Alternative titles; symbols
HGNC Approved Gene Symbol: KDM5C
Cytogenetic location: Xp11.22 Genomic coordinates (GRCh38): X:53,176,277-53,225,207 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xp11.22 | Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type | 300534 | X-linked recessive | 3 |
The KDM5C gene encodes a specific H3K4me3 and H3K4me2 demethylase, and acts as a transcriptional repressor through the RE-1-silencing transcription factor (REST) complex (Tahiliani et al., 2007).
Wu et al. (1994) reported the isolation and characterization of cDNAs for XE169, a non-pseudoautosomal region (PAR)-encoded human gene. The sequence appeared to represent a full-length or nearly full-length cDNA for the gene. Alternative splicing generates 2 distinct transcripts, either containing or missing 9 nucleotides, which in turn predicts 2 XE169 protein isoforms composed of 1,557 and 1,560 amino acids, respectively. XE169 is expressed in multiple human tissues, and homologous sequences exist on the human Y chromosome and in the genomes of 5 other eutherian mammals examined. RT-PCR analysis of somatic cell hybrids containing either an active or an inactive human X chromosome on a rodent background demonstrated that XE169 escapes X inactivation.
Jensen et al. (2005) reported that the JARID1C protein shares amino acid identity of 85%, 51%, and 47% with JARID1D/SMCY (426000), JARID1A (180202), and JARID1B (605393), respectively. The JARID1C protein contains several domains conserved among the JARID proteins, including a JmjN domain, an Arid/Bright domain, a JmjC domain, a C5HC2 zinc finger domain, and PHD zinc finger domains. Northern blot analysis detected varying expression of a 6.0-kb transcript in almost all adult human tissues examined, with strongest expression in brain and skeletal muscle and weakest expression in heart and liver.
The JARID1C gene was thought to escape X inactivation. Agulnik et al. (1994) observed that in hamster/human hybrids, Jarid1c was expressed when either an active or an inactive human X chromosome was present. Furthermore, 2 alleles of Smcx were found to be expressed in t(16;X)16H female mice despite the intact X chromosome being inactive in all cells. Lingenfelter et al. (1998) showed that Smcx is susceptible to complete X inactivation in a portion of mouse embryonic cells. Furthermore, Smcx inactivation persists in some cells at least until 13.5 days postcoitum. A highly variable Smcx expression found during mouse development progressively disappears in adult tissues where nearly equal expression between alleles is observed. Sheardown et al. (1996) demonstrated that the mouse Jarid1c gene exhibits partial X inactivation in embryos, in extraembryonic lineages, and in several adult tissues, showing an expression of 20 to 70% from the inactive, compared with the active, X allele. Xu et al. (2002) observed that Jarid1c and Jarid1d are expressed in mouse brain in a sex-specific fashion; in adult mouse brain, Jarid1c is expressed at a significantly higher level in females than in males, and expression of Jarid1d in males was not sufficient to compensate for the female bias in X-gene expression. Therefore, Jensen et al. (2005) suggested that the X-Y gene pair JARID1C and JARID1D may not be functionally equivalent, suggesting an indispensable role for JARID1C in normal brain function.
Tahiliani et al. (2007) showed that JARID1C/SMCX, a JmjC domain-containing protein implicated in X-linked mental retardation and epilepsy, possesses H3K4 tridemethylase activity and functions as a transcriptional repressor. An SMCX complex isolated from HeLa cells contained additional chromatin modifiers (the histone deacetylases HDAC1 (601241) and HDAC2 (605164), and the histone H3K9 methyltransferase G9a (604599)) and the transcriptional repressor REST (600571), suggesting a direct role for SMCX in chromatin dynamics and REST-mediated repression. Chromatin immunoprecipitation revealed that SMCX and REST co-occupy the neuron-restrictive silencing elements in the promoters of a subset of REST target genes. RNA interference-mediated depletion of SMCX derepressed several of these targets and simultaneously increased H3K4 trimethylation at the sodium channel type 2A (SCN2A; 182390) and synapsin I (SYN1; 313440) promoters. Tahiliani et al. (2007) proposed that loss of SMCX activity impairs REST-mediated neuronal gene regulation, thereby contributing to SMCX-associated X-linked mental retardation.
