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Relevance to Autism

Yamada et al., 2023 demonstrated that two de novo missense variants in the DHX9 gene (a p.Arg1052Gln variant that was previously reported in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2014, and a p.Gly414Arg variant that was identified in a novel patient presenting with developmental delay/intellectual disability, undergrowth, and ventricular non-compaction cardiomyopathy) resulted in aberrant localization and loss-of-function effects in transgenic Drosophila lines. In the same report, the authors also found that mice heterozygous for a p.Gly416Arg variant, which corresponded to the p.Gly414Arg variant, displayed reduced body weight, reduced emotionality, and cardiac conduction abnormalities (prolonged PR interval). Additional de novo variants in the DHX9 gene, including a de novo loss-of-function variant, have been identified in ASD probands from simplex families from the MSSNG cohort (Zhou et al., 2022), while a paternally-inherited DHX9 missense variant with a CADD score of 31 was identified in a Chinese ASD proband from the ACGC cohort (Guo et al., 2018). Calame et al., 2023 described 20 individuals with rare monoallelic DHX9 variants presenting with either a neurodevelopmental disorder characterized by developmental delay/intellectual disability, neuropsychiatric disorders (including autism spectrum disorder), seizures, axial hypotonia, and dysmorphic features, or Charcot-Marie-Tooth disease; subsequent functional studies demonstrated that DHX9 variants disrupted cellular localization and helicase activity and increased R-loops and double-stranded DNA breaks, while a Dhx9 -/- mice was shown to exhibit behavioral and neurological abnormalities in this report.

Molecular Function

This gene encodes a member of the DEAH-containing family of RNA helicases. The encoded protein is an enzyme that catalyzes the ATP-dependent unwinding of double-stranded RNA and DNA-RNA complexes. This protein localizes to both the nucleus and the cytoplasm and functions as a transcriptional regulator. This protein may also be involved in the expression and nuclear export of retroviral RNAs. Alternate splicing results in multiple transcript variants.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
ASD, DD, ID
Support
Integrating de novo and inherited variants in 42
ASD
Support
Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model.
ASD
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Recent Recommendation
DD, ID
ASD, epilepsy/seizures, Charcot-Marie-Tooth diseas

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1405R001 
 missense_variant 
 c.3155G>A 
 p.Arg1052Gln 
 De novo 
  
 Simplex 
 GEN1405R002 
 frameshift_variant 
 c.157_158insT 
 p.Asn53IlefsTer2 
 De novo 
  
 Simplex 
 GEN1405R003 
 missense_variant 
 c.359A>G 
 p.Lys120Arg 
 De novo 
  
 Simplex 
 GEN1405R004 
 synonymous_variant 
 c.3417T>C 
 p.Ser1139%3D 
 De novo 
  
 Simplex 
 GEN1405R005 
 missense_variant 
 c.2746G>A 
 p.Val916Ile 
 Familial 
 Paternal 
  
 GEN1405R006 
 missense_variant 
 c.1240G>A 
 p.Gly414Arg 
 De novo 
  
 Simplex 
 GEN1405R007 
 missense_variant 
 c.422G>A 
 p.Arg141Gln 
 De novo 
  
 Simplex 
 GEN1405R008 
 missense_variant 
 c.1822T>G 
 p.Cys608Gly 
 De novo 
  
 Simplex 
 GEN1405R009 
 missense_variant 
 c.3497G>C 
 p.Arg1166Pro 
 De novo 
  
 Simplex 
 GEN1405R010 
 splice_region_variant 
 c.627-4dup 
  
 De novo 
  
 Simplex 
 GEN1405R011 
 missense_variant 
 c.1417G>A 
 p.Val473Ile 
 De novo 
  
 Simplex 
 GEN1405R012 
 missense_variant 
 c.3488A>G 
 p.Lys1163Arg 
 De novo 
  
 Simplex 
 GEN1405R013 
 splice_site_variant 
 c.2786+1G>T 
  
 Unknown 
  
 Simplex 
 GEN1405R014 
 stop_gained 
 c.685C>T 
 p.Arg229Ter 
 De novo 
  
 Simplex 
 GEN1405R015 
 missense_variant 
 c.1232G>A 
 p.Gly411Glu 
 De novo 
  
 Simplex 
 GEN1405R016 
 frameshift_variant 
 c.2078_2079del 
 p.Glu693GlyfsTer7 
 De novo 
  
 Simplex 
 GEN1405R017 
 missense_variant 
 c.2282G>A 
 p.Arg761Gln 
 De novo 
  
 Simplex 
 GEN1405R018 
 missense_variant 
 c.3497G>C 
 p.Arg1166Pro 
 De novo 
  
 Simplex 
 GEN1405R019 
 missense_variant 
 c.2281C>T 
 p.Arg761Trp 
 De novo 
  
 Simplex 
 GEN1405R020 
 stop_gained 
 c.3787C>T 
 p.Gln1263Ter 
 Unknown 
  
 Simplex 
 GEN1405R021 
 splice_site_variant 
 c.674-1G>A 
  
 Unknown 
  
 Unknown 
 GEN1405R022 
 stop_gained 
 c.2290C>T 
 p.Arg764Ter 
 Unknown 
  
 Multiplex 
 GEN1405R023 
 missense_variant 
 c.2537A>G 
 p.Asp846Gly 
 De novo 
  
 Simplex 
 GEN1405R024 
 missense_variant 
 c.2510G>C 
 p.Arg837Thr 
 Unknown 
  
 Simplex 
 GEN1405R025 
 missense_variant 
 c.3763G>A 
 p.Ala1255Thr 
 Unknown 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
1
Duplication
 44
 
