L3MBTL1

L3MBTL histone methyl-lysine binding protein 1, the group of Zinc fingers C2HC-type|MBT domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 20:43489441-43550954

Previous symbols: [ "L3MBTL" ]

Links

ENSG00000185513 ∙ NCBI:26013 ∙ OMIM:608802 ∙ HGNC:15905 ∙ Uniprot:Q9Y468 ∙ 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 L3MBTL1 gene.

• Inborn genetic diseases (37 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the L3MBTL1 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				2		2
missense			34	3	1	38
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	34	5	1

Variants in L3MBTL1

This is a list of pathogenic ClinVar variants found in the L3MBTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-43513585-G-A		L3MBTL1-related disorder	Likely benign (Apr 22, 2022)
20-43514044-C-T		L3MBTL1-related disorder	Likely benign (Sep 22, 2020)
20-43514578-G-T		L3MBTL1-related disorder	Likely benign (Apr 21, 2020)
20-43514705-A-G		not specified	Likely benign (Jun 30, 2023)
20-43514755-G-A		L3MBTL1-related disorder	Likely benign (Sep 22, 2020)
20-43515022-G-C		not specified	Uncertain significance (May 10, 2022)
20-43515035-G-C		not specified	Uncertain significance (May 15, 2023)
20-43515054-C-T		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
20-43515078-G-T		not specified	Uncertain significance (Jan 17, 2024)
20-43515102-C-T		not specified	Uncertain significance (Nov 27, 2023)
20-43515296-G-A			Benign (Jan 19, 2018)
20-43515312-C-T		not specified	Uncertain significance (Mar 01, 2023)
20-43515316-A-G			Likely benign (Jul 01, 2022)
20-43515341-C-T		not specified	Uncertain significance (Jul 14, 2021)
20-43516145-C-G		not specified	Uncertain significance (Jun 03, 2022)
20-43528684-C-T		not specified	Uncertain significance (Jul 13, 2021)
20-43528692-T-C		not specified	Uncertain significance (Feb 16, 2023)
20-43528716-A-G		not specified	Likely benign (Jul 07, 2022)
20-43528744-A-G		not specified	Uncertain significance (Oct 03, 2023)
20-43529301-T-C		not specified	Uncertain significance (Aug 17, 2022)
20-43530287-T-C		not specified	Uncertain significance (Jun 29, 2023)
20-43530327-A-T		not specified	Uncertain significance (Jun 30, 2023)
20-43530333-A-G		not specified	Uncertain significance (May 31, 2022)
20-43530848-G-A		not specified	Uncertain significance (Apr 27, 2023)
20-43532782-C-T		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
L3MBTL1	protein_coding	protein_coding	ENST00000427442	21	43271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-12	0.997	125609	0	139	125748	0.000553

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	447	511	0.875	0.0000297	5470
Missense in Polyphen		110	143.1	0.7687		1612
Synonymous	1.16	189	210	0.898	0.0000137	1631
Loss of Function	2.80	27	47.9	0.564	0.00000248	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000951	0.000951
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00116	0.00116
European (Non-Finnish)	0.000547	0.000536
Middle Eastern	0.000109	0.000109
South Asian	0.000988	0.000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polycomb group (PcG) protein that specifically recognizes and binds mono- and dimethyllysine residues on target proteins, therey acting as a 'reader' of a network of post- translational modifications. PcG proteins maintain the transcriptionally repressive state of genes: acts as a chromatin compaction factor by recognizing and binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condense chromatin and repress transcription. Recognizes and binds p53/TP53 monomethylated at 'Lys-382', leading to repress p53/TP53-target genes. Also recognizes and binds RB1/RB monomethylated at 'Lys-860'. Participates in the ETV6-mediated repression. Probably plays a role in cell proliferation. Overexpression induces multinucleated cells, suggesting that it is required to accomplish normal mitosis. {ECO:0000269|PubMed:17540172, ECO:0000269|PubMed:18408754, ECO:0000269|PubMed:20870719, ECO:0000269|PubMed:20870725}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Methylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.79

Haploinsufficiency Scores

• pHI: 0.417
• hipred: Y
• hipred_score: 0.637
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: L3mbtl1

Gene ontology

• Biological process: chromatin organization;regulation of mitotic nuclear division;hemopoiesis;regulation of megakaryocyte differentiation;negative regulation of transcription, DNA-templated;regulation of cell cycle;regulation of signal transduction by p53 class mediator
• Cellular component: chromatin;condensed chromosome;nucleus;nucleoplasm;nucleolus;plasma membrane
• Molecular function: chromatin binding;DNA-binding transcription factor activity;protein binding;zinc ion binding;nucleosome binding;nucleosomal histone binding;SAM domain binding;methylated histone binding;histone binding;identical protein binding