BNC1

basonuclin 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 15:83255884-83284664

Previous symbols: [ "BNC" ]

Links

ENSG00000169594 ∙ NCBI:646 ∙ OMIM:601930 ∙ HGNC:1081 ∙ Uniprot:Q01954 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 46 XX gonadal dysgenesis (Supportive), mode of inheritance: AD
• premature ovarian failure 16 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Premature ovarian failure 16	AD	Obstetric	Genetic knowledge may allow reproductive capabilities such as via egg preservation	Obstetric	30010909

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BNC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BNC1 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				2	1	3
missense		1	47	3	1	52
nonsense			1			1
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	3	48	5	2

Variants in BNC1

This is a list of pathogenic ClinVar variants found in the BNC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-83257459-G-C		not specified	Uncertain significance (Oct 10, 2023)
15-83257510-G-A		Premature ovarian failure 16	Uncertain significance (Feb 16, 2020)
15-83257525-A-C		not specified	Uncertain significance (Jan 31, 2024)
15-83257570-G-A		not specified	Uncertain significance (Mar 06, 2023)
15-83257581-G-A		not specified	Uncertain significance (Apr 27, 2023)
15-83257676-C-G		not specified	Uncertain significance (Jun 22, 2021)
15-83257704-A-C		not specified	Uncertain significance (Feb 06, 2023)
15-83257837-T-A		not specified	Uncertain significance (Jun 29, 2023)
15-83257859-C-G			Likely benign (Apr 01, 2023)
15-83257875-C-T		not specified	Uncertain significance (Aug 22, 2023)
15-83257876-T-C		not specified	Uncertain significance (Nov 21, 2022)
15-83257959-C-G		not specified	Uncertain significance (Mar 02, 2023)
15-83258040-A-G		not specified	Uncertain significance (Oct 02, 2023)
15-83258053-G-A		not specified	Uncertain significance (Oct 05, 2023)
15-83258068-T-C			Benign (Apr 30, 2018)
15-83262967-G-A		not specified	Uncertain significance (May 23, 2023)
15-83262978-G-A		Premature ovarian failure	Likely pathogenic (Mar 02, 2020)
15-83263096-G-A		not specified	Uncertain significance (Jul 09, 2021)
15-83263108-T-C		not specified	Uncertain significance (Dec 18, 2023)
15-83263134-A-G		not specified	Uncertain significance (May 07, 2024)
15-83263173-G-A		not specified	Uncertain significance (Sep 14, 2022)
15-83263183-T-C		not specified	Uncertain significance (Apr 29, 2024)
15-83263221-C-T		not specified	Likely benign (Mar 01, 2023)
15-83263285-G-A		not specified	Uncertain significance (Sep 17, 2021)
15-83263290-T-C		not specified	Likely benign (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BNC1	protein_coding	protein_coding	ENST00000345382	5	28812

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0352	125729	0	11	125740	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	446	524	0.852	0.0000284	6646
Missense in Polyphen		150	191.66	0.78265		2344
Synonymous	-0.165	199	196	1.01	0.0000107	1903
Loss of Function	4.21	4	28.0	0.143	0.00000135	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000532	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator (By similarity). Likely specific for squamous epithelium and for the constituent keratinocytes at a stage either prior to or at the very beginning of terminal differentiation (PubMed:8034748). Required for the maintenance of spermatogenesis (By similarity). May also play a role in the differentiation of oocytes and the early development of embryos (By similarity). {ECO:0000250|UniProtKB:O35914, ECO:0000269|PubMed:8034748}.

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.0259
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.17

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.656
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bnc1
• Phenotype: vision/eye phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;spermatogenesis;positive regulation of cell population proliferation;epidermis development;cell differentiation
• Cellular component: nucleus;nucleoplasm;cytoplasm;intracellular membrane-bounded organelle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;metal ion binding