Using a genomewide small interfering RNA screen and secondary screens, Smith et al. (2010) identified 96 cellular genes that contributed to viral E2 protein-mediated repression of the human papillomavirus (HPV) long control region, which controls viral oncogene expression. In addition to the E2-binding protein BRD4 (608749), other genes implicated included the demethylase SMCX and EP400 (606265), a component of the NUA4/TIP60 histone acetyltransferase complex (see 601409). Smith et al. (2010) concluded that HPV E2 uses multiple cellular proteins to inhibit expression of its oncogenes.
By determining the chromatin landscape of RACK7-bound genomic locations in human breast cancer cells, Shen et al. (2016) found that RACK7 (ZMYND8; 615713) and KDM5C occupied many active enhancer sites, including almost all super-enhancers. Loss of RACK7 or KDM5C resulted in overactivation of enhancers, characterized by deposition of H3K4me3 and H3K27Ac and loss of H3K4me1, as well as increased transcription of enhancer RNAs and nearby genes. Loss of RACK7 significantly impaired KDM5C recruitment to enhancers. Human breast cancer cells lacking RACK7 or KDM5C displayed enhanced anchorage-independent growth, migration, and invasion abilities in vitro, as well as enhanced tumor growth in a mouse xenograft model. Shen et al. (2016) concluded that active enhancers are subject to negative regulation and that RACK7 and KDM5C act together as a 'brake' for active enhancers by controlling dynamic interchange between H3K4me1 and H3K4me3.
Jensen et al. (2005) stated that the SMCX gene comprises 26 exons.
By Southern hybridization analysis of a panel of human/mouse somatic cell hybrids containing various portions of translocated human X chromosomes, Wu et al. (1994) assigned the XE169 gene to the proximal half of the short arm of the X chromosome between Xp21.1 and the centromere.
Wu et al. (1994) assigned Xe169 to band F2/F3 on the mouse X chromosome by fluorescence in situ hybridization, and Southern analysis indicated that the gene is located outside the pseudoautosomal region.
Using direct in situ hybridization, Agulnik et al. (1994) mapped the mouse Smcx gene to the distal end of the X chromosome (XF2-XF4) and its human homolog, SMCX, to proximal Xp (Xp11.2-p11.1). Meiotic mapping in the mouse placed Smcx in the interval between Plp and Pdha1.
In a systematic screen of brain-expressed genes from the proximal Xp and pericentromeric regions of the X chromosome in 210 families with X-linked mental retardation (XLMR), Jensen et al. (2005) identified mutations in the JARID1C gene in affected members of 7 families with MRXSCJ (300534), including 1 frameshift and 2 nonsense mutations, as well as 4 missense mutations that altered evolutionarily conserved amino acids. In 2 of these families, expression studies revealed the almost complete absence of the mutated JARID1C transcript, suggesting that the phenotype in these families resulted from functional loss of the JARID1C protein. The JARID1C gene, formerly known as SMCX, is highly similar to the Y chromosome gene that encodes the H-Y antigen variously known as JARID1D, SMCY, and HYA (426000). Jensen et al. (2005) noted that in families with nonsyndromic XLMR, more than 30% of mutations seem to cluster on the proximal part of the short arm of the X chromosome and in the pericentric region. The authors estimated that the frequency of mutations in the JARID1C gene account for 2.8% to 3.3% families with XLMR.
In 4 of 287 probands with X-linked mental retardation, Abidi et al. (2008) identified 4 different mutations in the JARID1C gene (see, e.g., 314690.0007).
Poeta et al. (2013) found that ARX (300382) bound to conserved noncoding elements in the 5-prime region of the KDM5C gene, resulting in increased expression of KDM5C. In vitro cellular expression studies showed that transfection of 5 ARX mutants (see, e.g., 300382.0022) that cause intellectual disability or severe epilepsy resulted in variably decreased activation of the KDM5C gene compared to wildtype ARX. The changes in polyA repeats caused hypomorphic ARX alterations, which exhibit a decreased transactivity and reduced, but not abolished, binding to the KDM5C regulatory region. The altered functioning of the mutants tested correlated with the severity of the associated phenotype. Quantitative RT-PCR studies showed a dramatic decrease of Kdm5c mRNA in murine Arx-null embryonic and neural stem cells. The decrease in the KDM5C content during in vitro neuronal differentiation inversely correlated with increased histone regulation, as measured by H3K4me3 levels. The findings linked ARX polyA expansions to KDM5C, mutations of which cause a similar phenotype, and established that ARX polyA alterations damage the regulation of KDM5C expression, suggesting a pathogenic pathway involving changes in chromatin remodeling in these neurologic disorders.
