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 (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.

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.

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	29	10	40
missense			89	9	10	108
nonsense			1			1
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding			4	6	4	14
Total	0	0	96	44	24

Variants in BNC2

This is a list of pathogenic ClinVar variants found in the BNC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-16418996-A-G		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
9-16419194-T-C		Lower urinary tract obstruction, congenital	Uncertain significance (Jun 02, 2023)
9-16419197-C-G		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
9-16419200-C-T			Uncertain significance (Aug 30, 2023)
9-16419216-A-G		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
9-16419231-A-C			Uncertain significance (Aug 19, 2022)
9-16419263-G-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2021)
9-16419265-G-A			Benign (May 21, 2023)
9-16419267-C-T		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
9-16419270-C-T		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
9-16419272-G-A		BNC2-related disorder	Benign (Sep 08, 2023)
9-16419283-C-T			Likely benign (May 17, 2022)
9-16419284-G-A			Uncertain significance (Oct 03, 2023)
9-16419312-T-C		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
9-16419316-A-G			Likely benign (May 16, 2022)
9-16419337-G-A			Likely benign (Oct 28, 2021)
9-16419369-T-C		Hypotension	Benign (Jan 26, 2024)
9-16419429-C-T		Amelogenesis imperfecta • BNC2-related disorder	Benign/Likely benign (Aug 27, 2024)
9-16419487-G-A			Benign (Jan 02, 2023)
9-16419500-T-C		Hypotension • BNC2-related disorder	Likely benign (Dec 30, 2023)
9-16419501-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 11, 2023)
9-16419521-G-A		Hypotension • not specified • BNC2-related disorder	Benign/Likely benign (Jan 22, 2024)
9-16419521-G-C			Uncertain significance (May 15, 2023)
9-16419528-A-G		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
9-16419529-T-C		Inborn genetic diseases • BNC2-related disorder	Uncertain significance (Sep 17, 2021)

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