HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
MSL3
MSL complex subunit 3
Chromosome X Β· Xp22.2
NCBI Gene: 10943Ensembl: ENSG00000005302.19HGNC: HGNC:7370UniProt: Q8N5Y2
41PubMed Papers
21Diseases
0Drugs
39Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
DNA bindingprotein bindinghistone H4K16ac reader activityhistone reader activityBasilicata-Akhtar syndromegenetic disorderIntellectual disabilityneurodegenerative disease
✦AI Summary

MSL3 is a non-catalytic component of the male-specific lethal (MSL) histone acetyltransferase complex that mediates histone H4 acetylation at lysine-16 (H4K16ac), an epigenetic mark preventing chrX compaction and maintaining chromosome X and genome integrity 1. MSL3 acts as a histone reader that specifically recognizes histone H4 monomethylated at lysine-20 (H4K20me1) in a DNA-dependent manner, proposed to be involved in chrX targeting of the MSL complex 23. The protein forms extensive hydrophobic interactions with MSL1, serving as a scaffold for MSL complex assembly and targeting to the X chrX 4. MSL3 mutations cause Basilicata-Akhtar syndrome, an X-linked neurodevelopmental disorder affecting both males and females 5. Clinical manifestations include developmental delay, intellectual disability ranging from mild to severe, autism spectrum disorder, muscle tone abnormalities, macrocephaly, hearing impairment, and gastrointestinal problems 5. Neuroimaging commonly reveals hypoplasia of the cerebellar vermis and sometimes multifocal leukoencephalopathy 56. Most disease-causing variants are de novo loss-of-function mutations (nonsense, frameshift, or splice site variants), with clustering in terminal exons 5. Affected individuals benefit from early genetic diagnosis and multidisciplinary care to optimize outcomes 6.

Sources cited
1
MSL complex maintains H4K16ac levels required for chromosome stability and genome integrity
PMID: 33837287
2
MSL3 recognizes and binds histone H4K20me1 and is involved in chromosomal targeting of MSL complex
PMID: 20657587
3
MSL3 acts as histone H4K20me1 reader in DNA-dependent manner for MSL complex targeting
PMID: 20943666
4
MSL3 interacts with MSL1 forming extensive hydrophobic interface for complex assembly and X chromosome targeting
PMID: 21217699
5
MSL3 mutations cause Basilicata-Akhtar syndrome with developmental delay, intellectual disability, autism, dysmorphisms, and cerebellar vermis hypoplasia
PMID: 33173220
6
MSL3 pathogenic variants cause neurodevelopmental disorder with multifocal leukoencephalopathy; early diagnosis improves outcomes
PMID: 40767387
Disease Associationsβ“˜21
Basilicata-Akhtar syndromeOpen Targets
0.79Strong
genetic disorderOpen Targets
0.52Moderate
Intellectual disabilityOpen Targets
0.50Moderate
neurodegenerative diseaseOpen Targets
0.43Moderate
Feeding difficultiesOpen Targets
0.37Weak
HypotoniaOpen Targets
0.37Weak
Neurodevelopmental delayOpen Targets
0.37Weak
Global developmental delayOpen Targets
0.34Weak
Neurodevelopmental abnormalityOpen Targets
0.33Weak
X-linked non-syndromic intellectual disabilityOpen Targets
0.13Weak
attention deficit hyperactivity disorderOpen Targets
0.09Suggestive
attention deficit-hyperactivity disorder 8Open Targets
0.07Suggestive
hereditary attention deficit-hyperactivity disorderOpen Targets
0.07Suggestive
intellectual disability, autosomal recessive 59Open Targets
0.07Suggestive
movement disorderOpen Targets
0.07Suggestive
schizophrenia 15Open Targets
0.07Suggestive
Phelan-McDermid syndromeOpen Targets
0.05Suggestive
autismOpen Targets
0.05Suggestive
Tourette syndromeOpen Targets
0.05Suggestive
intellectual disability, autosomal dominant 50Open Targets
0.04Suggestive
Basilicata-Akhtar syndromeUniProt
Pathogenic Variants39