Carmignac et al. (2020) reported 19 female carriers of mutations in the KDM5C gene. Five females had de novo mutations, which were identified in 4 by whole-exome sequencing and in 1 by screening of a panel of genes associated with encephalopathy. Three of the mutations were predicted to lead to a frameshift and premature termination and one was a missense mutation. Skewing of X-chromosome inactivation was detected in all 4 patients tested; however, in 1 case the wildtype KDM5C mutation was preferentially expressed in blood, leading the authors to conclude that factors other than X-chromosome inactivation may be involved in disease expression. Mutations in the other 14 female carriers were from 5 families in which a brother or uncle had MRXSCJ. Four of these carriers were asymptomatic. X-chromosome inactivation was skewed in 3 and random in 7 of 10 patients tested. Among these patients, Carmignac et al. (2020) found no association between phenotype and X inactivation.
In monozygotic twins and their older brother with MRXSCJ, Guerra et al. (2020) identified a hemizygous mutation in the KDM5C gene (c.807delC; 314690.0010). Their asymptomatic mother was heterozygous for the mutation, and X-inactivation studies revealed complete skewing. DNA methylation analysis of the 3 sibs demonstrated 399 differentially methylated CpG sites compared to controls that were enriched for sites modulated during brain development; 72% of the sites were hypomethylated. These methylation abnormalities were not seen in the carrier mother.
Agulnik et al. (1994) isolated a mouse Y chromosome gene from the region encoding Spy, a spermatogenesis gene, and Hya and Sdma, the genes that, respectively, control the expression of the male specific minor histocompatibility antigen H-Y, as measured by specific T-cell assays, and the serologically detected male antigen SDMA. See 426000 for a discussion of SMCY (so named for 'selected mouse cDNA on Y') and its human homolog. The murine gene maps to Yp; the human homolog, SMCY, maps to Yq.
Iwase et al. (2016) found that Kdm5c-knockout mice exhibited smaller body size and reduced weight compared with wildtype mice, but that they were otherwise healthy and fertile. The authors observed adaptive and cognitive abnormalities in Kdm5c-knockout mice that were similar to those in human X-linked intellectual disability. Kdm5c-knockout brains exhibited abnormal dendritic arborization, spine anomalies, and altered transcriptomes. Studies of wildtype and Kdm5c-knockout neurons showed that Kdm5c was recruited to promoters harboring CpG islands decorated with high levels of H3K4me3, where it fine-tuned H3K4me3 levels. Kdm5c predominantly repressed these genes, some of which encoded proteins involved in key pathways regulating development and function of neuronal circuitries. Iwase et al. (2016) concluded that histone methylation dynamics sculpt the neuronal network, and they proposed that Kdm5c-knockout mice may help devise therapeutic strategies for X-linked intellectual disability.
In a study of 1,751 knockout alleles created by the International Mouse Phenotyping Consortium (IMPC), Dickinson et al. (2016) reported that knockout of the mouse homolog of human KDM5C is homozygous-lethal (defined as absence of homozygous mice after screening of at least 28 pups before weaning).
In affected members of a family with Claes-Jensen-type syndromic X-linked intellectual developmental disorder (MRXSCJ; 300534) originally reported by Claes et al. (2000), Jensen et al. (2005) detected a C-to-T transition at nucleotide 2191 in exon 15 of the JARID1C gene that changed leucine to phenylalanine at codon 731 (L731F). Jensen et al. (2005) suggested that the L731F mutation, which is located in an evolutionarily conserved C5HC2 zinc finger domain, may have a profound effect on that domain as a result of the difference in size and chemical properties between leucine and phenylalanine.
In 2 brothers with Claes-Jensen-type X-linked syndromic intellectual developmental disorder (MRXSCJ; 300534), Jensen et al. (2005) identified a single-nucleotide insertion of a cytidine (202_203insC) in exon 2 of the JARID1C gene that introduced a frameshift with premature stop codon (Arg68fsTer7). The change was not found in 312 control X chromosomes. The authors suggested that the mutation, which did not seem to undergo nonsense-mediated decay (NMD), may cause the aberrant phenotype through either extreme shortening of the protein and deletion of relevant domains, or through production of an abnormal protein by alternative use of a methionine downstream of exon 2. With an almost identical phenotype, both brothers had had removal of the gallbladder because of gallstones, at ages 20 and 31 years, respectively.
