BSN

bassoon presynaptic cytomatrix protein, the group of Zinc fingers PCLO-type

Basic information

Region (hg38): 3:49554477-49671549

Previous symbols: [ "ZNF231" ]

Links

ENSG00000164061 ∙ NCBI:8927 ∙ OMIM:604020 ∙ HGNC:1117 ∙ Uniprot:Q9UPA5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BSN 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				36	9	45
missense			262	24	7	293
nonsense			3			3
start loss						0
frameshift			2			2
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	268	61	16

Variants in BSN

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

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

Position	Type	Phenotype	Significance	ClinVar
3-49554625-A-G		not specified	Uncertain significance (Jun 17, 2022)
3-49554642-G-C		not specified	Uncertain significance (Nov 17, 2022)
3-49554652-C-T		not specified	Uncertain significance (Aug 26, 2022)
3-49554656-C-G			Likely benign (Oct 01, 2023)
3-49554677-G-GGGCCCC		BSN-related disorder	Likely benign (Apr 10, 2023)
3-49554693-C-G		not specified	Uncertain significance (Nov 16, 2021)
3-49554724-C-G		not specified	Uncertain significance (Aug 30, 2021)
3-49554726-G-T		not specified	Uncertain significance (Apr 20, 2024)
3-49554794-C-T			Likely benign (Dec 01, 2022)
3-49624980-C-T		not specified	Uncertain significance (Sep 01, 2023)
3-49625019-G-C		not specified	Uncertain significance (Apr 12, 2023)
3-49625033-A-G		not specified	Uncertain significance (Oct 20, 2023)
3-49625067-A-G		not specified	Likely benign (Sep 06, 2022)
3-49625078-C-T		BSN related epilepsy	Uncertain significance (Aug 16, 2023)
3-49625125-C-T			Likely benign (Nov 01, 2022)
3-49625131-G-T		not specified	Uncertain significance (Feb 26, 2024)
3-49625133-C-T		BSN-related disorder	Likely benign (Jun 16, 2022)
3-49625151-G-A		not specified	Uncertain significance (Dec 03, 2021)
3-49625187-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-49625221-C-T		BSN-related disorder	Likely benign (Nov 04, 2019)
3-49625286-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-49625325-A-C		not specified	Uncertain significance (Nov 22, 2022)
3-49625326-G-T		not specified	Uncertain significance (Jan 03, 2024)
3-49642334-C-A			Uncertain significance (Mar 07, 2024)
3-49642354-G-A		BSN-related disorder	Likely benign (Feb 26, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BSN	protein_coding	protein_coding	ENST00000296452	10	117057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.19e-10	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	2095	2.26e+3	0.925	0.000149	24933
Missense in Polyphen		36	35.452	1.0155		383
Synonymous	0.638	925	950	0.974	0.0000595	8761
Loss of Function	8.97	13	118	0.110	0.00000684	1304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.000113	0.000109
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000147	0.000132
Middle Eastern	0.000113	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Is thought to be involved in the organization of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. Seems to act through binding to ERC2/CAST1. Essential in regulated neurotransmitter release from a subset of brain glutamatergic synapses. Involved in the formation of the retinal photoreceptor ribbon synapses (By similarity). {ECO:0000250|UniProtKB:O88778}.

Recessive Scores

• pRec: 0.223

Intolerance Scores

• loftool: 0.126
• rvis_EVS: -3.96
• rvis_percentile_EVS: 0.19

Haploinsufficiency Scores

• pHI: 0.323
• hipred: Y
• hipred_score: 0.589
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.805

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bsn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; muscle phenotype

Gene ontology

• Biological process: chemical synaptic transmission;synapse assembly;protein localization to synapse;maintenance of presynaptic active zone structure;regulation of synaptic vesicle cycle;presynapse to nucleus signaling pathway
• Cellular component: nucleus;synaptic vesicle;cell surface;postsynaptic density;cell junction;axon;dendrite;synaptic vesicle membrane;neuron projection terminus;presynaptic active zone;cytoskeleton of presynaptic active zone;excitatory synapse;Schaffer collateral - CA1 synapse;glutamatergic synapse;GABA-ergic synapse
• Molecular function: metal ion binding;structural constituent of presynaptic active zone