NM_078629.4(MSL3):c.1125_1141dup (p.Met381fs)Pathogenic
Inborn genetic diseases|Basilicata-Akhtar syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 381
NM_078629.4(MSL3):c.973_974del (p.Gln326fs)Pathogenic
Basilicata-Akhtar syndrome|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 326
NM_078629.4(MSL3):c.1372C>T (p.Arg458Ter)Pathogenic
Intellectual disability|Basilicata-Akhtar syndrome|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 458
NM_078629.4(MSL3):c.1036C>T (p.Gln346Ter)Pathogenic
Intellectual disability|Basilicata-Akhtar syndrome|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 346
NM_078629.4(MSL3):c.1466+1G>APathogenic
Basilicata-Akhtar syndrome
β˜…β˜…β˜†β˜†2022
NM_078629.4(MSL3):c.749+5G>APathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2026
NM_078629.4(MSL3):c.588+1delLikely pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2025
NM_078629.4(MSL3):c.1281+1G>ALikely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025
NM_078629.4(MSL3):c.1211dup (p.Thr405fs)Likely pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 405
NM_078629.4(MSL3):c.980dup (p.Thr328fs)Likely pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 328
NM_078629.4(MSL3):c.590_593delPathogenic
Basilicata-Akhtar syndrome|not provided
β˜…β˜†β˜†β˜†2025
NM_078629.4(MSL3):c.909-1G>APathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024
NM_078629.4(MSL3):c.1347C>A (p.Tyr449Ter)Likely pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 449
NM_078629.4(MSL3):c.750-2A>GLikely pathogenic
Basilicata-Akhtar syndrome|Nonpapillary renal cell carcinoma
β˜…β˜†β˜†β˜†2023
NM_078629.4(MSL3):c.1373G>A (p.Arg458Gln)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 458
GRCh38/hg38 Xp22.2(chrX:11766227-11770962)x0Pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2023
NM_078629.4(MSL3):c.1105C>T (p.Gln369Ter)Pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 369
NM_078629.4(MSL3):c.547C>T (p.Gln183Ter)Pathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 183
NM_078629.4(MSL3):c.1282-249_1382-154delPathogenic
Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2022
NM_078629.4(MSL3):c.961C>T (p.Gln321Ter)Likely pathogenic
not provided|Basilicata-Akhtar syndrome
β˜…β˜†β˜†β˜†2022β†’ Residue 321
View on ClinVar β†—
Related Genes
H2BK1Shared pathway100%H2BW2Shared pathway100%ZCWPW2Shared pathway100%MSL3BShared pathway100%CDYL2Shared pathway100%ZNF618Shared pathway100%
Tissue Expression6 tissues
Lung
100%
Bone Marrow
91%
Brain
47%
Ovary
43%
Liver
40%
Heart
34%
Gene Interaction Network
Click a node to explore
MSL3H2BK1H2BW2ZCWPW2MSL3BCDYL2ZNF618
PROTEIN STRUCTURE
Preparing viewer…
PDB3OA6 Β· 2.35 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.28Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.13 [0.07–0.28]
RankingsWhere MSL3 stands among ~20K protein-coding genes
  • #10,037of 20,598
    Most Researched41
  • #1,574of 5,498
    Most Pathogenic Variants39
  • #1,007of 17,882
    Most Constrained (LOEUF)0.28 Β· top 10%
Genes detectedMSL3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Prevalence and architecture of de novo mutations in developmental disorders.
PMID: 28135719
Nature Β· 2017
1.00
2
MSL2 variants lead to a neurodevelopmental syndrome with lack of coordination, epilepsy, specific dysmorphisms, and a distinct episignature.
PMID: 38815585
Am J Hum Genet Β· 2024
0.90
3
Loss of function of male-specific lethal 3 (Msl3) does not affect spermatogenesis in rodents.
PMID: 37847071
Dev Dyn Β· 2024
0.80
4
Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder.
PMID: 33173220
Genet Med Β· 2021
0.70
5
Loss Of Chromodomain of Male-Specific Lethal 3 (MSL3) Does Not Affect Spermatogenesis In Rodents.
PMID: 36993289
bioRxiv Β· 2023
0.60