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LCORL ligand dependent nuclear receptor corepressor like [ Homo sapiens (human) ]

Gene ID: 254251, updated on 2-Nov-2024

Summary

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Official Symbol
LCORLprovided by HGNC
Official Full Name
ligand dependent nuclear receptor corepressor likeprovided by HGNC
Primary source
HGNC:HGNC:30776
See related
Ensembl:ENSG00000178177 MIM:611799; AllianceGenome:HGNC:30776
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
MLR1
Summary
This gene encodes a transcription factor that appears to function in spermatogenesis. Polymorphisms in this gene are associated with measures of skeletal frame size and adult height. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression
Ubiquitous expression in testis (RPKM 2.1), small intestine (RPKM 1.8) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See LCORL in Genome Data Viewer
Location:
4p15.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (17841187..18021875, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (17823534..18004228, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (17842810..18023498, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15312 Neighboring gene family with sequence similarity 184 member B Neighboring gene mediator complex subunit 28 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17812049-17812560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17812561-17813073 Neighboring gene DDB1 and CUL4 associated factor 16 Neighboring gene non-SMC condensin I complex subunit G Neighboring gene keratin 18 pseudogene 63 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21358 Neighboring gene uncharacterized LOC107986220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:18160933-18161439 Neighboring gene uncharacterized LOC107986262

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Identification and characterization of Mlr1,2: two mouse homologues of Mblk-1, a transcription factor from the honeybee brain(1). Kunieda T, et al. FEBS Lett, 2003 Jan 30. PMID 12560079
  2. A pathogenic CtBP1 missense mutation causes altered cofactor binding and transcriptional activity. Beck DB, et al. Neurogenetics, 2019 Aug. PMID 31041561, Free PMC Article
  3. New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism. Horikoshi M, et al. Nat Genet, 2013 Jan. PMID 23202124, Free PMC Article
  4. Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe). Carty CL, et al. Hum Mol Genet, 2012 Feb 1. PMID 22021425, Free PMC Article
  5. Genome-wide association study of height and body mass index in Australian twin families. Liu JZ, et al. Twin Res Hum Genet, 2010 Apr. PMID 20397748, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  2. Identification and characterization of an homologous gene in mouse.
    Title: Identification and characterization of Mlr1,2: two mouse homologues of Mblk-1, a transcription factor from the honeybee brain(1).
  3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
Submit: New GeneRIF Correction

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
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
EBI GWAS Catalog
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
EBI GWAS Catalog
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
EBI GWAS Catalog
Genome-wide association analysis identifies 20 loci that influence adult height.
EBI GWAS Catalog
Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe).
EBI GWAS Catalog
Genome-wide association study of height and body mass index in Australian twin families.
EBI GWAS Catalog
Genome-wide diet-gene interaction analyses for risk of colorectal cancer.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
EBI GWAS Catalog
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
EBI GWAS Catalog
New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30696

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone methyltransferase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ligand-dependent nuclear receptor corepressor-like protein
Names
LCOR-like protein
MBLK1-related protein
transcription factor MLR1

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

  1. NG_015822.2 RefSeqGene

    Range
    5106..185674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166139.2 → NP_001159611.1  ligand-dependent nuclear receptor corepressor-like protein isoform 1

    See identical proteins and their annotated locations for NP_001159611.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). There are no full-length human transcripts representing this variant; it is supported by partial human transcript alignments and by full-length homologous mouse transcripts (GeneID:209707).
    Source sequence(s)
    AC005768, AK055258, AL700364, BC037322, BC062661, BU902997, BX107807
    Consensus CDS
    CCDS54749.1
    UniProtKB/Swiss-Prot
    Q8N3X6, Q96NK1
    Related
    ENSP00000371661.5, ENST00000382226.5
    Conserved Domains (1) summary
    pfam05225
    Location:526 → 571
    HTH_psq; helix-turn-helix, Psq domain

