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Relevance to Autism

Musante et al., 2026 collected clinical and molecular information from 24 unrelated individuals with mostly heterozygous missense variants in the SF3B3 gene exhibiting a congruent phenotype including autism spectrum disorder, developmental delay, intellectual disability, language and motor delay, multiple congenital anomalies, and distinctive craniofacial features confirmed by GestaltMatcher analysis; three of the individuals included in this report were ASD probands from the Simons Simplex Collection and the SPARK cohort previously reported in Satterstrom et al., 2020, Zhou et al., 2022, and Trost et al., 2022. Additional functional assessment of fibroblasts from a subset of individuals with SF3B3 missense variants in Musante et al., 2026 identified reduced SF3B3 protein levels, differential gene expression, increased alternative splicing events, and cell-cycle abnormalities compared to controls.

Molecular Function

This gene encodes subunit 3 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence independent manner and may anchor the U2 snRNP to the pre-mRNA. Splicing factor 3b is also a component of the minor U12-type spliceosome. Subunit 3 has also been identified as a component of the STAGA (SPT3-TAF(II)31-GCN5L acetylase) transcription coactivator-HAT (histone acetyltransferase) complex, and the TFTC (TATA-binding-protein-free TAF(II)-containing complex). These complexes may function in chromatin modification, transcription, splicing, and DNA repair.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
A novel spliceosomopathy caused by de novo SF3B3 variants
ASD or autistic features, DD/ID
Epilepsy/seizures
Support
Genomic architecture of autism from comprehensive whole-genome sequence annotation
ASD
Support
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Recent ultra-rare inherited variants implicate new autism candidate risk genes
ASD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1536R001 
 missense_variant 
 c.2066C>T 
 p.Thr689Ile 
 De novo 
  
 Simplex 
 GEN1536R002 
 missense_variant 
 c.2183G>C 
 p.Arg728Pro 
 De novo 
  
 Simplex 
 GEN1536R003 
 missense_variant 
 c.2012A>G 
 p.Asn671Ser 
 De novo 
  
 Simplex 
 GEN1536R004 
 missense_variant 
 c.1922G>A 
 p.Cys641Tyr 
 De novo 
  
 Simplex 
 GEN1536R005 
 missense_variant 
 c.656A>C 
 p.His219Pro 
 De novo 
  
 Simplex 
 GEN1536R006 
 missense_variant 
 c.647G>A 
 p.Gly216Asp 
 De novo 
  
 Simplex 
 GEN1536R007 
 missense_variant 
 c.1480G>A 
 p.Val494Met 
 De novo 
  
 Simplex 
 GEN1536R008 
 missense_variant 
 c.3224C>A 
 p.Ala1075Asp 
 De novo 
  
 Simplex 
 GEN1536R009 
 missense_variant 
 c.452G>A 
 p.Arg151Gln 
 De novo 
  
 Simplex 
 GEN1536R010 
 missense_variant 
 c.1349C>T 
 p.Ser450Phe 
 De novo 
  
 Simplex 
 GEN1536R011 
 missense_variant 
 c.914C>T 
 p.Thr305Ile 
 De novo 
  
 Simplex 
 GEN1536R012 
 frameshift_variant 
 c.2364dupT 
 p.Val789CysfsTer5 
 De novo 
  
 Simplex 
 GEN1536R013 
 missense_variant 
 c.2066C>T 
 p.Thr689Ile 
 De novo 
  
 Simplex 
 GEN1536R014 
 missense_variant 
 c.2506G>A 
 p.Ala836Thr 
 De novo 
  
 Simplex 
 GEN1536R015 
 missense_variant 
 c.376A>G 
 p.Lys126Glu 
 De novo 
  
 Simplex 
 GEN1536R016 
 missense_variant 
 c.2066C>T 
 p.Thr689Ile 
 De novo 
  
 Simplex 
 GEN1536R017 
 inframe_deletion 
 c.1762_1764del 
 p.Val588del 
 De novo 
  
 Simplex 
 GEN1536R018 
 missense_variant 
 c.637C>A 
 p.Leu213Ile 
 De novo 
  
 Simplex 
 GEN1536R019 
 frameshift_variant 
 c.1242_1243insCTGGC 
 p.Asn417TrpfsTer21 
 De novo 
  
 Simplex 
 GEN1536R020 
 stop_gained 
 c.1390C>T 
 p.Arg464Ter 
 Unknown 
 Not maternal 
 Simplex 
 GEN1536R021 
 missense_variant 
 c.1574G>A 
 p.Arg525Gln 
 De novo 
  
 Simplex 
 GEN1536R022 
 missense_variant 
 c.1205A>C 
 p.Asp402Ala 
 De novo 
  
 Simplex 
 GEN1536R023 
 synonymous_variant 
 c.3579C>T 
 p.Val1193= 
 De novo 
  
  
 GEN1536R024 
 missense_variant 
 c.88A>G 
 p.Ile30Val 
 De novo 
  
 Multiplex 
 GEN1536R025 
 missense_variant 
 c.2384A>G 
 p.Asn795Ser 
 De novo 
  
 Simplex 
 GEN1536R026 
 splice_region_variant 
 c.2669+3_2669+5dup 
  
 De novo 
  
  
 GEN1536R027 
 frameshift_variant 
 c.996_1000del 
 p.Val333ArgfsTer9 
 Familial 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
16
Duplication
 1
 
16
Deletion
 4
 
16
Duplication
 2
 
16
Duplication
 1
 
16
Deletion-Duplication
 23
 
16
Deletion
 3
 
16
Duplication
 4
 
16
Deletion
 2
 
16
Duplication
 2
 

No Animal Model Data Available

 

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