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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
Diagnostic yield of whole-exome sequencing in non-syndromic intellectual disability
DD, ID
Epilepsy/seizures, autistic features
Support
Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C.
Support
The application of whole-exome sequencing in the early diagnosis of rare genetic diseases in children: a study from Southeastern China
ID
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
Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.
ID
Support
Decoding complex inherited phenotypes in rare disorders: the DECIPHERD initiative for rare undiagnosed diseases in Chile
DD
Support
Exploring the biological role of postzygotic and germinal de novo mutations in ASD
ASD
Support
A regulatory path associated with X-linked intellectual disability and epilepsy links KDM5C to the polyalanine expansions in ARX.
Support
Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort
Epilepsy/seizures
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
Novel JARID1C/SMCX mutations in patients with X-linked mental retardation.
ID
Epilepsy
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 c.2T>C mutation of the KDM5C/JARID1C gene in one large family with X-linked intellectual disability.
ID
Support
Whole-genome sequencing identifies novel genes for autism in Chinese trios
ASD
Support
Deep phenotyping and whole-exome sequencing improved the diagnostic yield for nuclear pedigrees with neurodevelopmental disorders
ASD, ADHD, DD, ID
Support
Xp11.2 microduplications including IQSEC2, TSPYL2 and KDM5C genes in patients with neurodevelopmental disorders.
DD, ID
ASD, epilepsy/seizures
Support
A novel mutation in JARID1C gene associated with mental retardation.
ID
Support
Claes-Jensen type of X-linked syndromic intellectu
Support
Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance.
Support
A novel nonsense mutation in KDM5C/JARID1C gene causing intellectual disability, short stature and speech delay.
ID
Support
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings
DD, ID, epilepsy/seizures
Support
Autism spectrum disorder and comorbid neurodevelopmental disorders (ASD-NDDs): Clinical and genetic profile of a pediatric cohort
ASD
Epilepsy/seizures
Support
Large-scale discovery of novel genetic causes of developmental disorders.
Cognitive impairment
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
Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1.
ID
Support
KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons
Intellectual developmental disorder, X-linked synd
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Support
Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing.
ID
Support
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: experience of two clinical units and 216 patients.
ID
Microcephaly
Support
A de novo paradigm for mental retardation.
ID
Support
The genetic landscape of autism spectrum disorder in the Middle Eastern population
ASD
Support
Comorbidities associated with genetic abnormalities in children with intellectual disability
ASD, DD/ID
Support
Exome sequencing in multiplex autism families suggests a major role for heterozygous truncating mutations.
ASD
Support
Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics.
DD
Behavioral abnormalities (stereotypic, self-injuri
Support
Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype-phenotype correlation.
ID
Support
The utility of exome sequencing in diagnosing pediatric neurodevelopmental disorders in a highly consanguineous population
DD, epilepsy/seizures
Highly Cited
Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation.
ID
Recent Recommendation
WNT signalling control by KDM5C during development affects cognition
Intellectual developmental disorder, X-linked synd
Recent Recommendation
Arachnoid cysts
ASD, DD, epilepsy/seizures
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.
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 
  
 GEN435R059 
 stop_gained 
 c.2080C>T 
 p.Arg694Ter 
 Unknown 
  
  
 GEN435R060 
 frameshift_variant 
  
 p.Ala241fs 
 Familial 
 Maternal 
 Unknown 
 GEN435R061 
 copy_number_gain 
  
  
 Familial 
 Maternal 
 Simplex 
 GEN435R062 
 copy_number_gain 
  
  
 Familial 
 Maternal 
 Extended multiplex 
 GEN435R063 
 copy_number_gain 
  
  
 Familial 
 Maternal 
 Simplex 
 GEN435R064 
 copy_number_gain 
  
  
 De novo 
  
 Simplex 
 GEN435R065 
 missense_variant 
 c.3745C>T 
 p.Arg1249Cys 
 De novo 
  
 Simplex 
 GEN435R066 
 stop_gained 
 c.2214C>A 
 p.Cys738Ter 
 De novo 
  
  
 GEN435R067 
 stop_gained 
 c.2851C>T 
 p.Arg951Ter 
 De novo 
  
 Simplex 
 GEN435R068 
 frameshift_variant 
 c.4030_4031dup 
 p.Met1344IlefsTer15 
 Unknown 
  
  
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
X
Deletion-Duplication
 27
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Deletion
 3
 
X
Deletion
 4
 
X
Deletion-Duplication
 1
 
X
Deletion
 1
 
X
Deletion-Duplication
 22
 

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
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
Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Gene expression1
Increased
 RNA sequencing
 P6
Differential gene expression1
Abnormal
 RNA sequencing
 P6
Targeted expression1
Decreased
 RNA sequencing
 P6
 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
Ntsr2 neurotensin receptor 2 18217 P70310 ChIP-Seq; RNA-Seq
Iwase S , et al. 2016
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
Slc29a1 solute carrier family 29 (nucleoside transporters), member 1 63959 Q9JIM1 ChIP-Seq; RNA-Seq
Iwase S , et al. 2016
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

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