L3MBTL3

L3MBTL histone methyl-lysine binding protein 3, the group of MBT domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 6:130013698-130141449

Links

ENSG00000198945 ∙ NCBI:84456 ∙ OMIM:618844 ∙ HGNC:23035 ∙ Uniprot:Q96JM7 ∙ 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 L3MBTL3 gene.

• Inborn genetic diseases (30 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the L3MBTL3 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					1	1
missense			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	29	2	2

Variants in L3MBTL3

This is a list of pathogenic ClinVar variants found in the L3MBTL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-130042725-G-A		not specified	Uncertain significance (Dec 12, 2023)
6-130042725-G-C		not specified	Uncertain significance (Oct 12, 2022)
6-130051371-T-G		not specified	Uncertain significance (Jun 27, 2022)
6-130051378-G-A		not specified	Uncertain significance (Feb 14, 2023)
6-130052894-A-G		not specified	Uncertain significance (Jan 06, 2023)
6-130052921-G-A		not specified	Uncertain significance (Jul 27, 2022)
6-130052957-C-A			Benign (Apr 20, 2019)
6-130052982-T-G		not specified	Uncertain significance (Aug 21, 2023)
6-130055161-C-A			Likely benign (Jul 26, 2018)
6-130055178-A-G		not specified	Uncertain significance (Feb 15, 2023)
6-130055205-C-T		not specified	Uncertain significance (May 17, 2023)
6-130055234-G-T		not specified	Uncertain significance (Feb 17, 2024)
6-130055238-C-T		not specified	Uncertain significance (Mar 28, 2023)
6-130055254-G-T		not specified	Uncertain significance (Aug 02, 2021)
6-130057456-G-A		not specified	Uncertain significance (Jul 20, 2022)
6-130057466-C-T		not specified	Uncertain significance (Jul 26, 2022)
6-130057478-C-T		not specified	Uncertain significance (Jun 05, 2023)
6-130057492-A-C		not specified	Uncertain significance (Sep 16, 2021)
6-130060093-G-A		not specified	Uncertain significance (Sep 15, 2021)
6-130060116-G-A			Benign (Jul 23, 2018)
6-130066402-A-G		not specified	Uncertain significance (Oct 13, 2023)
6-130066423-A-G		not specified	Uncertain significance (Dec 18, 2023)
6-130066464-G-A		not specified	Uncertain significance (May 17, 2023)
6-130068341-G-C		not specified	Uncertain significance (Oct 25, 2023)
6-130068424-A-G			Benign (Jul 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
L3MBTL3	protein_coding	protein_coding	ENST00000529410	21	127751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00256	125415	0	330	125745	0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	333	428	0.777	0.0000227	5177
Missense in Polyphen		100	174.14	0.57426		2164
Synonymous	-0.532	160	152	1.05	0.00000876	1390
Loss of Function	5.30	6	44.0	0.137	0.00000203	568

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00443	0.00427
Ashkenazi Jewish	0.000501	0.000496
East Asian	0.00183	0.00180
Finnish	0.00357	0.00352
European (Non-Finnish)	0.00117	0.00113
Middle Eastern	0.00183	0.00180
South Asian	0.0000329	0.0000327
Other	0.00201	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative Polycomb group (PcG) protein. PcG proteins maintain the transcriptionally repressive state of genes, probably via a modification of chromatin, rendering it heritably changed in its expressibility. Required for normal maturation of myeloid progenitor cells (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0984

Intolerance Scores

• loftool: 0.400
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.634
• hipred: Y
• hipred_score: 0.581
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.939

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: L3mbtl3
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated;macrophage differentiation;granulocyte differentiation;erythrocyte maturation
• Cellular component: nucleus;nucleolus
• Molecular function: molecular_function;DNA-binding transcription factor activity;protein binding;zinc ion binding