L3MBTL2

L3MBTL histone methyl-lysine binding protein 2, the group of MBT domain containing

Basic information

Region (hg38): 22:41205282-41231271

Links

ENSG00000100395 ∙ NCBI:83746 ∙ OMIM:611865 ∙ HGNC:18594 ∙ Uniprot:Q969R5 ∙ 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 L3MBTL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the L3MBTL2 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	2	3
missense			50	1	1	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	51	2	3

Variants in L3MBTL2

This is a list of pathogenic ClinVar variants found in the L3MBTL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41205371-G-T		not specified	Uncertain significance (Oct 27, 2021)
22-41205382-T-C		not specified	Uncertain significance (Jul 26, 2022)
22-41209711-G-A		Non-obstructive azoospermia	Pathogenic (Dec 18, 2023)
22-41209760-A-G		not specified	Uncertain significance (Jul 09, 2021)
22-41209772-G-C			Benign (Oct 29, 2020)
22-41209796-G-A		not specified	Uncertain significance (Apr 25, 2023)
22-41209836-A-T		not specified	Uncertain significance (Feb 17, 2024)
22-41209888-A-G		not specified	Uncertain significance (Mar 08, 2024)
22-41209901-C-A		not specified	Uncertain significance (Feb 27, 2023)
22-41209903-C-T		not specified	Uncertain significance (Mar 06, 2023)
22-41216260-A-T		not specified	Uncertain significance (Nov 08, 2022)
22-41217159-A-G		not specified	Uncertain significance (Jun 07, 2023)
22-41217177-C-T		not specified	Uncertain significance (Oct 26, 2022)
22-41219445-T-A		not specified	Uncertain significance (Jan 04, 2022)
22-41219470-G-C		not specified	Uncertain significance (Mar 01, 2023)
22-41219515-G-A		not specified	Uncertain significance (Sep 13, 2023)
22-41219521-G-A		not specified	Uncertain significance (Jun 28, 2022)
22-41220774-C-T			Benign (Jun 27, 2018)
22-41220782-A-T		not specified	Uncertain significance (Nov 06, 2023)
22-41220789-C-G		not specified	Uncertain significance (Oct 28, 2024)
22-41220794-G-A		not specified	Uncertain significance (Dec 09, 2024)
22-41220823-A-C		not specified	Uncertain significance (May 25, 2022)
22-41221219-G-A		not specified	Uncertain significance (Apr 25, 2023)
22-41221244-G-A		not specified	Uncertain significance (Jun 05, 2023)
22-41221246-C-G		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
L3MBTL2	protein_coding	protein_coding	ENST00000216237	17	26067

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-8	0.999	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	322	435	0.740	0.0000263	4639
Missense in Polyphen		75	125.11	0.59946		1347
Synonymous	0.137	174	176	0.987	0.0000119	1338
Loss of Function	2.99	20	40.6	0.493	0.00000227	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000666
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000973	0.0000924
European (Non-Finnish)	0.000167	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.0000981	0.0000980
Other	0.00	0.00

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. Its association with a chromatin-remodeling complex suggests that it may contribute to prevent expression of genes that trigger the cell into mitosis. Binds to monomethylated and dimethylated 'Lys-20' on histone H4. Binds histone H3 peptides that are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. {ECO:0000269|PubMed:19233876}.
• Pathway: Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.641
• rvis_EVS: -1.17
• rvis_percentile_EVS: 6.03

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.603
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.591

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: L3mbtl2
• Phenotype: skeleton phenotype; embryo 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); growth/size/body region phenotype

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm
• Molecular function: protein binding;zinc ion binding;methylated histone binding;histone binding