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Relevance to Autism

A two-stage analysis of rare de novo and inherited coding variants in 42,607 ASD cases, including 35,130 new cases from the SPARK cohort, in Zhou et al., 2022 identified SCAF1 as a gene reaching exome-wide significance (P < 2.5E-06); association of SCAF1 with ASD risk was driven by both de novo variants and rare loss-of-function variants. Wilfert et al., 2021 identified two ultra-rare inherited frameshift variants in SCAF1 that were exclusively transmitted to ASD probands from two independent families.

Molecular Function

Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Integrating de novo and inherited variants in 42
ASD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Recent ultra-rare inherited variants implicate new autism candidate risk genes
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1349R001 
 stop_gained 
 c.2185G>T 
 p.Glu729Ter 
 De novo 
  
  
 GEN1349R002 
 missense_variant 
 c.2282C>T 
 p.Ser761Phe 
 De novo 
  
 Simplex 
 GEN1349R003 
 missense_variant 
 c.3817C>T 
 p.Arg1273Cys 
 De novo 
  
 Simplex 
 GEN1349R004 
 missense_variant 
 c.2516T>C 
 p.Val839Ala 
 De novo 
  
 Simplex 
 GEN1349R005 
 missense_variant 
 c.2995T>A 
 p.Cys999Ser 
 De novo 
  
 Simplex 
 GEN1349R006 
 missense_variant 
 c.2969C>T 
 p.Pro990Leu 
 De novo 
  
  
 GEN1349R007 
 splice_site_variant 
 c.3361C>T 
 p.Arg1121Ter 
 De novo 
  
  
 GEN1349R008 
 splice_site_variant 
 c.166+1G>A 
  
 Familial 
  
 Multiplex 
 GEN1349R009 
 frameshift_variant 
 c.3540dup 
 p.Thr1181HisfsTer10 
 Familial 
  
 Multiplex 
 GEN1349R010 
 frameshift_variant 
 c.1787dup 
 p.Ser597GlnfsTer56 
 Familial 
 Maternal 
  
 GEN1349R011 
 frameshift_variant 
 c.2863_2866del 
 p.Gly955ProfsTer151 
 Familial 
 Maternal 
  
 GEN1349R012 
 frameshift_variant 
 c.1196del 
 p.Pro399ArgfsTer65 
 Familial 
 Paternal 
  
 GEN1349R013 
 frameshift_variant 
 c.2966del 
 p.Thr989IlefsTer118 
 Unknown 
 Not maternal 
  
 GEN1349R014 
 frameshift_variant 
 c.1234_1256del 
 p.Pro412TyrfsTer233 
 Unknown 
 Not maternal 
  
 GEN1349R015 
 frameshift_variant 
 c.3540dup 
 p.Thr1181HisfsTer10 
 Unknown 
 Not maternal 
  
 GEN1349R016 
 frameshift_variant 
 c.1496_1511dup 
 p.Pro505LeufsTer153 
 Unknown 
  
  
 GEN1349R017 
 frameshift_variant 
 c.3052del 
 p.Arg1018GlufsTer89 
 Unknown 
  
  
 GEN1349R018 
 frameshift_variant 
 c.2301del 
 p.Ser768LeufsTer64 
 Unknown 
  
  
 GEN1349R019 
 stop_gained 
 c.3717C>G 
 p.Tyr1239Ter 
 Unknown 
  
  
 GEN1349R020 
 frameshift_variant 
 c.3139dup 
 p.Ala1047GlyfsTer21 
 Unknown 
  
  
 GEN1349R021 
 frameshift_variant 
 c.240_241del 
 p.Gly82HisfsTer2 
 Unknown 
  
  
 GEN1349R022 
 stop_gained 
 c.874C>T 
 p.Gln292Ter 
 Unknown 
  
  
 GEN1349R023 
 frameshift_variant 
 c.3571_3572del 
 p.Lys1191GlufsTer8 
 Unknown 
  
  
 GEN1349R024 
 frameshift_variant 
 c.1787dup 
 p.Ser597GlnfsTer56 
 Familial 
  
 Simplex 
 GEN1349R025 
 frameshift_variant 
 c.2863_2866del 
 p.Gly955ProfsTer151 
 Familial 
  
 Simplex 
 GEN1349R026 
 missense_variant 
 c.2003C>T 
 p.Pro668Leu 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
19
Duplication
 1
 
19
Deletion-Duplication
 19
 
19
Deletion-Duplication
 4
 

No Animal Model Data Available

 

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