L3MBTL3 L3MBTL histone methyl-lysine binding protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: L3MBTL3provided by HGNC
Official Full Name: L3MBTL histone methyl-lysine binding protein 3provided by HGNC
Primary source: HGNC:HGNC:23035
See related: Ensembl:ENSG00000198945 MIM:618844; AllianceGenome:HGNC:23035
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MBT1; MBT-1
Summary: This gene encodes a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. Members of this family function as methyl-lysine readers, which recognize methylated lysine residues on histone protein tails, and are associated with the repression of gene expression. The encoded protein may regulate hematopoiesis. Homozygous deletion of this gene has been observed in human patients with medulloblastoma. [provided by RefSeq, Oct 2016]
Expression: Ubiquitous expression in endometrium (RPKM 5.0), spleen (RPKM 4.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q23.1

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (130018581..130141438)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (131211018..131336219)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (130339726..130462583)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Association of the L3MBTL3 rs1125970 and rs4897367 Gene Polymorphisms With Coronary Heart Disease Susceptibility in the Chinese Population: A Case-Control Study.
Title: Association of the L3MBTL3 rs1125970 and rs4897367 Gene Polymorphisms With Coronary Heart Disease Susceptibility in the Chinese Population: A Case-Control Study.
The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3.
Title: The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3.
Identification of the genetic mechanism that associates L3MBTL3 to multiple sclerosis.
Title: Identification of the genetic mechanism that associates L3MBTL3 to multiple sclerosis.
Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.
Title: Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.
L3MBTL3 rs4364506 was found neither as a predisposing nor a protective variant against multiple sclerosis
Title: Association of SHMT1, MAZ, ERG, and L3MBTL3 Gene Polymorphisms with Susceptibility to Multiple Sclerosis.
The direct binding of L3MBTL3 to the methylated SOX2 protein leads to the recruitment of the CRL4(DCAF5) ubiquitin E3 ligase to target SOX2 protein for ubiquitin-dependent proteolysis.
Title: Proteolysis of methylated SOX2 protein is regulated by L3MBTL3 and CRL4(DCAF5) ubiquitin ligase.
RBPJ interacts with L3MBTL3 to promote repression of Notch signaling via histone demethylase KDM1A.
Title: RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1.
Mutation in L3MBTL3 gene is associated with insulin-resistant cardiometabolic disease.
Title: Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance.
The mouse MBT-1 protein influences myelopoiesis by transiently enhancing p57(KIP2) expression levels.
Title: Impaired maturation of myeloid progenitors in mice lacking novel Polycomb group protein MBT-1.

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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
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Many sequence variants affecting diversity of adult human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel 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

STS-N22856 (e-PCR)
- UniSTS:46643

SHGC-79187 (e-PCR)
- UniSTS:102731

RH98682 (e-PCR)
- UniSTS:92123

SHGC-143035 (e-PCR)
- UniSTS:171772

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables methylation-dependent protein binding	IPI Inferred from Physical Interaction 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 erythrocyte maturation	IEA Inferred from Electronic Annotation more info
involved_in granulocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in macrophage differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA methylation-dependent heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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

Names: H-l(3)mbt-like protein 3; L3MBTL3, histone methyl-lysine binding protein; L3mbt-like 3; l(3)mbt-like 3

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.

Genomic

NG_051942.1 RefSeqGene

Range

5213..128070

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001007102.4 → NP_001007103.1 lethal(3)malignant brain tumor-like protein 3 isoform b

See identical proteins and their annotated locations for NP_001007103.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2-4 encode the same isoform (b).

Source sequence(s)

AB058701, AI123736, AK094137, DA927626, DB059438, DB080397

Consensus CDS

CCDS34538.1

UniProtKB/TrEMBL

A8K2F4

Related

ENSP00000437185.1, ENST00000533560.5

Conserved Domains (4) summary

cd09582
Location:680 → 745

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:680 → 746

SAM; Sterile alpha motif

smart00561
Location:211 → 307

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

pfam01530
Location:532 → 559

zf-C2HC; Zinc finger, C2HC type
NM_001346550.2 → NP_001333479.1 lethal(3)malignant brain tumor-like protein 3 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2-4 encode the same isoform (b).

