KDM3A
lysine demethylase 3A, the group of Lysine demethylases
Basic information
Region (hg38): 2:86440647-86492716
Previous symbols: [ "JMJD1", "JMJD1A" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (127 variants)
- KDM3A-related_disorder (22 variants)
- not_provided (8 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM3A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018433.6. 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 | 10 | 18 | ||||
| missense | 122 | 131 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 123 | 17 | 10 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KDM3A | protein_coding | protein_coding | ENST00000409556 | 25 | 52070 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000112 | 125734 | 0 | 12 | 125746 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 573 | 695 | 0.824 | 0.0000351 | 8677 |
| Missense in Polyphen | 215 | 339.83 | 0.63268 | 4131 | ||
| Synonymous | -2.16 | 294 | 251 | 1.17 | 0.0000129 | 2500 |
| Loss of Function | 6.86 | 9 | 71.7 | 0.125 | 0.00000398 | 841 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.000220 | 0.000198 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000440 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000101 | 0.0000980 |
| 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. Preferentially demethylates mono- and dimethylated H3 'Lys-9' residue, with a preference for dimethylated residue, while it has weak or no activity on trimethylated H3 'Lys-9'. Demethylation of Lys residue generates formaldehyde and succinate. Involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes, resulting in H3 'Lys-9' demethylation and transcriptional activation. Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TNP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1. {ECO:0000269|PubMed:16603237, ECO:0000269|PubMed:28262558}.;
- Pathway
- Thermogenesis - Homo sapiens (human);HDMs demethylate histones;Chromatin modifying enzymes;AndrogenReceptor;Coregulation of Androgen receptor activity;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.377
- rvis_EVS
- -0.73
- rvis_percentile_EVS
- 14.24
Haploinsufficiency Scores
- pHI
- 0.383
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.532
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.925
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kdm3a
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; reproductive system phenotype; liver/biliary system phenotype;
Gene ontology
- Biological process
- spermatid nucleus elongation;hormone-mediated signaling pathway;androgen receptor signaling pathway;histone H3-K9 demethylation;histone H3-K9 dimethylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;formaldehyde biosynthetic process;negative regulation of histone H3-K9 methylation;oxidation-reduction process;positive regulation of cold-induced thermogenesis;cellular response to leukemia inhibitory factor;regulation of stem cell population maintenance;regulation of stem cell differentiation
- Cellular component
- chromatin;nucleus;nucleoplasm;cytoplasm;membrane
- Molecular function
- transcription regulatory region sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity;iron ion binding;protein binding;chromatin DNA binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);androgen receptor binding;dioxygenase activity