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

ENSG00000070495 ∙ NCBI:23210 ∙ OMIM:604914 ∙ HGNC:19355 ∙ Uniprot:Q6NYC1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the JMJD6 gene.

• not_specified (44 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000015167.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2		1	3
missense			45			45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	49	0	1

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

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

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