L3MBTL2

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

Basic information

Region (hg38): 22:41205282-41231271

Links

ENSG00000100395NCBI:83746OMIM:611865HGNC:18594Uniprot:Q969R5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
2
clinvar
3
missense
50
clinvar
1
clinvar
1
clinvar
52
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)2257688
22-41205382-T-C not specified Uncertain significance (Jul 26, 2022)2303457
22-41209760-A-G not specified Uncertain significance (Jul 09, 2021)2235985
22-41209772-G-C Benign (Oct 29, 2020)771544
22-41209796-G-A not specified Uncertain significance (Apr 25, 2023)2540060
22-41209836-A-T not specified Uncertain significance (Feb 17, 2024)3117265
22-41209888-A-G not specified Uncertain significance (Mar 08, 2024)3117268
22-41209901-C-A not specified Uncertain significance (Feb 27, 2023)2489813
22-41209903-C-T not specified Uncertain significance (Mar 06, 2023)2461975
22-41216260-A-T not specified Uncertain significance (Nov 08, 2022)2323030
22-41217159-A-G not specified Uncertain significance (Jun 07, 2023)2523392
22-41217177-C-T not specified Uncertain significance (Oct 26, 2022)2228901
22-41219445-T-A not specified Uncertain significance (Jan 04, 2022)2269305
22-41219470-G-C not specified Uncertain significance (Mar 01, 2023)2492803
22-41219515-G-A not specified Uncertain significance (Sep 13, 2023)2601877
22-41219521-G-A not specified Uncertain significance (Jun 28, 2022)2298174
22-41220774-C-T Benign (Jun 27, 2018)777726
22-41220782-A-T not specified Uncertain significance (Nov 06, 2023)3117270
22-41220789-C-G not specified Uncertain significance (Oct 28, 2024)3536741
22-41220794-G-A not specified Uncertain significance (Dec 09, 2024)3536750
22-41220823-A-C not specified Uncertain significance (May 25, 2022)2290563
22-41221219-G-A not specified Uncertain significance (Apr 25, 2023)2509935
22-41221244-G-A not specified Uncertain significance (Jun 05, 2023)2523373
22-41221246-C-G not specified Uncertain significance (Aug 12, 2021)2206293
22-41221270-G-A not specified Uncertain significance (May 25, 2022)2410893

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
L3MBTL2protein_codingprotein_codingENST00000216237 1726067
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.03e-80.9991257080401257480.000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.923224350.7400.00002634639
Missense in Polyphen75125.110.599461347
Synonymous0.1371741760.9870.00001191338
Loss of Function2.992040.60.4930.00000227430

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006680.000666
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.00009730.0000924
European (Non-Finnish)0.0001670.000158
Middle Eastern0.0001630.000163
South Asian0.00009810.0000980
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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