NRBF2

protein-coding

nuclear receptor binding factor 2, the group of PIK3C3 complex subunits

Gene summary

Involved in autophagy. Located in cytoplasm and phosphatidylinositol 3-kinase complex, class III. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_030759.5

Inheritance

—

ClinVar variants

U:31B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr10:63,133,247-63,155,031

External References & Databases

Ensembl (ENSG00000148572)

Transcript & Mutation Effects

hg38 • Region Span ~21.8 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 NRBF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030759.5. 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			29 clinvar	2 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	31	3	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030759.5	RefSeq	NP_110386.2	4	MANE Select
ENST00000277746.11	Ensembl	ENSP00000277746.6	4	MANE Select
NM_001282405.2	RefSeq	NP_001269334.1	3	Standard
ENST00000435510.6	Ensembl	ENSP00000397502.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Autophagy - animal - Homo sapiens (human)
Gene expression (Transcription)
Generic Transcription Pathway
Nuclear Receptor transcription pathway
RNA Polymerase II Transcription

Biological Process

transcription initiation from RNA polymerase II promoter
autophagy
response to endoplasmic reticulum stress
regulation of lipid kinase activity

Molecular Function

protein binding

Cellular Component

nucleoplasm
cytoplasm
autophagosome
cytoplasmic vesicle
phosphatidylinositol 3-kinase complex, class III

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000277746
Coding exons: 4
Length: 21734
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.279	138	148	0.935	0.00000694	1890
Missense (PolyPhen)		31	34.93	0.88748		510
Synonymous	-0.180	55	53.3	1.03	0.00000257	534
Loss of Function	1.43	7	12.4	0.563	6.23e-7	155

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May modulate transcriptional activation by target nuclear receptors. Can act as transcriptional activator (in vitro). {ECO:0000269|PubMed:15610520}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.355
RVIS EVS: 0.53
RVIS percentile EVS: 80.58

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.985

Gene Damage Prediction

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