KDM5D

lysine demethylase 5D, the group of AT-rich interaction domain containing|PHD finger proteins|Minor histocompatibility antigens|Lysine demethylases

Basic information

Region (hg38): Y:19703864-19744939

Previous symbols: [ "HYA", "HY", "SMCY", "JARID1D" ]

Links

ENSG00000012817 ∙ NCBI:8284 ∙ OMIM:426000 ∙ HGNC:11115 ∙ Uniprot:Q9BY66 ∙ 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 KDM5D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM5D 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM5D	protein_coding	protein_coding	ENST00000317961	26	41075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.928	0.0721	67931	13	0	67944	0.0000957

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.372	259	243	1.07	0.0000401	10069
Missense in Polyphen		56	83.025	0.67449		3352
Synonymous	-2.81	118	85.0	1.39	0.0000131	3059
Loss of Function	3.71	3	21.6	0.139	0.00000362	844

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000140	0.000140
Ashkenazi Jewish	0.000388	0.000193
East Asian	0.000221	0.000110
Finnish	0.00	0.00
European (Non-Finnish)	0.000227	0.000110
Middle Eastern	0.000221	0.000110
South Asian	0.000174	0.0000867
Other	0.000718	0.000312

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase that specifically demethylates 'Lys- 4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks. {ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320162, ECO:0000269|PubMed:17351630, ECO:0000269|PubMed:26747897, ECO:0000269|PubMed:27185910, ECO:0000269|PubMed:27427228, ECO:0000269|PubMed:27477906}.
• Pathway: HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Haploinsufficiency Scores

• pHI: 0.223
• hipred: N
• hipred_score: 0.170
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.163

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdm5d

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;T cell antigen processing and presentation;chromatin remodeling;histone H3-K4 demethylation;histone H3-K4 demethylation, trimethyl-H3-K4-specific;oxidation-reduction process;regulation of androgen receptor signaling pathway
• Cellular component: fibrillar center;cellular_component;nucleus;nucleoplasm;histone methyltransferase complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;histone demethylase activity;histone demethylase activity (H3-K4 specific);histone demethylase activity (H3-trimethyl-K4 specific);metal ion binding;androgen receptor binding;dioxygenase activity