KDM4A
Basic information
Region (hg38): 1:43650149-43705518
Previous symbols: [ "JMJD2", "JMJD2A" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (96 variants)
- not_provided (8 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM4A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014663.3. 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 | 7 | |||||
| missense | 94 | 96 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 94 | 4 | 5 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KDM4A | protein_coding | protein_coding | ENST00000372396 | 21 | 55358 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 3.80e-7 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.68 | 351 | 606 | 0.579 | 0.0000344 | 7021 |
| Missense in Polyphen | 110 | 247.69 | 0.4441 | 2730 | ||
| Synonymous | 0.797 | 201 | 216 | 0.931 | 0.0000120 | 1999 |
| Loss of Function | 6.62 | 4 | 58.7 | 0.0681 | 0.00000329 | 669 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000121 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000364 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000383 | 0.0000327 |
| 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 (PubMed:26741168). 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. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively. {ECO:0000269|PubMed:16024779, ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:26741168}.;
- Pathway
- DNA Repair;DNA Double-Strand Break Repair;HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.274
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.25
Haploinsufficiency Scores
- pHI
- 0.181
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.520
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.920
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kdm4a
- Phenotype
- homeostasis/metabolism phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin remodeling;negative regulation of autophagy;positive regulation of gene expression;negative regulation of gene expression;cardiac muscle hypertrophy in response to stress;viral process;histone demethylation;response to nutrient levels;histone H3-K9 demethylation;positive regulation of neuron differentiation;negative regulation of transcription, DNA-templated;negative regulation of astrocyte differentiation;oxidation-reduction process;negative regulation of cell death;histone H3-K36 demethylation;negative regulation of histone H3-K9 trimethylation
- Cellular component
- fibrillar center;nucleus;nucleoplasm;pericentric heterochromatin;cytosol;histone methyltransferase complex
- Molecular function
- protein binding;zinc ion binding;ubiquitin protein ligase binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);methylated histone binding;histone demethylase activity (H3-K36 specific)