BRF2

BRF2 RNA polymerase III transcription initiation factor subunit

Basic information

Region (hg38): 8:37843268-37849861

Links

ENSG00000104221 ∙ NCBI:55290 ∙ OMIM:607013 ∙ HGNC:17298 ∙ Uniprot:Q9HAW0 ∙ 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 BRF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRF2 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			41	1		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	0

Variants in BRF2

This is a list of pathogenic ClinVar variants found in the BRF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-37844512-G-A		not specified	Uncertain significance (Jun 07, 2024)
8-37844521-T-C		not specified	Uncertain significance (Jan 05, 2022)
8-37844537-C-A		not specified	Uncertain significance (Nov 18, 2022)
8-37844540-T-C		not specified	Uncertain significance (Jan 30, 2024)
8-37844564-G-A		not specified	Uncertain significance (Dec 28, 2023)
8-37844569-C-T		not specified	Uncertain significance (Aug 07, 2023)
8-37844614-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-37844620-G-A		not specified	Uncertain significance (Nov 30, 2022)
8-37844638-G-C		not specified	Uncertain significance (Dec 14, 2022)
8-37844647-C-T		not specified	Uncertain significance (May 11, 2022)
8-37844648-G-A		not specified	Uncertain significance (Jun 23, 2021)
8-37844696-C-A		not specified	Uncertain significance (Sep 27, 2021)
8-37844702-G-A		not specified	Uncertain significance (Nov 03, 2022)
8-37844720-C-T		not specified	Uncertain significance (Jul 30, 2024)
8-37844737-A-C		not specified	Uncertain significance (Sep 22, 2021)
8-37844749-C-T		not specified	Uncertain significance (Oct 27, 2023)
8-37844758-T-A		not specified	Uncertain significance (Feb 05, 2024)
8-37844770-G-A		not specified	Uncertain significance (Sep 22, 2022)
8-37844813-G-A		not specified	Uncertain significance (Feb 16, 2023)
8-37844824-C-T		not specified	Uncertain significance (Dec 10, 2024)
8-37844831-G-C		not specified	Uncertain significance (May 08, 2023)
8-37844840-G-C		not specified	Uncertain significance (Sep 14, 2021)
8-37844879-G-A		not specified	Uncertain significance (Jul 02, 2024)
8-37844899-C-T		not specified	Likely benign (Feb 05, 2024)
8-37844926-C-A		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRF2	protein_coding	protein_coding	ENST00000220659	4	6637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.75e-12	0.168	125627	0	121	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0239	253	252	1.00	0.0000155	2650
Missense in Polyphen		47	54.812	0.85748		555
Synonymous	0.0287	108	108	0.996	0.00000641	921
Loss of Function	0.785	20	24.2	0.828	0.00000190	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00106
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000490	0.000489
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000432	0.000431
Middle Eastern	0.000490	0.000489
South Asian	0.00121	0.00121
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: General activator of RNA polymerase III transcription. Factor exclusively required for RNA polymerase III transcription of genes with promoter elements upstream of the initiation sites (PubMed:11040218, PubMed:11121026, PubMed:11564744, PubMed:26638071). Contributes to the regulation of gene expression; functions as activator in the absence of oxidative stress (PubMed:26638071). Down-regulates expression of target genes in response to oxidative stress (PubMed:26638071). Overexpression protects cells against apoptosis in response to oxidative stress (PubMed:26638071). {ECO:0000269|PubMed:11040218, ECO:0000269|PubMed:11121026, ECO:0000269|PubMed:11564744, ECO:0000269|PubMed:26638071}.
• Pathway: Gene expression (Transcription);RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.315
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.762
• hipred: Y
• hipred_score: 0.510
• ghis: 0.546

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brf2

Gene ontology

• Biological process: DNA-templated transcription, initiation;regulation of transcription by RNA polymerase III;cellular response to oxidative stress;transcription preinitiation complex assembly;RNA polymerase III preinitiation complex assembly
• Cellular component: transcription factor TFIIIB complex;nucleus;nucleoplasm
• Molecular function: RNA polymerase III type 3 promoter sequence-specific DNA binding;RNA polymerase III type 3 promoter DNA binding;transcription factor binding;metal ion binding