N4BP2L2

protein-coding

NEDD4 binding protein 2 like 2

Gene summary

Enables enzyme binding activity. Involved in negative regulation of hematopoietic stem cell differentiation and positive regulation of hematopoietic stem cell proliferation. Located in nucleus. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014887.3

Inheritance

—

ClinVar variants

U:18B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr13:32,432,417-32,538,885

External References & Databases

Ensembl (ENSG00000244754)

Transcript & Mutation Effects

hg38 • Region Span ~106.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to N4BP2L2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014887.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			17 clinvar	2 clinvar		19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	2	0	20

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 106 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014887.3	RefSeq	NP_055702.1	5	MANE Select
ENST00000267068.6	Ensembl	ENSP00000267068.3	5	MANE Select
NM_001278432.2	RefSeq	NP_001265361.1	7	Standard
NM_001320836.3	RefSeq	NP_001307765.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
positive regulation of hematopoietic stem cell proliferation
negative regulation of hematopoietic stem cell differentiation

Molecular Function

molecular_function
transcription corepressor activity
protein binding
enzyme binding

Cellular Component

nucleus
transcriptional repressor complex
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399396
Coding exons: 8
Length: 106417
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125740
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.400	343	365	0.941	0.0000173	4989
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0614

Intolerance Scores

LoFtool: 0.418
RVIS EVS: 1.83
RVIS percentile EVS: 97.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.762

Gene Damage Prediction

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