KDM4E

lysine demethylase 4E, the group of Lysine demethylases

Basic information

Region (hg38): 11:95025258-95027596

Previous symbols: [ "KDM4DL" ]

Links

ENSG00000235268 ∙ NCBI:390245 ∙ OMIM:616581 ∙ HGNC:37098 ∙ Uniprot:B2RXH2 ∙ 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 KDM4E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM4E 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				4		4
missense			34	2	2	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	6	2

Variants in KDM4E

This is a list of pathogenic ClinVar variants found in the KDM4E region.

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

Position	Type	Phenotype	Significance	ClinVar
11-95025587-C-A		not specified	Uncertain significance (Sep 14, 2023)
11-95025609-T-G		not specified	Uncertain significance (Jun 07, 2023)
11-95025682-A-G			Benign (May 14, 2018)
11-95025738-G-C		not specified	Uncertain significance (Nov 13, 2024)
11-95025759-A-G		not specified	Likely benign (Sep 26, 2022)
11-95025799-G-A		not specified	Uncertain significance (Aug 15, 2024)
11-95025849-T-C		not specified	Uncertain significance (Sep 17, 2021)
11-95025852-C-T		not specified	Uncertain significance (Sep 29, 2022)
11-95025853-G-A		not specified	Uncertain significance (Sep 30, 2021)
11-95025855-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-95025883-C-T		not specified	Uncertain significance (Dec 06, 2023)
11-95025886-C-T		not specified	Uncertain significance (Oct 04, 2022)
11-95025896-G-T		not specified	Uncertain significance (Nov 13, 2024)
11-95025913-A-G		not specified	Uncertain significance (Jul 14, 2024)
11-95025919-G-C		not specified	Uncertain significance (Mar 07, 2023)
11-95025988-A-G		not specified	Uncertain significance (May 08, 2023)
11-95026004-G-C		not specified	Uncertain significance (Aug 05, 2024)
11-95026065-G-C		not specified	Uncertain significance (Sep 03, 2024)
11-95026067-G-C		not specified	Uncertain significance (May 14, 2024)
11-95026100-G-A		not specified	Uncertain significance (Oct 25, 2024)
11-95026118-C-T			Likely benign (Aug 29, 2018)
11-95026127-A-G			Likely benign (Aug 29, 2018)
11-95026164-T-C		not specified	Likely benign (Jul 05, 2022)
11-95026173-C-G		not specified	Uncertain significance (Jun 25, 2024)
11-95026191-G-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM4E	protein_coding	protein_coding	ENST00000450979	1	2339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.513	0.425	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.166	282	290	0.973	0.0000160	3298
Missense in Polyphen		94	94.802	0.99154		1171
Synonymous	-1.21	123	107	1.15	0.00000588	1002
Loss of Function	1.33	0	2.06	0.00	8.68e-8	26

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. {ECO:0000269|PubMed:21914792}.

Intolerance Scores

• rvis_EVS: 2.19
• rvis_percentile_EVS: 98.1

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.348

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin remodeling;histone H3-K9 demethylation;oxidation-reduction process
• Cellular component: nucleus;histone methyltransferase complex
• Molecular function: histone demethylase activity;histone demethylase activity (H3-K9 specific);metal ion binding;dioxygenase activity