KDM1B

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

Basic information

Region (hg38): 6:18155328-18223854

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.

• Inborn genetic diseases (13 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.

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			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	13	0	1

Variants in KDM1B

This is a list of pathogenic ClinVar variants found in the KDM1B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-18159975-G-C		not specified	Uncertain significance (Jan 05, 2022)
6-18161328-C-T		not specified	Uncertain significance (Nov 18, 2022)
6-18161343-C-T			Benign (Jun 26, 2018)
6-18161348-A-G		not specified	Uncertain significance (Mar 14, 2023)
6-18166306-A-C		not specified	Uncertain significance (Jun 24, 2022)
6-18171364-T-C		not specified	Uncertain significance (Dec 17, 2023)
6-18171384-T-A		not specified	Uncertain significance (Mar 02, 2023)
6-18197123-G-A		not specified	Uncertain significance (May 10, 2022)
6-18197598-C-G		not specified	Uncertain significance (Sep 01, 2021)
6-18197644-C-T		not specified	Uncertain significance (Jan 22, 2024)
6-18200439-G-A		not specified	Uncertain significance (Apr 22, 2022)
6-18207477-C-T		not specified	Uncertain significance (Feb 06, 2023)
6-18208162-G-C		not specified	Uncertain significance (Dec 21, 2022)
6-18215071-A-G		not specified	Uncertain significance (Dec 14, 2022)
6-18215083-T-C		not specified	Uncertain significance (Jan 03, 2024)
6-18215104-C-T		not specified	Uncertain significance (May 08, 2023)
6-18215110-G-A		not specified	Uncertain significance (Mar 04, 2024)
6-18215120-C-G		not specified	Uncertain significance (Oct 05, 2023)
6-18215122-A-G		not specified	Uncertain significance (Dec 13, 2021)
6-18217725-G-C			Benign (Jun 26, 2018)
6-18217776-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-18221960-G-A		not specified	Uncertain significance (Sep 26, 2023)
6-18221973-G-A		not specified	Uncertain significance (Feb 15, 2023)

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