.941	0.0000173	4989
Missense in Polyphen		49	70.687	0.6932		1067
Synonymous	0.951	116	130	0.894	0.00000659	1330
Loss of Function	1.98	19	30.9	0.616	0.00000136	457

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000364	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0614

Intolerance Scores

• loftool: 0.418
• rvis_EVS: 1.83
• rvis_percentile_EVS: 97.03

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.123
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.762

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: N4bp2l2

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of hematopoietic stem cell proliferation;negative regulation of hematopoietic stem cell differentiation
• Cellular component: nucleus;transcriptional repressor complex;extracellular exosome
• Molecular function: molecular_function;transcription corepressor activity;protein binding;enzyme binding