KDM4D
Basic information
Region (hg38): 11:94973709-94999519
Previous symbols: [ "JMJD2D" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (56 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM4D gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018039.3. 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 | 0 | |||||
| missense | 56 | 1 | 2 | 59 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 56 | 1 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KDM4D | protein_coding | protein_coding | ENST00000335080 | 1 | 25838 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.432 | 0.468 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.16 | 204 | 311 | 0.655 | 0.0000184 | 3416 |
| Missense in Polyphen | 34 | 102.42 | 0.33196 | 1273 | ||
| Synonymous | -0.377 | 119 | 114 | 1.04 | 0.00000612 | 1070 |
| Loss of Function | 1.07 | 0 | 1.34 | 0.00 | 5.46e-8 | 22 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys- 9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238}.;
- Pathway
- HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- loftool
- 0.414
- rvis_EVS
- 0.64
- rvis_percentile_EVS
- 83.98
Haploinsufficiency Scores
- pHI
- 0.201
- hipred
- N
- hipred_score
- 0.309
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.848
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kdm4d
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;double-strand break repair via homologous recombination;regulation of protein phosphorylation;chromatin remodeling;histone H3-K9 demethylation;positive regulation of chromatin binding;oxidation-reduction process;cellular response to ionizing radiation;negative regulation of histone H3-K9 trimethylation;positive regulation of double-strand break repair via nonhomologous end joining
- Cellular component
- nucleus;nucleoplasm;pericentric heterochromatin;histone methyltransferase complex;site of double-strand break;blood microparticle
- Molecular function
- damaged DNA binding;chromatin DNA binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);metal ion binding;dioxygenase activity