Human Gene Module / Chromosome 3 / BSN

BSNbassoon presynaptic cytomatrix protein

SFARI Gene Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
8 / 12
Rare Variants / Common Variants
39 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
3p21.31
Associated Disorders
-
Relevance to Autism

De novo loss-of-function variants in the BSN gene have been identified in an ASD proband from the SPARK cohort (Trost et al., 2022) and in a Japanese ASD proband who also presented with developmental delay, intellectual disability, and epilepsy (Furukawa et al., 2025), while additional de novo missense and synonymous variants in this gene have been reported in ASD probands from the Autism Sequencing Consortium, the SPARK cohort, and the MSSNG cohort (De Rubeis et al., 2014; Yuen et al., 2017; Feliciano et al., 2019; Satterstrom et al., 2020; Zhou et al., 2022; Fu et al., 2022; Trost et al., 2022). Heterozygous and compound heterozygous variants in BSN have also been reported in individuals with epilepsy (Ye et al., 2023), and a genome-wide association study of febrile seizures in 7635 cases and 83,966 controls in Skotte et al., 2022 identified BSN as a novel loci with a P-value < 5.0E-10. Altrock et al., 2003 had previously demonstrated that mutant mice expressing a form of Bsn lacking the central exons critical for anchoring Bsn to the cytomatrix at the presynaptic active zone displayed a reduction in normal synaptic transmission that was attributable to inactivation of a significant fraction of glutamatergic synapses, an inability of vesicles at these synapses to fuse, and spontaneous epileptic seizures. More recently, Guzman et al., 2025 described 14 individuals with potentially disruptive de novo variants in the BSN gene and identified 15 additional individuals with protein-truncating variants (PTVs) from large biobanks; clinical features were standardized using the Human Phenotype Ontology (HPO) across all 29 individuals, which revealed common clinical characteristics including epilepsy (13/29, 45%), behavioral phenotypes (14/29, 48%) including ADHD (7/29, 25%) and autistic behavior (5/29, 17%), developmental delay (11/29, 38%), obesity (10/29, 34%), and delayed speech (8/29, 28%).

Molecular Function

Neurotransmitters are released from a specific site in the axon terminal called the active zone, which is composed of synaptic vesicles and a meshwork of cytoskeleton underlying the plasma membrane. The protein encoded by this gene is thought to be a scaffolding protein involved in organizing the presynaptic cytoskeleton. The gene is expressed primarily in neurons in the brain. A similar gene product in rodents is concentrated in the active zone of axon terminals and tightly associated with cytoskeletal structures, and is essential for regulating neurotransmitter release from a subset of synapses.

SFARI Genomic Platforms
Reports related to BSN (12 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support - Wilko D Altrock et al. (2003) No -
2 Support Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
3 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
4 Support Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes Feliciano P et al. (2019) Yes -
5 Support Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
6 Positive association - Line Skotte et al. (2022) No -
7 Support - Zhou X et al. (2022) Yes -
8 Support - Fu JM et al. (2022) Yes -
9 Support - Trost B et al. (2022) Yes -
10 Support - Tingting Ye et al. (2023) No -
11 Primary - Sawako Furukawa et al. (2025) Yes -
12 Support - Stacy G Guzman et al. (2025) No ASD or autistic behavior, ADHD, ODD, ID, learning
Rare Variants   (39)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.10615G>C p.Asp3539His missense_variant De novo - - 35982160 Fu JM et al. (2022)
c.11479A>C p.Thr3827Pro missense_variant De novo - - 35982160 Fu JM et al. (2022)
c.3322G>T p.Glu1108Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.6684C>A p.Tyr2228Ter stop_gained Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.7126G>T p.Glu2376Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.7351C>T p.Gln2451Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.7801C>T p.Arg2601Ter stop_gained Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.7916C>G p.Ser2639Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.8095G>T p.Glu2699Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.8614C>T p.Gln2872Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.8614C>T p.Gln2872Ter stop_gained Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.9988C>T p.Arg3330Ter stop_gained Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.10255C>T p.Gln3419Ter stop_gained De novo - - 40393460 Stacy G Guzman et al. (2025)
c.1986+1G>A p.? splice_site_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.620C>A p.Pro207His missense_variant De novo - - 40393460 Stacy G Guzman et al. (2025)
c.7882C>T p.Arg2628Cys missense_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.7804C>T p.Arg2602Cys missense_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.8980C>T p.Arg2994Trp missense_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.5919A>G p.Pro1973= synonymous_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.5869G>A p.Ala1957Thr missense_variant De novo - - 40393460 Stacy G Guzman et al. (2025)
c.9499C>A p.Pro3167Thr missense_variant De novo - - 40393460 Stacy G Guzman et al. (2025)
c.10436C>T p.Ala3479Val missense_variant De novo - Unknown 35982159 Zhou X et al. (2022)
c.4838C>T p.Pro1613Leu missense_variant De novo - Simplex 36368308 Trost B et al. (2022)
c.11249G>A p.Arg3750Gln missense_variant De novo - - 31981491 Satterstrom FK et al. (2020)
c.6263dupC p.Ala2088fs frameshift_variant De novo - Unknown 36368308 Trost B et al. (2022)
c.1027C>T p.Gln343Ter stop_gained Familial Paternal - 40393460 Stacy G Guzman et al. (2025)
c.2301G>A p.Thr767= synonymous_variant De novo - Multiplex 28263302 C Yuen RK et al. (2017)
c.4257T>C p.Tyr1419= synonymous_variant De novo - Simplex 31452935 Feliciano P et al. (2019)
c.81delC p.Gly28AlafsTer104 frameshift_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.867dupG p.Pro290AlafsTer27 frameshift_variant De novo - - 40393460 Stacy G Guzman et al. (2025)
c.1602delC p.Thr535ProfsTer7 frameshift_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.4138delA p.Thr1380ProfsTer19 frameshift_variant De novo - - 40393460 Stacy G Guzman et al. (2025)
c.5840delC p.Pro1947LeufsTer73 frameshift_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.2613_2621del p.His872ProfsTer10 frameshift_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.9707_9708delAC p.Ile3237GlnfsTer2 frameshift_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.8628_8629delinsA p.Leu2877TrpfsTer17 frameshift_variant Unknown - - 40393460 Stacy G Guzman et al. (2025)
c.8158_8162delACGGA p.Thr2720AlafsTer38 frameshift_variant De novo - - 40393460 Stacy G Guzman et al. (2025)
c.4971dupC p.Arg1659GlnfsTer23 frameshift_variant De novo - Simplex 39610113 Sawako Furukawa et al. (2025)
c.3001_3006delinsCCCTT p.Ser1001ProfsTer16 frameshift_variant Familial Paternal - 40393460 Stacy G Guzman et al. (2025)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

4/1/2025
3

Initial score established: 3

Krishnan Probability Score

Score 0.64568764715992

Ranking 43/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.99999999207718

Ranking 133/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.94988926143554

Ranking 18273/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score 0.56800886936304

Ranking 184/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
Submit New Gene

Report an Error