BNC2

basonuclin 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 9:16409503-16870843

Links

ENSG00000173068NCBI:54796OMIM:608669HGNC:30988Uniprot:Q6ZN30AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Lower urinary tract obstruction, congenitalADRenalThe 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 functionRenal31051115

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
BNC2protein_codingprotein_codingENST00000380672 7461341
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9280.07241257380101257480.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3605846090.9590.00003507327
Missense in Polyphen157222.80.704672747
Synonymous-1.642682361.140.00001432145
Loss of Function4.53634.80.1720.00000242415

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001850.000185
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00005280.0000527
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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