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Relevance to Autism

A missense mutation in the KDM5C gene was detected in a nondysmorphic patient with developmental delay and autism spectrum disorder (Adegbola et al., 2008).

Molecular Function

This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
A novel mutation in JARID1C/SMCX in a patient with autism spectrum disorder (ASD).
ASD
DD
Support
Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance.
Support
Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1.
ID
Support
Autism spectrum disorder and comorbid neurodevelopmental disorders (ASD-NDDs): Clinical and genetic profile of a pediatric cohort
ASD
Epilepsy/seizures
Support
Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing.
ID
Support
Intellectual developmental disorder, X-linked synd
Support
Altered Gene-Regulatory Function of KDM5C by a Novel Mutation Associated With Autism and Intellectual Disability.
ASD, DD
Microcephaly, cognitive impairment
Support
A de novo paradigm for mental retardation.
ID
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Support
Exome sequencing in multiplex autism families suggests a major role for heterozygous truncating mutations.
ASD
Support
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: experience of two clinical units and 216 patients.
ID
Microcephaly
Support
Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype-phenotype correlation.
ID
Support
Comorbidities associated with genetic abnormalities in children with intellectual disability
ASD, DD/ID
Support
Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C.
Support
Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics.
DD
Behavioral abnormalities (stereotypic, self-injuri
Support
Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.
ID
Support
DD, epilepsy/seizures
Support
Diagnostic yield of whole-exome sequencing in non-syndromic intellectual disability
DD, ID
Epilepsy/seizures, autistic features
Support
A regulatory path associated with X-linked intellectual disability and epilepsy links KDM5C to the polyalanine expansions in ARX.
Support
Integrating de novo and inherited variants in 42
ASD
Support
Patient Mutations of the Intellectual Disability Gene KDM5C Downregulate Netrin G2 and Suppress Neurite Growth in Neuro2a Cells.
Support
Novel JARID1C/SMCX mutations in patients with X-linked mental retardation.
ID
Epilepsy
Support
DD
Support
Exploring the biological role of postzygotic and germinal de novo mutations in ASD
ASD
Support
A novel c.2T>C mutation of the KDM5C/JARID1C gene in one large family with X-linked intellectual disability.
ID
Support
Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability
ID
Support
Comprehensive molecular testing in patients with high functioning autism spectrum disorder.
ASD
Support
A novel mutation in JARID1C gene associated with mental retardation.
ID
Support
Further delineation of the female phenotype with KDM5C disease causing variants: 19 new individuals and review of the literature
DD, ID
Behavioral abnormalities
Support
A novel nonsense mutation in KDM5C/JARID1C gene causing intellectual disability, short stature and speech delay.
ID
Support
Deep phenotyping and whole-exome sequencing improved the diagnostic yield for nuclear pedigrees with neurodevelopmental disorders
ASD, ADHD, DD, ID
Support
Large-scale discovery of novel genetic causes of developmental disorders.
Cognitive impairment
Support
Claes-Jensen type of X-linked syndromic intellectu
Highly Cited
Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation.
ID
Recent Recommendation
Histone demethylase KDM5C is a SAHA-sensitive central hub at the crossroads of transcriptional axes involved in multiple neurodevelopmental disorders.
Recent Recommendation
A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation.
Recent Recommendation
Intellectual developmental disorder, X-linked synd
Recent Recommendation
Arachnoid cysts
ASD, DD, epilepsy/seizures

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN435R001 
 missense_variant 
 c.2296C>T 
 p.Arg766Trp 
 Familial 
 Maternal 
  
 GEN435R002 
 missense_variant 
 c.2191C>T 
 p.Leu731Phe 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R003 
 frameshift_variant 
 c.151-2899dup 
  
 Familial 
 Maternal 
 Multiplex 
 GEN435R004 
 missense_variant 
 c.1162G>C 
 p.Ala388Pro 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R005 
 stop_gained 
 c.2080C>T 
 p.Arg694Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN435R006 
 stop_gained 
 c.3864G>A 
 p.Trp1288Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN435R007 
 missense_variant 
 c.2092G>A 
 p.Glu698Lys 
 Unknown 
  
 Multiplex 
 GEN435R008 
 missense_variant 
 c.1204G>T 
 p.Asp402Tyr 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R009 
 missense_variant 
 c.1353C>G 
 p.Ser451Arg 
 Familial 
 Maternal 
 Multiplex 
 GEN435R010 
 stop_gained 
 c.994C>T 
 p.Arg332Ter 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R011 
 missense_variant 
 c.260A>G 
 p.Asp87Gly 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R012 
 missense_variant 
 c.1924T>C 
 p.Phe642Leu 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R013 
 missense_variant 
 c.2248C>T 
 p.Arg750Trp 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R014 
 missense_variant 
 c.2252A>G 
 p.Tyr751Cys 
 Familial 
 Maternal 
 Multiplex 
 GEN435R015 
 missense_variant 
 c.229G>A 
 p.Ala77Thr 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R016 
 missense_variant 
 c.1510G>A 
 p.Val504Met 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R017 
 splice_site_variant 
 c.1382+5G>A 
  
 Unknown 
  
 Unknown 
 GEN435R018 
 frameshift_variant 
 c.4046+289_4046+290del 
  
 Familial 
 Maternal 
 Multiplex 
 GEN435R019 
 frameshift_variant 
 c.3057dup 
 p.Lys1020GlnfsTer43 
 Familial 
 Maternal 
 Multiplex 
 GEN435R020 
 missense_variant 
 c.1160C>A 
 p.Pro554Thr 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R021 
 stop_gained 
 c.2172C>A 
 p.Cys724Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN435R022 
 initiator_codon_variant 
 c.2T>C 
 p.Met1? 
 Familial 
 Maternal 
 Multiplex 
 GEN435R023 
 synonymous_variant 
 c.1827C>T 
 p.Tyr609= 
  
  
  
 GEN435R024 
 missense_variant 
 c.1251A>C 
 p.Thr418Ala 
 Familial 
 Maternal 
 Multiplex 
 GEN435R025 
 splice_site_variant 
 c.658-1G>T 
  
 Familial 
 Maternal 
 Multiplex 
 GEN435R026 
 missense_variant 
 c.2152G>C 
 p.Ala718Pro 
 De novo 
  
 Simplex 
 GEN435R027 
 frameshift_variant 
 c.1296dup 
 p.Glu433Ter 
 Familial 
 Maternal 
 Simplex 
 GEN435R028 
 missense_variant 
 c.3357G>A 
 p.Met1119Ile 
 Unknown 
  
  
 GEN435R029 
 missense_variant 
 c.3068A>G 
 p.Lys1023Arg 
 Unknown 
  
  
 GEN435R030 
 missense_variant 
 c.1919G>A 
 p.Cys640Tyr 
 Familial 
 Maternal 
 Simplex 
 GEN435R031 
 stop_gained 
 c.2482C>T 
 p.Arg828Ter 
 Familial 
 Maternal 
 Simplex 
 GEN435R032 
 missense_variant 
 c.3344G>A 
 p.Arg1115His 
 Familial 
 Maternal 
 Simplex 
 GEN435R033 
 frameshift_variant 
 c.-172del 
  
 De novo 
  
 Simplex 
 GEN435R034 
 frameshift_variant 
 c.589dup 
 p.Leu197ProfsTer23 
 De novo 
  
 Simplex 
 GEN435R035 
 splice_site_variant 
 c.845A>G 
 p.Tyr282Cys 
 De novo 
  
 Simplex 
 GEN435R036 
 missense_variant 
 c.1866G>T 
 p.Trp622Cys 
 De novo 
  
 Simplex 
 GEN435R037 
 frameshift_variant 
 c.2383_234del 
 p.Arg795GlyfsTer5 
 De novo 
  
 Simplex 
 GEN435R038 
 missense_variant 
 c.260A>G 
 p.Asp87Gly 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R039 
 missense_variant 
 c.156G>T 
 p.Trp52Cys 
 Familial 
 Maternal 
 Multiplex 
 GEN435R040 
 missense_variant 
 c.1795C>T 
 p.Arg599Cys 
 Familial 
 Maternal 
 Multiplex 
 GEN435R041 
 missense_variant 
 c.1837G>A 
 p.Glu613Lys 
 Unknown 
  
