BNC2

basonuclin 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 9:16409503-16870843

Links

ENSG00000173068

∙ NCBI:54796 ∙ OMIM:608669 ∙ HGNC:30988 ∙ Uniprot:Q6ZN30 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

posterior urethral valve (Supportive), mode of inheritance: AR
lower urinary tract obstruction, congenital (Strong), mode of inheritance: AD
lower urinary tract obstruction, congenital (Definitive), mode of inheritance: AD
lower urinary tract obstruction, congenital (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lower urinary tract obstruction, congenital	AD	Renal	The condition may involve occult urinary tract obstruction, which may manifest as frequent urinary tract infections and other sequelae, leading to renal damage, and awareness may allow interventions to preserve kidney function	Renal	31051115

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BNC2 gene.

not_provided (151 variants)
Inborn_genetic_diseases (133 variants)
BNC2-related_disorder (27 variants)
Hypotension (17 variants)
Lower_urinary_tract_obstruction,_congenital (10 variants)
not_specified (2 variants)
Lower_Urinary_Tract_Obstruction (2 variants)
Amelogenesis_imperfecta (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BNC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017637.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	34 clinvar	12 clinvar	49
missense	1 clinvar		180 clinvar	15 clinvar	10 clinvar	206
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	1	0	185	49	22

Highest pathogenic variant AF is 0.000023339995

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BNC2	protein_coding	protein_coding	ENST00000380672	7	461341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.928	0.0724	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.360	584	609	0.959	0.0000350	7327
Missense in Polyphen		157	222.8	0.70467		2747
Synonymous	-1.64	268	236	1.14	0.0000143	2145
Loss of Function	4.53	6	34.8	0.172	0.00000242	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probable transcription factor specific for skin keratinocytes. May play a role in the differentiation of spermatozoa and oocytes.;

Recessive Scores

pRec: 0.122

Intolerance Scores

loftool: 0.168
rvis_EVS: 0.63
rvis_percentile_EVS: 83.58

Haploinsufficiency Scores

pHI: 0.606
hipred: Y
hipred_score: 0.644
ghis: 0.507

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.330

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Bnc2
Phenotype: growth/size/body region phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; skeleton phenotype;

Zebrafish Information Network

Gene name: bnc2
Affected structure: xanthophore
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: endochondral bone growth;regulation of transcription by RNA polymerase II;tongue development;roof of mouth development;mesenchyme development
Cellular component: nucleoplasm
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding