KDM4D

lysine demethylase 4D, the group of Lysine demethylases

Basic information

Region (hg38): 11:94973709-94999519

Previous symbols: [ "JMJD2D" ]

Links

ENSG00000186280 ∙ NCBI:55693 ∙ OMIM:609766 ∙ HGNC:25498 ∙ Uniprot:Q6B0I6 ∙ 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 KDM4D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM4D 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			26	1	2	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in KDM4D

This is a list of pathogenic ClinVar variants found in the KDM4D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-94997556-A-T		not specified	Uncertain significance (Jul 30, 2023)
11-94997571-A-G		not specified	Uncertain significance (Mar 24, 2023)
11-94997572-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-94997593-C-T		not specified	Uncertain significance (Jul 12, 2023)
11-94997676-C-T		not specified	Uncertain significance (Oct 12, 2024)
11-94997838-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-94998018-C-G		not specified	Uncertain significance (Aug 12, 2024)
11-94998046-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-94998078-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-94998157-A-G		not specified	Likely benign (Oct 18, 2021)
11-94998160-G-T		not specified	Uncertain significance (Mar 01, 2024)
11-94998202-A-G		not specified	Uncertain significance (Dec 10, 2024)
11-94998315-G-T		not specified	Uncertain significance (Mar 15, 2024)
11-94998319-G-C		not specified	Uncertain significance (Mar 15, 2024)
11-94998351-A-G		not specified	Uncertain significance (Apr 05, 2023)
11-94998375-C-G		not specified	Uncertain significance (Oct 27, 2022)
11-94998430-C-T		not specified	Uncertain significance (Aug 26, 2024)
11-94998437-C-G			Benign (May 09, 2018)
11-94998475-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-94998490-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-94998520-G-A		not specified	Uncertain significance (Aug 16, 2022)
11-94998526-C-T		not specified	Uncertain significance (Nov 11, 2024)
11-94998546-C-T		not specified	Uncertain significance (Jun 25, 2024)
11-94998547-G-A		not specified	Uncertain significance (Mar 04, 2024)
11-94998559-G-A		not specified	Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM4D	protein_coding	protein_coding	ENST00000335080	1	25838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.432	0.468	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	204	311	0.655	0.0000184	3416
Missense in Polyphen		34	102.42	0.33196		1273
Synonymous	-0.377	119	114	1.04	0.00000612	1070
Loss of Function	1.07	0	1.34	0.00	5.46e-8	22

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: dbNSFP

• Function: FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys- 9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238}.
• Pathway: HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.414
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.98

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.309

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kdm4d
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;double-strand break repair via homologous recombination;regulation of protein phosphorylation;chromatin remodeling;histone H3-K9 demethylation;positive regulation of chromatin binding;oxidation-reduction process;cellular response to ionizing radiation;negative regulation of histone H3-K9 trimethylation;positive regulation of double-strand break repair via nonhomologous end joining
• Cellular component: nucleus;nucleoplasm;pericentric heterochromatin;histone methyltransferase complex;site of double-strand break;blood microparticle
• Molecular function: damaged DNA binding;chromatin DNA binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);metal ion binding;dioxygenase activity