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Relevance to Autism

De novo variants in the CTR9 gene have been identified in ASD probands, including a rare and potentially deleterious de novo missense variant in a proband from the Autism Sequencing Consortium (De Rubeis et al., 2014; Sanders et al., 2015; Yuen et al., 2017; Turner et al., 2017). Additional de novo variants in this gene have been identified in probands with intellectual disability in Lelieveld et al., 2016, probands from the 2017 Deciphering Developmental Disorders study, and an NDD proband in Hamanaka et al., 2022. Moreover, Hamanaka et al., 2022 classified CTR9 as a high-confidence candidate gene for neurodevelopmental disorders following gene-based enrichment of de novo deleterious SNVs and CNVs in 41,165 novel and previously reported cases and subsequent prioritization based on its similarity to known NDD genes using a deep learning model. Meuwissen et al., 2022 described the clinical and molcular profiles of 13 probands harboring likely pathogenic CTR9 missense variants who presented with a neurodevelopmental disorder characterized by variable degrees of intellectual disability, hypotonia, joint hyperlaxity, speech delay, coordination problems, tremor, and autism spectrum disorder.

Molecular Function

The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD
Support
Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability
ID
Support
Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants
NDD
Support
Genomic Patterns of De Novo Mutation in Simplex Autism
ASD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Prevalence and architecture of de novo mutations in developmental disorders
Developmental disorders
Recent Recommendation
Heterozygous variants in CTR9
DD, ID
ASD, ADHD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1334R001 
 missense_variant 
 c.2488C>T 
 p.Arg830Trp 
 De novo 
  
  
 GEN1334R002 
 5_prime_UTR_variant 
 c.-32_-31dup 
  
 De novo 
  
  
 GEN1334R003 
 5_prime_UTR_variant 
 c.-32_-31dup 
  
 De novo 
  
  
 GEN1334R004 
 intron_variant 
 c.1598-469_1598-468insAGAGACATTTCCTAGTGC 
  
 De novo 
  
 Multiplex 
 GEN1334R005 
 intron_variant 
 c.144+848G>A 
  
 De novo 
  
 Multiplex 
 GEN1334R006 
 intron_variant 
 c.2508+170G>A 
  
 De novo 
  
 Simplex 
 GEN1334R007 
 intron_variant 
 c.45+112T>G 
  
 De novo 
  
 Simplex 
 GEN1334R008 
 inframe_insertion 
 c.86delinsTCAT 
 p.Glu29delinsValIle 
 De novo 
  
 Simplex 
 GEN1334R009 
 missense_variant 
 c.1405G>A 
 p.Glu469Lys 
 De novo 
  
 Simplex 
 GEN1334R010 
 missense_variant 
 c.2515C>T 
 p.Arg839Trp 
 De novo 
  
 Simplex 
 GEN1334R011 
 splice_site_variant 
 c.46-2A>C 
  
 De novo 
  
 Simplex 
 GEN1334R012 
 missense_variant 
 c.74C>G 
 p.Pro25Arg 
 De novo 
  
 Simplex 
 GEN1334R013 
 missense_variant 
 c.43G>A 
 p.Glu15Lys 
 De novo 
  
 Simplex 
 GEN1334R014 
 missense_variant 
 c.109G>C 
 p.Glu37Gln 
 De novo 
  
 Simplex 
 GEN1334R015 
 missense_variant 
 c.50T>C 
 p.Ile17Thr 
 Familial 
 Paternal 
  
 GEN1334R016 
 missense_variant 
 c.1405G>A 
 p.Glu469Lys 
 De novo 
  
 Simplex 
 GEN1334R017 
 missense_variant 
 c.254G>A 
 p.Cys85Tyr 
 De novo 
  
 Simplex 
 GEN1334R018 
 missense_variant 
 c.76G>C 
 p.Glu26Gln 
 De novo 
  
 Simplex 
 GEN1334R019 
 missense_variant 
 c.1126G>A 
 p.Glu376Lys 
 De novo 
  
 Simplex 
 GEN1334R020 
 missense_variant 
 c.1126G>A 
 p.Glu376Lys 
 De novo 
  
 Simplex 
 GEN1334R021 
 missense_variant 
 c.1364A>G 
 p.Asn455Ser 
 De novo 
  
 Simplex 
 GEN1334R022 
 missense_variant 
 c.2296A>G 
 p.Thr766Ala 
 Unknown 
 Not maternal 
  
 GEN1334R023 
 missense_variant 
 c.74C>G 
 p.Pro25Arg 
 De novo 
  
 Simplex 
 GEN1334R024 
 missense_variant 
 c.2633G>A 
 p.Arg878Gln 
 De novo 
  
 Simplex 
 GEN1334R025 
 missense_variant 
 c.1126G>A 
 p.Glu376Lys 
 De novo 
  
 Simplex 
 GEN1334R026 
 initiator_codon_variant 
 c.1A>T 
 p.Met1? 
 De novo 
  
 Multiplex 
 GEN1334R027 
 splice_region_variant 
 c.1687-7G>T 
  
 De novo 
  
 Simplex 
 GEN1334R028 
 missense_variant 
 c.2273C>T 
 p.Ala758Val 
 De novo 
  
 Simplex 
 GEN1334R029 
 frameshift_variant 
 c.1557_1558del 
 p.Tyr520Ter 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
11
Duplication
 1
 

No Animal Model Data Available

 

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