 Multiplex 
 GEN435R042 
 splice_site_variant 
 c.2228dup 
 p.Leu744AlafsTer11 
 Familial 
 Maternal 
 Multiplex 
 GEN435R043 
 missense_variant 
 c.1487G>T 
 p.Gly496Val 
 De novo 
  
 Simplex 
 GEN435R044 
 missense_variant 
 c.145C>T 
 p.Pro49Ser 
 Familial 
 Maternal 
 Multiplex 
 GEN435R045 
 missense_variant 
 c.2233C>G 
 p.Gln745Glu 
 Unknown 
  
 Unknown 
 GEN435R046 
 missense_variant 
 c.2233C>G 
 p.Gln745Glu 
 Unknown 
  
 Unknown 
 GEN435R047 
 frameshift_variant 
 c.3191_3192del 
 p.Glu1064AlafsTer72 
 Unknown 
  
 Unknown 
 GEN435R048 
 missense_variant 
 c.1354G>A 
 p.Gly452Ser 
 Unknown 
  
  
 GEN435R049 
 frameshift_variant 
 c.440dup 
 p.Arg148GlufsTer5 
 Familial 
 Maternal 
  
 GEN435R050 
 splice_site_variant 
 c.2517_2622del 
 p.Pro840ValfsTer60 
 Unknown 
  
 Multiplex 
 GEN435R051 
 missense_variant 
 c.1226T>C 
 p.Phe409Ser 
 Familial 
 Maternal 
  
 GEN435R052 
 missense_variant 
 c.1112G>A 
 p.Cys371Tyr 
 Familial 
 Maternal 
  
 GEN435R053 
 stop_gained 
 c.2041C>T 
 p.Arg681Ter 
 De novo 
  
  
 GEN435R054 
 stop_gained 
 c.3533C>A 
 p.Ser1178Ter 
 De novo 
  
 Simplex 
 GEN435R055 
 stop_gained 
 c.4259G>A 
 p.Trp1420Ter 
 Familial 
 Maternal 
 Multi-generational 
 GEN435R056 
 missense_variant 
 c.1204G>A 
 p.Asp402Asn 
 Familial 
 Maternal 
 Multiplex 
 GEN435R057 
 stop_gained 
 c.709C>T 
 p.Gln237Ter 
 Unknown 
  
 Simplex 
 GEN435R058 
 missense_variant 
 c.860C>T 
 p.Ser287Leu 
 Familial 
 Maternal 
  
  et al.  
 GEN435R059 
 stop_gained 
 c.2080C>T 
 p.Arg694Ter 
 Unknown 
  
  
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
X
Deletion-Duplication
 25
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Deletion
 2
 
X
Deletion
 4
 
X
Deletion-Duplication
 1
 
X
Deletion
 1
 
X
Deletion-Duplication
 21
 

Model Summary

Kdm5c is associated with X-linked syndromic Claes-Jensen type intellectual developmental disorder. The hemizygous male mouse model shows complete ablation of the gene, while the heterozygous female shows a reduction of half of the level of expression, compared to sex-matched wildtypes. In the female mouse model this reduction results in differential expressed genes, some of which are also differentially expressed in the hemizygous male model, while others are uniquely differentially expressed in the female heterozygous model. The female heterozygous mice show increased foot shock sensitivity and decreased social approach. A double heterozygote mutant female mouse of Kdm5c and Kmt2a also shows decreased social approach, in addition to decreased contextual memory in the fear conditioning paradigm and decreased social dominance in the tube test of social dominance.

References

Type
Title
Author, Year

M_KDM5C_1_KO_HE

Model Type: Genetic
Model Genotype: Hemizygous
Mutation: Kdm5c knockout allele was generated through Cre-mediated deletion of exons 11 and 12 in a conditional-ready construct (MGI:6163735). Kdm5c knockout was maintained in a mixed background of C57BL/6J and 129S1/SvImJ.
Allele Type: Knockout
Strain of Origin: 129; 129S4/SvJae-Tg(Prm-cre)70Og
Genetic Background: C57BL/6J; 129S1/SvImJ
ES Cell Line: Not specified
Mutant ES Cell Line:
Model Source: Yang Shi lab

