KDM2A
lysine demethylase 2A, the group of F-box and leucine rich repeat proteins|Zinc fingers CXXC-type|Lysine demethylases|PHD finger proteins
Basic information
Region (hg38): 11:67119263-67258082
Previous symbols: [ "FBXL11" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (62 variants)
- KDM2A-related_neurodevelopmental_disorder (18 variants)
- not_provided (2 variants)
- Neurodevelopmental_disorder (1 variants)
- KDM2A_related_condition (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012308.3. 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 | 2 | |||||
| missense | 65 | 73 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 5 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 7 | 9 | 65 | 1 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KDM2A | protein_coding | protein_coding | ENST00000529006 | 20 | 138819 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 4.03e-11 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 5.31 | 302 | 696 | 0.434 | 0.0000428 | 7615 |
| Missense in Polyphen | 40 | 261.68 | 0.15286 | 2818 | ||
| Synonymous | -0.410 | 260 | 252 | 1.03 | 0.0000142 | 2247 |
| Loss of Function | 7.50 | 0 | 65.5 | 0.00 | 0.00000416 | 676 |
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- 36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys- 36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis. {ECO:0000269|PubMed:16362057, ECO:0000269|PubMed:19001877, ECO:0000269|PubMed:28262558}.;
- Pathway
- The oncogenic action of Succinate;The oncogenic action of Fumarate;The oncogenic action of 2-hydroxyglutarate;The oncogenic action of L-2-hydroxyglutarate in Hydroxygluaricaciduria;The oncogenic action of D-2-hydroxyglutarate in Hydroxygluaricaciduria ;HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- 0.0344
- rvis_EVS
- -1.2
- rvis_percentile_EVS
- 5.76
Haploinsufficiency Scores
- pHI
- 0.417
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.633
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.668
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kdm2a
- Phenotype
- embryo 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- kdm2aa
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- present
Gene ontology
- Biological process
- double-strand break repair via nonhomologous end joining;regulation of transcription by RNA polymerase II;oxidation-reduction process;histone H3-K36 demethylation
- Cellular component
- nucleoplasm
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding;histone demethylase activity;histone demethylase activity (H3-K36 specific)