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
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.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 26 | 29 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 26 | 1 | 2 |
Variants in KDM4D
This is a list of pathogenic ClinVar variants found in the KDM4D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-94997556-A-T | not specified | Uncertain significance (Jul 30, 2023) | ||
11-94997571-A-G | not specified | Uncertain significance (Mar 24, 2023) | ||
11-94997572-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
11-94997593-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
11-94997838-C-T | not specified | Uncertain significance (Oct 26, 2022) | ||
11-94998046-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
11-94998078-C-T | not specified | Uncertain significance (Feb 03, 2022) | ||
11-94998157-A-G | not specified | Likely benign (Oct 18, 2021) | ||
11-94998160-G-T | not specified | Uncertain significance (Mar 01, 2024) | ||
11-94998315-G-T | not specified | Uncertain significance (Mar 15, 2024) | ||
11-94998319-G-C | not specified | Uncertain significance (Mar 15, 2024) | ||
11-94998351-A-G | not specified | Uncertain significance (Apr 05, 2023) | ||
11-94998375-C-G | not specified | Uncertain significance (Oct 27, 2022) | ||
11-94998437-C-G | Benign (May 09, 2018) | |||
11-94998475-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
11-94998490-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
11-94998520-G-A | not specified | Uncertain significance (Aug 16, 2022) | ||
11-94998547-G-A | not specified | Uncertain significance (Mar 04, 2024) | ||
11-94998559-G-A | not specified | Uncertain significance (Dec 20, 2022) | ||
11-94998566-C-A | not specified | Uncertain significance (Nov 21, 2023) | ||
11-94998586-T-A | not specified | Uncertain significance (Nov 19, 2022) | ||
11-94998591-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
11-94998598-C-A | not specified | Uncertain significance (Dec 06, 2022) | ||
11-94998627-C-T | not specified | Uncertain significance (Dec 13, 2021) | ||
11-94998727-G-T | not specified | Uncertain significance (Nov 18, 2023) |
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