M_KDM5C_2_KO_HT

Model Type: Genetic
Model Genotype: Heterozygous
Mutation: Kdm5c knockout allele was generated through Cre-mediated deletion of exons 11 and 12 in a conditional-ready construct (MGI:6163735). Kdm5c knockout was maintained in a mixed background of C57BL/6J and 129S1/SvImJ.
Allele Type: Knockout
Strain of Origin: 129
Genetic Background: C57BL/6J; 129S1/SvImJ
ES Cell Line: Not specified
Mutant ES Cell Line:
Model Source: Yang Shi lab

M_KDM5C_3_KO_HT_KMT2A_KO_HT

Model Type: Genetic
Model Genotype: Heterozygous; Heterozygous
Mutation: Double knockout F1 hybrids were generated by crossing female mice carrying the Kdm5c knockout allele (MGI:6163735) on a congenic C57BL/6J background with mice heterozygous for loss of Kmt2a (MGI:3849323) on a congenic 129S1/SvImJ background.
Allele Type: Knockout
Strain of Origin: 129; 129S4/SvJae-Tg(Prm-cre)70Og
Genetic Background: C57BL/6J; 129S1/SvImJ
ES Cell Line: Not specified; PC3
Mutant ES Cell Line:
Model Source: Yang Shi lab; Hugh Brady lab

M_KDM5C_1_KO_HE

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Targeted expression1
Decreased
Description: There is an absence of RNA-seq reads of exons 11 and 12 in brain tissue from hemizygous males compared to wildtype males.
Exp Paradigm: cortex and hippocampus
 RNA sequencing
 P6
Gene expression1
Increased
Description: The gene with the greatest level of differential expression in Kdm5c hemizygous males is Gap junction protein, beta 1 (Gjb1) (Log2FC = 1.96, q = 1.92 Ã? 10â??82). Gjb1 encodes connexin-32, whose expression increases across postnatal cortical development to form gap junctions in oligodendrocytes and neurons and is implicated in epilepsy. Another gene with a significant level of differential expression is cyclin-dependent kinase inhibitor 1c (Cdkn1c) (Log2FC = 0.89, q = 8.02 Ã? 10â??20). Cdkn1c is a paternally imprinted gene involved in neocortical development and aggressive behavior. Pnmt and Gal genes are significantly upregulated in the hemizygous Kdm5c males but not in the heterozygous females.
Exp Paradigm: cortex and hippocampus; Gjb1, Cdkn1c, Pnmt, Gal
 RNA sequencing
 P6
Differential gene expression1
Abnormal
Description: Kdm5c hemizygous males showed 708 genes upregulated and 371 genes downregulated compared to wildtype males. Most differentially expressed genes are upregulated in the mutants, consistent with Kdm5c being a transcriptional repressor.
Exp Paradigm: cortex and hippocampus
 RNA sequencing
 P6
 Not Reported:

M_KDM5C_2_KO_HT

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Pain or nociception1
Increased
Description: Kdm5c heterozygous female mice show increased foot shock sensitivity, measured by maximum velocity during the acquisition phase of the fear conditioning paradigm. No change in average velocity was observed.
 Fear conditioning test
 4-8 months
Social approach1
Decreased
Description: Kdm5c heterozygous female mice show an exploratory preference for the non-social chamber with a toy mouse over the social chamber with a stranger mouse, contrary to wildtype mice.
 Three-chamber social approach test
 4-8 months
Targeted expression1
Decreased
Description: There is approximately a half level of expression of RNA-seq reads of exons 11 and 12 in brain tissue from hemizygous females compared to wildtype females.
Exp Paradigm: cortex and hippocampus
 RNA sequencing
 P6
Gene expression1
Increased
Description: The gene with the greatest level of differential expression in Kdm5c heterozygous females is Gap junction protein, beta 1 (Gjb1) (Log2FC = 1.17, q = 4.01 Ã? 10â??37). Gjb1 encodes connexin-32, whose expression increases across postnatal cortical development to form gap junctions in oligodendrocytes and neurons and is implicated in epilepsy. Another gene with a significant level of differential expression is cyclin-dependent kinase inhibitor 1c (Cdkn1c) (Log2FC = 0.472, q = 1.48 Ã? 10â??5). Cdkn1c is a paternally imprinted gene involved in neocortical development and aggressive behavior. Mdk and Jpx genes are significantly upregulated in the heterozygous Kdm5c females but not in the hemizygous males.
Exp Paradigm: cortex and hippocampus; Gjb1, Cdkn1c, Jpx, Mdk
 RNA sequencing
 P6
Differential gene expression1
Abnormal
Description: Kdm5c heterozygous females showed 122 genes upregulated and 14 genes downregulated compared to wildtype females. Most differentially expressed genes are upregulated in the mutants, consistent with Kdm5c being a transcriptional repressor.
Exp Paradigm: cortex and hippocampus
 RNA sequencing
 P6
Exploratory activity1
 No change
 Three-chamber social approach test
 4-8 months
Cued or contextual fear conditioning: memory of context1
 No change
 Fear conditioning test
 4-8 months
Aggression1
 No change
 Resident-intruder test
 4-8 months
Social dominance1
 No change
 Tube test of social dominance
 4-8 months
 Not Reported:

