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.

• not_specified (90 variants)
• not_provided (4 variants)
• Breast_ductal_adenocarcinoma (1 variants)

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. These statistics are base on transcript: NM_001161630.1. 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		2
missense			89	2	2	93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	89	4	2

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