  2. NM_001365658.1 → NP_001352587.1  ligand-dependent nuclear receptor corepressor-like protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variant 5, encodes isoform 3.
    Source sequence(s)
    AC005768, AC079399
    Conserved Domains (1) summary
    pfam05225
    Location:366 → 411
    HTH_psq; helix-turn-helix, Psq domain

  3. NM_001365659.1 → NP_001352588.1  ligand-dependent nuclear receptor corepressor-like protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variant 4, encodes isoform 3.
    Source sequence(s)
    AC005768, AC079399
    Conserved Domains (1) summary
    pfam05225
    Location:366 → 411
    HTH_psq; helix-turn-helix, Psq domain

  4. NM_001365660.1 → NP_001352589.1  ligand-dependent nuclear receptor corepressor-like protein isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
    Consensus CDS
    CCDS93484.1
    UniProtKB/TrEMBL
    A0A6Q8PG24, A0A6Q8PHE0
    Related
    ENSP00000502692.1, ENST00000675143.1

  5. NM_001365661.1 → NP_001352590.1  ligand-dependent nuclear receptor corepressor-like protein isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC079399
    Consensus CDS
    CCDS93486.1
    UniProtKB/TrEMBL
    A0A6Q8PG24, A0A6Q8PHT2
    Related
    ENSP00000502833.1, ENST00000674942.1

  6. NM_001365662.1 → NP_001352591.1  ligand-dependent nuclear receptor corepressor-like protein isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
    UniProtKB/TrEMBL
    A0A6Q8PG24

  7. NM_001365663.1 → NP_001352592.1  ligand-dependent nuclear receptor corepressor-like protein isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
    UniProtKB/TrEMBL
    A0A6Q8PG24

  8. NM_001365665.1 → NP_001352594.1  ligand-dependent nuclear receptor corepressor-like protein isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

  9. NM_001394446.1 → NP_001381375.1  ligand-dependent nuclear receptor corepressor-like protein isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
    Consensus CDS
    CCDS93485.1
    UniProtKB/TrEMBL
    A0A1B0GVP4
    Related
    ENSP00000490600.1, ENST00000635767.2
    Conserved Domains (1) summary
    pfam15090
    Location:1416 → 1866
    DUF4553; Domain of unknown function (DUF4553)

  10. NM_153686.8 → NP_710153.2  ligand-dependent nuclear receptor corepressor-like protein isoform 2

    See identical proteins and their annotated locations for NP_710153.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 3' terminal exon compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC005768, AK299939, AL133031, BC037322, BU902997
    Consensus CDS
    CCDS3425.1
    UniProtKB/TrEMBL
    A0A6Q8PG24
    Related
    ENSP00000317566.3, ENST00000326877.8

RNA

  1. NR_136669.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two non-consecutive exons and contains an alternate 3' terminal exon compared to variant 1. It is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005768, AK299939, AL133031, BC037322

  2. NR_158563.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
    Related
    ENST00000675131.1

  3. NR_158564.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

  4. NR_158565.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

  5. NR_158566.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

  6. NR_158567.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

  7. NR_158568.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

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

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    17841187..18021875 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449965.1 → XP_047305921.1  ligand-dependent nuclear receptor corepressor-like protein isoform X1

  2. XM_017007965.2 → XP_016863454.1  ligand-dependent nuclear receptor corepressor-like protein isoform X3

  3. XM_047449966.1 → XP_047305922.1  ligand-dependent nuclear receptor corepressor-like protein isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    17823534..18004228 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349513.1 → XP_054205488.1  ligand-dependent nuclear receptor corepressor-like protein isoform X1

  2. XM_054349515.1 → XP_054205490.1  ligand-dependent nuclear receptor corepressor-like protein isoform X3

  3. XM_054349514.1 → XP_054205489.1  ligand-dependent nuclear receptor corepressor-like protein isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N3X6.4 GenPept UniProtKB/Swiss-Prot:Q8N3X6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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