KDM4C
Basic information
Region (hg38): 9:6720863-7175648
Previous symbols: [ "JMJD2C" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (139 variants)
- not_provided (9 variants)
- KDM4C-related_disorder (2 variants)
- Enchondromatosis (1 variants)
- Maffucci_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM4C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015061.6. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | |||||
| missense | 133 | 141 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 133 | 11 | 6 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KDM4C | protein_coding | protein_coding | ENST00000381309 | 21 | 454786 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.52e-7 | 1.00 | 125711 | 0 | 37 | 125748 | 0.000147 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.489 | 622 | 589 | 1.06 | 0.0000310 | 6985 |
| Missense in Polyphen | 138 | 195.38 | 0.70633 | 2277 | ||
| Synonymous | -2.39 | 262 | 217 | 1.21 | 0.0000125 | 1908 |
| Loss of Function | 4.34 | 21 | 56.1 | 0.375 | 0.00000282 | 704 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000326 | 0.000326 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000185 | 0.000185 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000660 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:28262558}.;
- Pathway
- Signal Transduction;HDMs demethylate histones;Chromatin modifying enzymes;AndrogenReceptor;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;RHO GTPase Effectors;Signaling by Rho GTPases;Coregulation of Androgen receptor activity;Chromatin organization
(Consensus)
Intolerance Scores
- loftool
- 0.689
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 29.62
Haploinsufficiency Scores
- pHI
- 0.707
- hipred
- N
- hipred_score
- 0.414
- ghis
- 0.549
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Kdm4c
- Phenotype
- immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;blastocyst formation;chromatin remodeling;regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;positive regulation of gene expression;histone H3-K9 demethylation;positive regulation of neuron differentiation;oxidation-reduction process;histone H3-K36 demethylation;negative regulation of histone H3-K9 trimethylation;regulation of stem cell population maintenance;regulation of stem cell differentiation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;pericentric heterochromatin;histone methyltransferase complex
- Molecular function
- zinc ion binding;enzyme binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);androgen receptor binding;histone demethylase activity (H3-K36 specific)