Source sequence(s)

AL355581, AL356579, AL583846

Consensus CDS

CCDS34538.1

UniProtKB/TrEMBL

A8K2F4
NM_001346551.2 → NP_001333480.1 lethal(3)malignant brain tumor-like protein 3 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2-4 encode the same isoform (b).

Source sequence(s)

AL355581, AL356579, AL583846

Consensus CDS

CCDS34538.1

UniProtKB/TrEMBL

A8K2F4
NM_032438.4 → NP_115814.1 lethal(3)malignant brain tumor-like protein 3 isoform a

See identical proteins and their annotated locations for NP_115814.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AL355581, AL356579, AL583846

Consensus CDS

CCDS34537.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Related

ENSP00000354526.2, ENST00000361794.7

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type

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_000006.12 Reference GRCh38.p14 Primary Assembly

Range

130018581..130141438

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419407.1 → XP_047275363.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_011536184.3 → XP_011534486.1 lethal(3)malignant brain tumor-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_011534486.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type
XM_047419410.1 → XP_047275366.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_006715576.4 → XP_006715639.1 lethal(3)malignant brain tumor-like protein 3 isoform X1

UniProtKB/TrEMBL

A8K2F4

Conserved Domains (4) summary

cd09582
Location:740 → 805

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:740 → 806

SAM; Sterile alpha motif

smart00561
Location:271 → 367

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

pfam01530
Location:592 → 619

zf-C2HC; Zinc finger, C2HC type
XM_047419401.1 → XP_047275357.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_047419408.1 → XP_047275364.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_011536181.3 → XP_011534483.1 lethal(3)malignant brain tumor-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_011534483.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type
XM_047419400.1 → XP_047275356.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_011536180.3 → XP_011534482.1 lethal(3)malignant brain tumor-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_011534482.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type
XM_006715578.4 → XP_006715641.1 lethal(3)malignant brain tumor-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_006715641.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type
XM_047419412.1 → XP_047275368.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_047419404.1 → XP_047275360.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_047419405.1 → XP_047275361.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_011536179.4 → XP_011534481.1 lethal(3)malignant brain tumor-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_011534481.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type
XM_047419409.1 → XP_047275365.1 lethal(3)malignant brain tumor-like protein 3 isoform X3

Related

ENSP00000436706.1, ENST00000526019.5
XM_005267161.5 → XP_005267218.1 lethal(3)malignant brain tumor-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_005267218.1

UniProtKB/Swiss-Prot

Q4VXE1, Q5VUM9, Q6P9B5, Q96JM7

UniProtKB/TrEMBL

A8K2F4

Related

ENSP00000357118.2, ENST00000368136.3

Conserved Domains (4) summary

cd09582
Location:705 → 770

SAM_Scm-like-3MBT3,4; SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group

smart00454
Location:705 → 771

SAM; Sterile alpha motif

smart00561
Location:236 → 332

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

pfam01530
Location:557 → 584

zf-C2HC; Zinc finger, C2HC type
XM_047419403.1 → XP_047275359.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_047419402.1 → XP_047275358.1 lethal(3)malignant brain tumor-like protein 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

131211018..131336219

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356530.1 → XP_054212505.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_054356537.1 → XP_054212512.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356544.1 → XP_054212519.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_054356542.1 → XP_054212517.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356547.1 → XP_054212522.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_054356532.1 → XP_054212507.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_054356545.1 → XP_054212520.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_054356538.1 → XP_054212513.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356531.1 → XP_054212506.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_054356541.1 → XP_054212516.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356543.1 → XP_054212518.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356548.1 → XP_054212523.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_054356535.1 → XP_054212510.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_054356536.1 → XP_054212511.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_054356539.1 → XP_054212514.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356546.1 → XP_054212521.1 lethal(3)malignant brain tumor-like protein 3 isoform X3
XM_054356540.1 → XP_054212515.1 lethal(3)malignant brain tumor-like protein 3 isoform X2
XM_054356534.1 → XP_054212509.1 lethal(3)malignant brain tumor-like protein 3 isoform X1
XM_054356533.1 → XP_054212508.1 lethal(3)malignant brain tumor-like protein 3 isoform X1