NRBF2

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

Basic information

Region (hg38): 10:63133247-63155031

Links

ENSG00000148572 ∙ NCBI:29982 ∙ OMIM:616477 ∙ HGNC:19692 ∙ Uniprot:Q96F24 ∙ 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 NRBF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRBF2 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			13	2		15
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	3	0

Variants in NRBF2

This is a list of pathogenic ClinVar variants found in the NRBF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-63146242-T-G		not specified	Uncertain significance (Jan 04, 2024)
10-63146287-G-A		not specified	Uncertain significance (Jun 16, 2024)
10-63146290-G-A		not specified	Uncertain significance (Aug 22, 2023)
10-63153511-G-A		not specified	Uncertain significance (Dec 07, 2021)
10-63153595-G-A		not specified	Uncertain significance (Feb 13, 2024)
10-63153601-A-G		not specified	Uncertain significance (Dec 17, 2024)
10-63153635-C-T		not specified	Likely benign (Jun 13, 2023)
10-63153687-C-T			Likely benign (Nov 01, 2024)
10-63153794-A-T		not specified	Uncertain significance (Dec 31, 2024)
10-63153880-G-A		not specified	Uncertain significance (Aug 01, 2022)
10-63153918-G-C		not specified	Uncertain significance (Aug 08, 2022)
10-63153928-T-G		not specified	Uncertain significance (Dec 21, 2023)
10-63153985-A-G		not specified	Likely benign (Sep 20, 2023)
10-63153991-A-G		not specified	Uncertain significance (Mar 07, 2024)
10-63154000-G-A		not specified	Uncertain significance (Jun 22, 2023)
10-63154112-C-G		not specified	Uncertain significance (Sep 20, 2023)
10-63154134-T-G		not specified	Uncertain significance (Feb 07, 2025)
10-63154175-T-C		not specified	Uncertain significance (Jan 26, 2025)
10-63154204-T-A		not specified	Uncertain significance (Feb 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRBF2	protein_coding	protein_coding	ENST00000277746	4	21734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000504	0.891	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.279	138	148	0.935	0.00000694	1890
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.000165	0.000163
South Asian	0.0000669	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate transcriptional activation by target nuclear receptors. Can act as transcriptional activator (in vitro). {ECO:0000269|PubMed:15610520}.
• Pathway: Autophagy - animal - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.355
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.849
• hipred: N
• hipred_score: 0.480
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nrbf2

Gene ontology

• Biological process: transcription initiation from RNA polymerase II promoter;autophagy;response to endoplasmic reticulum stress;regulation of lipid kinase activity
• Cellular component: nucleoplasm;cytoplasm;autophagosome;cytoplasmic vesicle;phosphatidylinositol 3-kinase complex, class III
• Molecular function: protein binding