BNC2
Basic information
Region (hg38): 9:16409503-16870843
Links
Phenotypes
GenCC
Source:
- 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:
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
- 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 | 34 | 12 | 49 | |||
missense | 180 | 15 | 10 | 206 | ||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 1 | 0 | 185 | 49 | 22 |
Highest pathogenic variant AF is 0.000023339995
GnomAD
Source:
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:
- 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