L3MBTL2 L3MBTL histone methyl-lysine binding protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: L3MBTL2provided by HGNC
Official Full Name: L3MBTL histone methyl-lysine binding protein 2provided by HGNC
Primary source: HGNC:HGNC:18594
See related: Ensembl:ENSG00000100395 MIM:611865; AllianceGenome:HGNC:18594
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: L3MBT; H-l(3)mbt-l
Summary: Enables methylated histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including ectoderm development; stem cell differentiation; and stem cell proliferation. Located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in lymph node (RPKM 7.9), testis (RPKM 7.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.2

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (41205312..41231271)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (41680250..41706208)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (41601316..41627275)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Augmenting L3MBTL2-induced condensates suppresses tumor growth in osteosarcoma.
Title: Augmenting L3MBTL2-induced condensates suppresses tumor growth in osteosarcoma.
L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage, regulating the DNA damage response pathway.
Title: L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage.
L3MBTL2 polymorphism is associated with neuroticism.
Title: Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders.
Our findings highlight a PcG/L3MBTL2 collaboration that attains repressive chromatin without entailing histone lysine methylation marks.
Title: L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure.
determination of the solution structure of the FCS zinc finger of L3MBTL2; structure consists of a beta-hairpin followed by an alpha-helix; structure is consistent with the proposal that FCS zinc fingers bind to regulatory RNAs
Title: Solution structure of the FCS zinc finger domain of the human polycomb group protein L(3)mbt-like 2.
High-resolution crystallographic analysis of the four MBT repeats of L3MBTL2 reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides.
Title: Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G43605 (e-PCR)
- UniSTS:95040

MARC_6537-6538:992007286:1 (e-PCR)
- UniSTS:231241

MARC_6537-6538:996689759:1 (e-PCR)
- UniSTS:231241

D22S1539 (e-PCR)
- UniSTS:26256

GDB:631802 (e-PCR)
- UniSTS:158429

D22S1539 (e-PCR)
- UniSTS:16382

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IPI Inferred from Physical Interaction more info	PubMed
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: lethal(3)malignant brain tumor-like protein 2

Names: H-l(3)mbt-like protein 2; L(3)mbt-like protein 2; L3MBTL2, polycomb repressive complex 1 subunit; l(3)mbt-like 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_031488.5 → NP_113676.2 lethal(3)malignant brain tumor-like protein 2

See identical proteins and their annotated locations for NP_113676.2

Status: VALIDATED

Source sequence(s)

AJ305226, AJ305227, AK097052, BU184979

Consensus CDS

CCDS14011.1

UniProtKB/Swiss-Prot

Q8TEN1, Q969R5, Q96SC4, Q9BQI2, Q9UGS4

UniProtKB/TrEMBL

A0A0S2Z5X6, B3KPJ8

Related

ENSP00000216237.5, ENST00000216237.10

Conserved Domains (1) summary

smart00561
Location:511 → 604

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

41205312..41231271

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017028976.2 → XP_016884465.1 lethal(3)malignant brain tumor-like protein 2 isoform X2
XM_047441536.1 → XP_047297492.1 lethal(3)malignant brain tumor-like protein 2 isoform X1
XM_047441537.1 → XP_047297493.1 lethal(3)malignant brain tumor-like protein 2 isoform X4
XM_017028977.2 → XP_016884466.1 lethal(3)malignant brain tumor-like protein 2 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060946.1 Alternate T2T-CHM13v2.0

Range

41680250..41706208

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054326000.1 → XP_054181975.1 lethal(3)malignant brain tumor-like protein 2 isoform X2
XM_054325999.1 → XP_054181974.1 lethal(3)malignant brain tumor-like protein 2 isoform X1
XM_054326002.1 → XP_054181977.1 lethal(3)malignant brain tumor-like protein 2 isoform X4
XM_054326001.1 → XP_054181976.1 lethal(3)malignant brain tumor-like protein 2 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001003689.1: Suppressed sequence

Description

NM_001003689.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.