1
Deletion
 2
 
1
Deletion
 2
 
1
Deletion
 1
 
1
Deletion-Duplication
 18
 
1
Deletion
 3
 

Model Summary

Variation in DHX genes, including DHX9, has been linked to neurodevelopmental disorders including autism spectrum disorder (ASD). The homozygous knockout model shows no change in viability but exhibits decreased body weight compared to sex-matched wildtypes. The model also shows altered behavioral and neurological function. Male and female model mice show decreased locomotion, with a decrease in distance traveled in the periphery of the open field and a decrease in locomotor speed. Additionally, model male and female mice demonstrate decreased grip strength, increased tremor, and decreased auditory functioning, as measured by the auditory brainstem response test. Furthermore, the model shows altered metabolic function, with possible altered renal function, decreased glucose clearance, and decreased cholesterol levels.

References

Type
Title
Author, Year

M_DHX9_1_KO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Mice were generated by allele conversion of the C57BL/6NCrl-Dhx9^Tm1a (EUCOMM) Hmgu mouse line. The tm1b allele (MGI:6472605) was produced by deletion of exon 4 of Dhx9 and the neomycin cassette by a cell-permeable Cre recombinase. The allele is a knockout given that skipping over of the LacZ cassette does not produce a functional protein. The cassette produces LacZ under the control of the Dhx9 promoter as a fusion protein with exon 3.
Allele Type: Knockout
Strain of Origin: C57BL/6N-A
Genetic Background: C57BL/6NCrl
ES Cell Line: JM8A1.N3
Mutant ES Cell Line:
Model Source: Helmholtz Zentrum Muenchen GmbH

M_DHX9_1_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Grip strength1
Decreased
Description: Dhx9 mutant male and female mice exhibited decreased 2-paw and 4-paw grip strength, as measured by mean force (grams).
 Grip strength test
 9 weeks
Tremor1
Increased
Description: 20% of Dhx9 mutant mice (3 of 15 mutants, 2 of 6 males, and 1 of 9 females) showed tremors in SHIRPA analysis, compared to 0% of wildtype controls.
Exp Paradigm: SHIRPA analysis
 Tremor activity measurements
 9 weeks
Rearing behavior1
Increased
Description: Dhx9 mutant mice exhibited an increase in rearing activity during the active dark period of the light/dark cycle in a familiar home cage environment,
Exp Paradigm: dark period of the light/dark cycle
 Home cage behavior
 11 weeks
Hyperactivity1
Decreased
Description: Dhx9 mutant male and female mice exhibited a decrease in the distance traveled in the periphery of the open field and a decrease in locomotor speed.
 Open field test
 8 weeks
Startle response: acoustic stimulus1
Decreased
Description: Dhx9 male and female mutant mice exhibited a decreased startle response compared to wildtype controls.
 Acoustic startle reflex test
 10 weeks
Hearing1
Decreased
Description: Dhx9 male and female mutant mice exhibited deafness, as evidenced by absent hearing curves in ABR analysis.
 Auditory brainstem response test
 14 weeks
Satiety response1
Decreased
Description: Dhx9 mutant male and female mice exhibited reduced food intake and more weight loss compared to wildtype controls in a 21 hour period after transfer to a new home cage.
 Food intake measurements
 11 weeks
Renal function1
Decreased
Description: Dhx9 mutant female mice showed increased creatinine and urea levels, suggesting possible altered renal function.
 Urine/blood electrolyte analysis
 16 weeks
Metabolic function1
Decreased
Description: Dhx9 male mutant mice exhibited impaired glucose clearance in the ipGTT, as measured by blood glucose concentration.
 Glucose tolerance test
 13 weeks
Serum lipid levels1
Decreased
Description: Dhx9 mutant male and female mice exhibited decreased cholesterol levels compared to wildtype controls.
 Measurement of blood lipids
 16 weeks
Glucose levels1
Decreased
Description: Dhx9 mutant male and female mice exhibited decreased ad libitum fed glucose.
 Measurement of blood glucose
 13 weeks
Size/growth1
Decreased
Description: Dhx9 mutant male and female mice exhibited decreased body weight compared to wildtype controls.
 Body weight measurement
 11 weeks
Exploratory activity1
Decreased
Description: Dhx9 mutant mice exhibited decreased rearing behavior in response to a novel home cage.
Exp Paradigm: novel home cage
 Novel cage test
 11 weeks
Cell differentiation: hematopoiesis1
Abnormal
Description: Dhx9 mutant male and female mice exhibited mild hypochromic microcytosis of erythrocytes, as indexed by increased red blood cell counts, decreased mean corpuscular volume (MCV), and decreased mean corpuscular hemoglobin (MCH). Moreover, lowered platelet counts in males were associated with higher mean platelet volumes and increased anisocytosis of platelets.
 Hematological analysis
 16 weeks
Mortality/lethality1
 No change
 General observations
 P0
 Not Reported:

 

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