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Relevance to Autism

Rare nonsynonymous variants in the EFR3A gene were found to be more common among cases (16/2196; 0.73%) than matched controls (12/3389; 0.35%), and were statistically more common at conserved nucleotides based on an experiment-wide significance threshold (P=0.0077, permutation test); variants likely to be deleterious were also statistically more common in cases than controls (P=0.017, Fisher exact test) (Gupta et al., 2014).

Molecular Function

This gene encodes a membrane protein that is a component of a protein complex required for PtdIns4P synthesis. Studies with orthologous gene in mouse show that it is differentially expressed in the auditory brainstem neurons of mice with hearing deficit, compared to mice with normal hearing ability, suggesting a role for this gene in hearing.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Rare deleterious mutations of the gene EFR3A in autism spectrum disorders.
ASD
Support
Genome-wide characteristics of de novo mutations in autism
ASD
Support
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD
Support
De novo mutations revealed by whole-exome sequencing are strongly associated with autism.
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior.
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN613R001 
 missense_variant 
 c.1013T>C 
 p.Phe338Ser 
 De novo 
  
 Simplex 
 GEN613R002 
 missense_variant 
 c.208C>T 
 p.Arg70Cys 
 Familial 
 Paternal 
 Simplex 
 GEN613R003 
 missense_variant 
 c.353T>C 
 p.Leu118Pro 
 Familial 
 Paternal 
 Simplex 
 GEN613R004 
 missense_variant 
 c.728G>C 
 p.Gly243Ala 
 Familial 
 Maternal 
 Simplex 
 GEN613R005 
 missense_variant 
 c.1601T>C 
 p.Ile534Thr 
 Familial 
 Maternal 
 Simplex 
 GEN613R006 
 inframe_insertion 
 c.1621_1622insATT 
 p.Ala541delinsAspSer 
 Familial 
 Maternal 
 Simplex 
 GEN613R007 
 missense_variant 
 c.2353A>G 
 p.Thr785Ala 
 Familial 
 Maternal 
 Simplex 
 GEN613R008 
 missense_variant 
 c.367T>C 
 p.Phe123Leu 
 Familial 
 Maternal 
 Simplex 
 GEN613R009 
 frameshift_variant 
 c.538_539insTCGCATA 
 p.Gly180ValfsTer3 
 Familial 
 Maternal 
 Simplex 
 GEN613R010 
 missense_variant 
 c.148A>G 
 p.Lys50Glu 
 Unknown 
  
 Unknown 
 GEN613R011 
 missense_variant 
 c.961G>T 
 p.Ala321Ser 
 Unknown 
  
 Unknown 
 GEN613R012 
 missense_variant 
 c.1009G>C 
 p.Val337Leu 
 Unknown 
  
 Unknown 
 GEN613R013 
 missense_variant 
 c.1511A>G 
 p.Asp504Gly 
 Unknown 
  
 Unknown 
 GEN613R014 
 missense_variant 
 c.1523T>C 
 p.Leu508Pro 
 Unknown 
  
 Unknown 
 GEN613R015 
 missense_variant 
 c.1528A>G 
 p.Ile510Val 
 Unknown 
  
 Unknown 
 GEN613R016 
 missense_variant 
 c.1583A>G 
 p.Gln528Arg 
 Unknown 
  
 Unknown 
 GEN613R017 
 missense_variant 
 c.1828A>G 
 p.Met610Val 
 Unknown 
  
 Unknown 
 GEN613R018 
 missense_variant 
 c.44G>A 
 p.Arg15His 
 De novo 
  
 Simplex 
 GEN613R019 
 upstream_gene_variant 
  
  
 De novo 
  
 Simplex 
 GEN613R020 
 intergenic_variant 
 delTAAA 
  
  
  
 Unknown 
 GEN613R021 
 missense_variant 
 c.1750A>G 
 p.Ile584Val 
 Unknown 
  
  
 GEN613R022 
 missense_variant 
 c.2432A>G 
 p.Tyr811Cys 
 De novo 
  
  
 GEN613R023 
 missense_variant 
 c.929T>C 
 p.Val310Ala 
 De novo 
  
 Simplex 
 GEN613R024 
 frameshift_variant 
 c.3del 
 p.Met1? 
 Familial 
 Paternal 
 Multiplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
8
Duplication
 1
 
8
Duplication
 1
 
8
Duplication
 3
 
8
Duplication
 3
 
8
Deletion
 2
 
8
Deletion
 1
 
8
Duplication
 2
 
8
Deletion-Duplication
 8
 

No Animal Model Data Available

 

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