JMJD6
jumonji domain containing 6, arginine demethylase and lysine hydroxylase, the group of Iron (II) and 2-oxoglutarate dependent oxygenases
Basic information
Region (hg38): 17:76712832-76726799
Previous symbols: [ "PTDSR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 JMJD6 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 | 1 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 1 |
Variants in JMJD6
This is a list of pathogenic ClinVar variants found in the JMJD6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-76716699-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 17-76718790-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 17-76718839-C-T | not specified | Uncertain significance (Dec 07, 2021) | ||
| 17-76718853-G-C | not specified | Uncertain significance (Oct 03, 2022) | ||
| 17-76718857-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 17-76720364-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 17-76720454-G-C | not specified | Uncertain significance (Dec 22, 2023) | ||
| 17-76723796-G-T | not specified | Uncertain significance (Feb 26, 2024) | ||
| 17-76723816-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 17-76723852-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 17-76723968-G-C | not specified | Uncertain significance (Jun 17, 2024) | ||
| 17-76723976-G-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 17-76724003-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 17-76725508-G-A | Benign (Feb 08, 2018) | |||
| 17-76725564-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 17-76725654-T-C | not specified | Uncertain significance (Jun 21, 2023) | ||
| 17-76725740-T-C | not specified | Uncertain significance (Oct 25, 2022) | ||
| 17-76725833-G-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 17-76726375-C-T | not specified | Uncertain significance (Apr 06, 2022) | ||
| 17-76726432-C-G | not specified | Uncertain significance (May 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| JMJD6 | protein_coding | protein_coding | ENST00000445478 | 7 | 13948 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.934 | 0.0665 | 124800 | 0 | 7 | 124807 | 0.0000280 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.48 | 183 | 249 | 0.736 | 0.0000140 | 2727 |
| Missense in Polyphen | 37 | 76.275 | 0.48509 | 840 | ||
| Synonymous | -0.896 | 110 | 98.7 | 1.11 | 0.00000621 | 773 |
| Loss of Function | 3.74 | 3 | 21.8 | 0.137 | 0.00000106 | 245 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000158 | 0.000158 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000442 | 0.0000265 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses. {ECO:0000269|PubMed:17947579, ECO:0000269|PubMed:19574390, ECO:0000269|PubMed:20684070, ECO:0000269|PubMed:21060799}.;
- Pathway
- HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.192
Intolerance Scores
- loftool
- 0.236
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.44
Haploinsufficiency Scores
- pHI
- 0.233
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.549
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Jmjd6
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; muscle phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; hematopoietic system 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); vision/eye phenotype; digestive/alimentary phenotype; 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); renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- jmjd6
- Affected structure
- neural tube
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- kidney development;sprouting angiogenesis;mRNA processing;cell surface receptor signaling pathway;heart development;RNA splicing;peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine;lung development;T cell differentiation in thymus;macrophage activation;recognition of apoptotic cell;positive regulation of transcription, DNA-templated;regulation of mRNA splicing, via spliceosome;erythrocyte development;oxidation-reduction process;retina development in camera-type eye;histone H3-R2 demethylation;histone H4-R3 demethylation
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytosol;plasma membrane;ribonucleoprotein complex
- Molecular function
- transcription coactivator activity;RNA binding;single-stranded RNA binding;iron ion binding;protein binding;histone demethylase activity;histone demethylase activity (H3-R2 specific);histone demethylase activity (H4-R3 specific);signaling receptor activity;identical protein binding;protein homodimerization activity;peptidyl-lysine 5-dioxygenase activity