KDM5C
Homo sapiens
Gene Name: lysine demethylase 5C
Aliases: RP11-258C19.2, DXS1272E, JARID1C, MRXJ, MRXSCJ, MRXSJ, SMCX, XE169
Chromosome No: X
Chromosome Band: Xp11.22
Genetic Category: Syndromic-Rare single gene variant--Multigenic CNV/Functional-Functional-Rare single gene variant/Functional-Syndromic/Functional
Aliases: RP11-258C19.2, DXS1272E, JARID1C, MRXJ, MRXSCJ, MRXSJ, SMCX, XE169
Chromosome No: X
Chromosome Band: Xp11.22
Genetic Category: Syndromic-Rare single gene variant--Multigenic CNV/Functional-Functional-Rare single gene variant/Functional-Syndromic/Functional
Summary Statistics:
ASD Reports: 48
Recent Reports: 4
Annotated variants: 68
Associated CNVs: 9
Evidence score: 3
ASD Reports: 48
Recent Reports: 4
Annotated variants: 68
Associated CNVs: 9
Evidence score: 3
Gene Score: 3
Associated Disorders: |
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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.
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
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
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
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
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
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.
Rare
Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
GEN435R002
missense_variant
c.2191C>T
p.Leu731Phe
Familial
Maternal
Multi-generational
GEN435R004
missense_variant
c.1162G>C
p.Ala388Pro
Familial
Maternal
Multi-generational
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
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
GEN435R025
splice_site_variant
c.658-1G>T
Familial
Maternal
Multiplex
GEN435R030
missense_variant
c.1919G>A
p.Cys640Tyr
Familial
Maternal
Simplex
GEN435R032
missense_variant
c.3344G>A
p.Arg1115His
Familial
Maternal
Simplex
GEN435R037
frameshift_variant
c.2383_234del
p.Arg795GlyfsTer5
De novo
Simplex
GEN435R038
missense_variant
c.260A>G
p.Asp87Gly
Familial
Maternal
Multi-generational
GEN435R040
missense_variant
c.1795C>T
p.Arg599Cys
Familial
Maternal
Multiplex
GEN435R042
splice_site_variant
c.2228dup
p.Leu744AlafsTer11
Familial
Maternal
Multiplex
GEN435R044
missense_variant
c.145C>T
p.Pro49Ser
Familial
Maternal
Multiplex
GEN435R047
frameshift_variant
c.3191_3192del
p.Glu1064AlafsTer72
Unknown
Unknown
GEN435R050
splice_site_variant
c.2517_2622del
p.Pro840ValfsTer60
Unknown
Multiplex
GEN435R056
missense_variant
c.1204G>A
p.Asp402Asn
Familial
Maternal
Multiplex
Common
No Common Variants Available