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Relevance to Autism

Krall et al., 2019 reported five individuals, including two sib pairs, with biallelic variants in the INTS1 gene who presented with absent or severely limited speech, abnormal gait, hypotonia, cataracts, and dysmorphic features; three of these individuals were diagnosed with ASD, while a fourth individual presented with autistic features. Oegema et al., 2017 had previously described three unrelated individuals with the same homozygous truncating variant in the INTS1 gene who presented with similar features.

Molecular Function

INTS1 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1) and U2 (RNU2).

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies.
DD
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
ASD
Support
ID
Support
Contribution of rare and common variants to intellectual disability in a sub-isolate of Northern Finland.
ID
Support
Human mutations in integrator complex subunits link transcriptome integrity to brain development.
DD
Epilepsy/seizures

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1056R001a 
 missense_variant 
 c.229C>T 
 p.Arg77Cys 
 Familial 
  
 Multiplex 
 GEN1056R001b 
 frameshift_variant 
 c.5398dup 
 p.Arg1800ProfsTer20 
 Familial 
  
 Multiplex 
 GEN1056R002a 
 missense_variant 
 c.5621C>T 
 p.Pro1874Leu 
 Familial 
 Both parents 
 Multiplex 
 GEN1056R003a 
 frameshift_variant 
 c.5290del 
 p.Leu1764CysfsTer16 
 Familial 
  
 Simplex 
 GEN1056R003b 
 missense_variant 
 c.6491T>C 
 p.Leu2164Pro 
 Familial 
  
 Simplex 
 GEN1056R004a 
 stop_gained 
 c.5351C>A 
 p.Ser1784Ter 
 Familial 
 Both parents 
 Simplex 
 GEN1056R005a 
 stop_gained 
 c.5351C>A 
 p.Ser1784Ter 
 Familial 
 Both parents 
 Simplex 
 GEN1056R006a 
 stop_gained 
 c.5351C>A 
 p.Ser1784Ter 
 Familial 
 Both parents 
 Simplex 
 GEN1056R007a 
 missense_variant 
 c.3950A>G 
 p.Asp1317Gly 
 Familial 
 Both parents 
 Unknown 
 GEN1056R008 
 frameshift_variant 
 c.618_619del 
 p.Leu207GlyfsTer3 
 Familial 
 Maternal 
 Multiplex 
 GEN1056R009 
 missense_variant 
 c.6299G>A 
 p.Arg2100His 
 Unknown 
  
  
 GEN1056R010 
 synonymous_variant 
 c.2055C>A 
 p.Ala685%3D 
 Unknown 
  
  
 GEN1056R011 
 missense_variant 
 c.5494G>A 
 p.Val1832Ile 
 Unknown 
  
  
 GEN1056R012 
 splice_site_variant 
 c.*109G>C 
  
 De novo 
  
  
 GEN1056R013 
 missense_variant 
 c.4970G>A 
 p.Arg1657His 
 De novo 
  
  
 GEN1056R014 
 splice_region_variant 
 c.3921G>A 
 p.Leu1307%3D 
 De novo 
  
  
 GEN1056R015 
 missense_variant 
 c.575C>T 
 p.Ala192Val 
 De novo 
  
  
 GEN1056R016 
 frameshift_variant 
 c.482del 
 p.Tyr161SerfsTer2 
 De novo 
  
  
 GEN1056R017 
 synonymous_variant 
 c.*150C>T 
  
 De novo 
  
  
 GEN1056R018 
 missense_variant 
 c.6089C>T 
 p.Ser2030Phe 
 De novo 
  
  
 GEN1056R019 
 synonymous_variant 
 c.5910T>C 
 p.Asn1970%3D 
 De novo 
  
  
 GEN1056R020 
 missense_variant 
 c.4936A>G 
 p.Lys1646Glu 
 De novo 
  
  
 GEN1056R021 
 synonymous_variant 
 c.1188C>T 
 p.Asn396%3D 
 De novo 
  
  
 GEN1056R022 
 missense_variant 
 c.1361G>T 
 p.Arg454Leu 
 De novo 
  
 Simplex 
 GEN1056R023 
 splice_site_variant 
 c.6255+1G>T 
  
 De novo 
  
  
 GEN1056R024 
 splice_site_variant 
 c.6255+1G>T 
  
 De novo 
  
 Simplex 
 GEN1056R025 
 splice_site_variant 
 c.3429+7_3429+22del 
  
 Familial 
 Paternal 
 Multiplex 
 GEN1056R026a 
 missense_variant 
 c.3010C>T 
 p.Arg1004Trp 
 Familial 
 Both parents 
  
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
7
Deletion-Duplication
 19
 
7
Duplication
 1
 
7
Duplication
 1
 
7
Duplication
 1
 
7
Duplication
 2
 
7
Deletion-Duplication
 1
 
7
Deletion
 5
 
7
Deletion
 2
 

No Animal Model Data Available

 

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