KDM1B

lysine demethylase 1B, the group of Zinc fingers CW-type|Lysine demethylases

Basic information

Region (hg38): 6:18155329-18223854

Previous symbols: [ "C6orf193", "AOF1" ]

Links

ENSG00000165097

∙ NCBI:221656 ∙ OMIM:613081 ∙ HGNC:21577 ∙ Uniprot:Q8NB78 ∙ 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 KDM1B gene.

not_specified (60 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001364614.2. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			58 clinvar	1 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM1B	protein_coding	protein_coding	ENST00000297792	16	68525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00140	0.999	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	252	338	0.745	0.0000184	3878
Missense in Polyphen		43	68.393	0.62872		875
Synonymous	-0.326	131	126	1.04	0.00000772	1109
Loss of Function	3.80	12	36.9	0.325	0.00000195	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.000167	0.000163
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri- methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-, di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys- 36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of histone H4. {ECO:0000269|PubMed:23260659, ECO:0000269|PubMed:23357850}.;
Pathway: Post-translational protein modification;Metabolism of proteins;HDMs demethylate histones;Chromatin modifying enzymes;UCH proteinases;Deubiquitination;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.123

Intolerance Scores

loftool: 0.300
rvis_EVS: 0.0000761
rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

pHI: 0.186
hipred: Y
hipred_score: 0.601
ghis: 0.497

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Kdm1b
Phenotype: reproductive system phenotype;

Gene ontology

Biological process: regulation of gene expression by genetic imprinting;multicellular organism development;protein deubiquitination;histone H3-K4 demethylation;DNA methylation involved in gamete generation;regulation of DNA methylation;oxidation-reduction process
Cellular component: nucleosome;nucleus;nucleoplasm
Molecular function: DNA binding;protein binding;zinc ion binding;oxidoreductase activity;histone demethylase activity;histone demethylase activity (H3-dimethyl-K4 specific);histone demethylase activity (H3-monomethyl-K4 specific);histone binding;FAD binding