In a family with 4 males who presented with intellectual developmental disorder and microcephaly (MRXSCJ; 300534), Jensen et al. (2005) observed a 1162G-C transversion in exon 9 of the JARID1C gene that caused an ala388-to-pro (A388P) amino acid substitution.
In 2 brothers with X-linked intellectual developmental disorder and short stature (MRXSCJ; 300534), Jensen et al. (2005) found a 2080C-T transition in exon 15 of the JARID1C gene that caused a premature termination at arg694 (R694X). KDM5C mRNA expression was almost undetectable, indicating nonsense-mediated decay (NMD).
In 2 male sibs with Claes-Jensen-type X-linked syndromic intellectual developmental disorder (MRXSCJ; 300534), Santos et al. (2006) identified a 1353C-G transversion in exon 10 of the JARID1C gene, resulting in a ser451-to-arg (S451R) substitution. The unaffected mother was heterozygous for the mutation, which was not identified in 250 control chromosomes.
In a 4-year-old boy with cognitive impairment (MRXSCJ; 300534), Adegbola et al. (2008) identified a hemizygous 2296C-T transition in exon 16 of the JARID1C gene, resulting in an arg766-to-trp (R766W) substitution. His unaffected mother also carried the mutation. Detailed neuropsychologic testing of the patient showed significant delays in perception, fine motor skills, cognitive and language skills, and difficulty with self-regulation. He also showed impairments in social reciprocity and use of nonverbal behavior, stereotyped mannerisms, and adherence to routine, consistent with autistic spectrum disorder. Although he had no dysmorphic features as observed in many patients with KDM5C-related mental retardation, Adegbola et al. (2008) noted that the phenotype associated with mutations in the KDM5C gene is variable with regard to dysmorphism and cognitive impairment; the authors suggested that this patient falls within a milder end of the spectrum.
In affected members of a family with X-linked syndromic intellectual developmental disorder (MRXSCJ; 300534), Abidi et al. (2008) identified a 229G-A transition in exon 3 of the JARID1C gene, resulting in an ala77-to-thr (A77T) substitution in the ARID/BRIGHT domain. Additional features included short stature, deep-set eyes, prominent nasal bridge, prominent ears, clubfeet, and aggressive behavior. Three carrier females had mild mental retardation. The mutation was not identified in 782 control X chromosomes.
In affected members of a Brazilian family with X-linked syndromic intellectual developmental disorder (MRXSCJ; 300534), Santos-Reboucas et al. (2011) identified a 2172C-A transversion in exon 15 of the KDM5C gene, resulting in a cys724-to-ter (C724X) substitution in the C5HC2 zinc finger domain, resulting in decreased protein expression likely from nonsense-mediated mRNA decay. There were 3 affected brothers with severe mental retardation, poor speech, short stature, low weight, microcephaly, high palate, slight maxillary hypoplasia, and small feet. Their mother, who also carried the mutation, was mildly cognitively impaired.
In affected members of a family with X-linked syndromic intellectual developmental disorder (MRXSCJ; 300534), Rujirabanjerd et al. (2010) identified a 1160C-A transversion in exon 12 of the KDM5C gene, resulting in a pro554-to-thr (P554T) substitution at a highly conserved residue in the core of the JmjC domain. Although the family had previously been designated as nonsyndromic MRX13 (Kerr et al., 1992), Rujirabanjerd et al. (2010) noted that affected individuals had short stature, large ears, and microcephaly in addition to moderately impaired intellectual development. Two of 6 female carriers had learning difficulties. In vitro functional expression studies showed that the mutant protein had significantly decreased demethylase activity compared to wildtype. In an erratum, the authors confirmed that the mutation was P554T; the mutation was incorrectly stated as P544T in the abstract and text of their article.
In monozygotic twins and their older brother, Guerra et al. (2020) identified hemizygosity for a 1-bp deletion (c.807delC, NM_004187.3) in exon 7 of the KDM5C gene, resulting in a frameshift and premature termination (Thr270GlnfsTer2). The mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing, segregated with disease in the family. The asymptomatic mother was heterozygous for the mutation, and X-inactivation studies revealed complete skewing. The mutation was predicted to result in loss of the JmjC catalytic domain, leading to absence of a functional protein.
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