KDM5D
Basic information
Region (hg38): Y:19703865-19744939
Previous symbols: [ "HYA", "HY", "SMCY", "JARID1D" ]
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 KDM5D 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KDM5D | protein_coding | protein_coding | ENST00000317961 | 26 | 41075 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.928 | 0.0721 | 67931 | 13 | 0 | 67944 | 0.0000957 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.372 | 259 | 243 | 1.07 | 0.0000401 | 10069 |
| Missense in Polyphen | 56 | 83.025 | 0.67449 | 3352 | ||
| Synonymous | -2.81 | 118 | 85.0 | 1.39 | 0.0000131 | 3059 |
| Loss of Function | 3.71 | 3 | 21.6 | 0.139 | 0.00000362 | 844 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000140 | 0.000140 |
| Ashkenazi Jewish | 0.000388 | 0.000193 |
| East Asian | 0.000221 | 0.000110 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000227 | 0.000110 |
| Middle Eastern | 0.000221 | 0.000110 |
| South Asian | 0.000174 | 0.0000867 |
| Other | 0.000718 | 0.000312 |
dbNSFP
Source:
- Function
- FUNCTION: Histone demethylase that specifically demethylates 'Lys- 4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks. {ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320162, ECO:0000269|PubMed:17351630, ECO:0000269|PubMed:26747897, ECO:0000269|PubMed:27185910, ECO:0000269|PubMed:27427228, ECO:0000269|PubMed:27477906}.;
- Pathway
- HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.223
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.406
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.163
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kdm5d
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;T cell antigen processing and presentation;chromatin remodeling;histone H3-K4 demethylation;histone H3-K4 demethylation, trimethyl-H3-K4-specific;oxidation-reduction process;regulation of androgen receptor signaling pathway
- Cellular component
- fibrillar center;cellular_component;nucleus;nucleoplasm;histone methyltransferase complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;histone demethylase activity;histone demethylase activity (H3-K4 specific);histone demethylase activity (H3-trimethyl-K4 specific);metal ion binding;androgen receptor binding;dioxygenase activity