KDM4D

lysine demethylase 4D, the group of Lysine demethylases

Basic information

Region (hg38): 11:94973709-94999519

Previous symbols: [ "JMJD2D" ]

Links

ENSG00000186280NCBI:55693OMIM:609766HGNC:25498Uniprot:Q6B0I6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
clinvar
2
clinvar
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)2614682
11-94997571-A-G not specified Uncertain significance (Mar 24, 2023)2529797
11-94997572-G-A not specified Uncertain significance (Dec 15, 2022)2208357
11-94997593-C-T not specified Uncertain significance (Jul 12, 2023)2611024
11-94997838-C-T not specified Uncertain significance (Oct 26, 2022)2321001
11-94998046-G-A not specified Uncertain significance (Jan 23, 2023)2470532
11-94998078-C-T not specified Uncertain significance (Feb 03, 2022)2276025
11-94998157-A-G not specified Likely benign (Oct 18, 2021)2370608
11-94998160-G-T not specified Uncertain significance (Mar 01, 2024)3113823
11-94998315-G-T not specified Uncertain significance (Mar 15, 2024)3287928
11-94998319-G-C not specified Uncertain significance (Mar 15, 2024)3287929
11-94998351-A-G not specified Uncertain significance (Apr 05, 2023)2533292
11-94998375-C-G not specified Uncertain significance (Oct 27, 2022)2218153
11-94998437-C-G Benign (May 09, 2018)775297
11-94998475-G-A not specified Uncertain significance (Jan 09, 2024)3113815
11-94998490-G-A not specified Uncertain significance (Jun 24, 2022)2214148
11-94998520-G-A not specified Uncertain significance (Aug 16, 2022)2407418
11-94998547-G-A not specified Uncertain significance (Mar 04, 2024)3113816
11-94998559-G-A not specified Uncertain significance (Dec 20, 2022)3113817
11-94998566-C-A not specified Uncertain significance (Nov 21, 2023)3113818
11-94998586-T-A not specified Uncertain significance (Nov 19, 2022)2370480
11-94998591-C-T not specified Uncertain significance (Dec 11, 2023)3113819
11-94998598-C-A not specified Uncertain significance (Dec 06, 2022)2333172
11-94998627-C-T not specified Uncertain significance (Dec 13, 2021)2324014
11-94998727-G-T not specified Uncertain significance (Nov 18, 2023)3113820

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KDM4Dprotein_codingprotein_codingENST00000335080 125838
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4320.46800000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.162043110.6550.00001843416
Missense in Polyphen34102.420.331961273
Synonymous-0.3771191141.040.000006121070
Loss of Function1.0701.340.005.46e-822

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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