M_KDM5C_3_KO_HT_KMT2A_KO_HT

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Social dominance1
Decreased
Description: Double mutant female mice show a submissive phenotype compared to wildtype mice.
 Tube test of social dominance
 4-8 months
Social approach1
Decreased
Description: Double mutant female mice show no exploratory preference for the social chamber with a stranger mouse over the non-social chamber with a toy mouse, whereas wildtype female mice show preference for the social chamber.
 Three-chamber social approach test
 4-8 months
Cued or contextual fear conditioning: memory of context1
Decreased
Description: Double mutant female mice show decreased freezing level in re-exposure to foreground context after fear conditioning compared to wildtype female mice.
 Fear conditioning test
 4-8 months
Exploratory activity1
 No change
 Three-chamber social approach test
 4-8 months
Pain or nociception1
 No change
 Fear conditioning test
 4-8 months
Aggression1
 No change
 Resident-intruder test
 4-8 months
 Not Reported:


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
ARHGAP25 Rho GTPase-activating protein 25 9938 P42331-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
CHD8 chromodomain helicase DNA binding protein 8 57680 Q9HCK8 CHIP-seq
Cotney J , et al. 2015
DEF8 differentially expressed in FDCP 8 homolog (mouse) 54849 Q6ZN54 IP; LC-MS/MS
Huttlin EL , et al. 2015
HLA-F HLA class I histocompatibility antigen, alpha chain F 3134 P30511-3 IP; LC-MS/MS
Huttlin EL , et al. 2015
IER2 immediate early response 2 9592 Q9BTL4 IP; LC-MS/MS
Huttlin EL , et al. 2015
KIAA1683 KIAA1683 80726 Q9H0B3 IP; LC-MS/MS
Huttlin EL , et al. 2015
LHX6 LIM/homeobox protein Lhx6 26468 Q9UPM6-3 IP; LC-MS/MS
Huttlin EL , et al. 2015
OLFM2 Noelin-2 93145 O95897 IP; LC-MS/MS
Huttlin EL , et al. 2015
SCML4 Sex comb on midleg-like protein 4 256380 Q8N228-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
SKP2 S-phase kinase-associated protein 2, E3 ubiquitin protein ligase 6502 B4DJT4 IP; LC-MS/MS
Huttlin EL , et al. 2015
SPATA1 spermatogenesis associated 1 NM_001081472 Q5VX52 IP; LC-MS/MS
Huttlin EL , et al. 2015
SSH3 Protein phosphatase Slingshot homolog 3 54961 Q8TE77-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
TKT transketolase 7086 P29401 IP; LC-MS/MS
Huttlin EL , et al. 2015
TRIM35 tripartite motif containing 35 23087 Q9UPQ4 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZMYND8 zinc finger, MYND-type containing 8 23613 Q9ULU4 IP; LC-MS/MS; IP/WB; in vitro binding assay; Co-localization
Shen H , et al. 2016
Ntsr2 neurotensin receptor 2 18217 P70310 ChIP-Seq; RNA-Seq
Iwase S , et al. 2016
Slc29a1 solute carrier family 29 (nucleoside transporters), member 1 63959 Q9JIM1 ChIP-Seq; RNA-Seq
Iwase S , et al. 2016

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