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MSL3 MSL complex subunit 3 [ Homo sapiens (human) ]

Gene ID: 10943, updated on 13-Apr-2024

Summary

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Official Symbol
MSL3provided by HGNC
Official Full Name
MSL complex subunit 3provided by HGNC
Primary source
HGNC:HGNC:7370
See related
Ensembl:ENSG00000005302 MIM:300609; AllianceGenome:HGNC:7370
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
MRSXBA; MRXS36; MRXSBA; MSL3L1
Summary
This gene encodes a nuclear protein that is similar to the product of the Drosophila male-specific lethal-3 gene. The Drosophila protein plays a critical role in a dosage-compensation pathway, which equalizes X-linked gene expression in males and females. Thus, the human protein is thought to play a similar function in chromatin remodeling and transcriptional regulation, and it has been found as part of a complex that is responsible for histone H4 lysine-16 acetylation. This gene can undergo X inactivation. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 2, 7 and 8. [provided by RefSeq, Jul 2010]
Expression
Ubiquitous expression in lymph node (RPKM 13.7), appendix (RPKM 11.8) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
Xp22.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (11758159..11775772)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (11340708..11358321)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (11776278..11793891)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20661 Neighboring gene Sharpr-MPRA regulatory region 2065 Neighboring gene MSL3 divergent transcript Neighboring gene FERM and PDZ domain containing 4 Neighboring gene MPRA-validated peak7357 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:12327767-12328270 Neighboring gene FRMPD4 antisense RNA 1 Neighboring gene ribosomal protein L17 pseudogene 49

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
  • 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. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder. Brunet T, et al. Genet Med, 2021 Feb. PMID 33173220, Free PMC Article
  2. Characterization of a novel chromo domain gene in xp22.3 with homology to Drosophila msl-3. Prakash SK, et al. Genomics, 1999 Jul 1. PMID 10395802
  3. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation. Basilicata MF, et al. Nat Genet, 2018 Oct. PMID 30224647, Free PMC Article
  4. Origin and evolution of the regulatory gene male-specific lethal-3. Marín I, et al. Mol Biol Evol, 2000 Aug. PMID 10908644
  5. Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain. Kim D, et al. Nat Struct Mol Biol, 2010 Aug. PMID 20657587, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder.
    Title: Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder.
  2. Characterization of syndrome that allowed us to decipher the developmental importance of MSL3 in humans.
    Title: De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation.
  3. MSL3 plays an important role in targeting the male specific lethal complex to chromatin in both humans and flies by binding to H4K20Me(1).
    Title: Structural and biochemical studies on the chromo-barrel domain of male specific lethal 3 (MSL3) reveal a binding preference for mono- or dimethyllysine 20 on histone H4.
  4. A multisubunit human histone acetylase complex that contains homologs of the Drosophila MSL proteins MOF, MSL1 (hampin A), MSL2, and MSL3 was described. This complex is responsible for histone H4 lysine-16 acetylation of all cellular chromosomes.
    Title: A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16.
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

Associated conditions

Description Tests
Basilicata-Akhtar syndrome
MedGen: C5231394 OMIM: 301032 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2023-08-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2023-08-23)

ClinGen Genome Curation PagePubMed

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp586J1822

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H4K16 acetyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of MSL complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of MSL complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of NuA4 histone acetyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
male-specific lethal 3 homolog
Names
MSL3-like 1
male-specific lethal-3 protein-like 1

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_012564.1 RefSeqGene

    Range
    5079..22614
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001193270.2 → NP_001180199.1  male-specific lethal 3 homolog isoform e

    See identical proteins and their annotated locations for NP_001180199.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, and uses a distinct start codon, compared to variant 1. The resulting isoform (e) has a distinct N-terminus and is 12 aa shorter than isoform a.
    Source sequence(s)
    AK300814, BC031210, DA172776, DC395802
    Consensus CDS
    CCDS55369.1
    UniProtKB/TrEMBL
    A0A3B3IT59
    Related
    ENSP00000381538.2, ENST00000398527.7
    Conserved Domains (3) summary
    smart00298
    Location:24 → 66
    CHROMO; Chromatin organization modifier domain
    pfam05712
    Location:145 → 494
    MRG; MRG
    pfam12258
    Location:297 → 401
    Microcephalin; Microcephalin protein

  2. NM_001282174.1 → NP_001269103.1  male-specific lethal 3 homolog isoform f

    See identical proteins and their annotated locations for NP_001269103.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in its 5' UTR and 5' coding region, and uses a distinct start codon, compared to variant 1. The resulting isoform (f) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AF117065, AK294255, AL713667
    Consensus CDS
    CCDS65213.1
    UniProtKB/TrEMBL
    A0A3F2YNX2
    Related
    ENSP00000354562.2, ENST00000361672.6
    Conserved Domains (2) summary
    pfam05712
    Location:4 → 357
    MRG; MRG
    pfam12258
    Location:160 → 264
    Microcephalin; Microcephalin protein

  3. NM_006800.4 → NP_006791.2  male-specific lethal 3 homolog isoform c

    See identical proteins and their annotated locations for NP_006791.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The resulting isoform (c) is 166 aa shorter shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC004554, AK025642, CT002798, DA961602
    Consensus CDS
    CCDS14149.1
    UniProtKB/TrEMBL
    A0A3F2YNX2
    Related
    ENSP00000498017.1, ENST00000649078.1
    Conserved Domains (2) summary
    pfam05712
    Location:6 → 340
    MRG
    pfam12258
    Location:143 → 247
    Microcephalin; Microcephalin protein

  4. NM_078628.2 → NP_523352.1  male-specific lethal 3 homolog isoform d

    See identical proteins and their annotated locations for NP_523352.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (d) has a distinct C-terminus and is 105 aa shorter than isoform a.
    Source sequence(s)
    AF117065, AK000793, AK289780, DB240082
    Consensus CDS
    CCDS14148.1
    UniProtKB/TrEMBL
    A0A3B3ITF3
    Related
    ENSP00000338078.2, ENST00000337339.7
    Conserved Domains (3) summary
    pfam05712
    Location:157 → 289
    MRG; MRG
    pfam11717
    Location:14 → 73
    Tudor-knot; RNA binding activity-knot of a chromodomain
    pfam12258
    Location:309 → 392
    Microcephalin; Microcephalin protein

  5. NM_078629.4 → NP_523353.2  male-specific lethal 3 homolog isoform a

    See identical proteins and their annotated locations for NP_523353.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC004554, AF117065, BC031210
    Consensus CDS
    CCDS14147.1
    UniProtKB/Swiss-Prot
    A6NCU2, A6NHW8, A8K165, B4DUV8, B7Z227, Q8N5Y2, Q9UG70, Q9Y5Z8
    UniProtKB/TrEMBL
    A0A3B3IT59
    Related
    ENSP00000312244.4, ENST00000312196.10
    Conserved Domains (2) summary
    cd18983
    Location:15 → 81
    CBD_MSL3_like; chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins
    pfam05712
    Location:156 → 506
    MRG

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    11758159..11775772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    11340708..11358321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_078630.1: Suppressed sequence

    Description
    NM_078630.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N5Y2.1 GenPept UniProtKB/Swiss-Prot:Q8N5Y2

Gene LinkOut

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