MSL3
Basic information
Region (hg38): X:11758159-11775772
Previous symbols: [ "MSL3L1" ]
Links
Phenotypes
GenCC
Source:
- Basilicata-Akhtar syndrome (Strong), mode of inheritance: XL
- Basilicata-Akhtar syndrome (Strong), mode of inheritance: XL
- Basilicata-Akhtar syndrome (Definitive), mode of inheritance: XL
- Basilicata-Akhtar syndrome (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Basilicata-Akhtar syndrome | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 30224647 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (60 variants)
- Inborn_genetic_diseases (36 variants)
- Basilicata-Akhtar_syndrome (31 variants)
- MSL3-related_disorder (12 variants)
- Intellectual_disability (9 variants)
- not_specified (2 variants)
- X-linked_neurodevelopmental_delay,_dysmorphism,_and_progressive_neurological_disorder (1 variants)
- Global_developmental_delay (1 variants)
- Neurodevelopmental_abnormality (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000078629.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 8 | |||||
missense | 66 | 11 | 80 | |||
nonsense | 10 | |||||
start loss | 0 | |||||
frameshift | 16 | |||||
splice donor/acceptor (+/-2bp) | 9 | |||||
Total | 20 | 17 | 67 | 17 | 2 |
Highest pathogenic variant AF is 9.5177813e-7
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MSL3 | protein_coding | protein_coding | ENST00000312196 | 13 | 17593 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.997 | 0.00335 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.93 | 121 | 197 | 0.613 | 0.0000157 | 3439 |
Missense in Polyphen | 24 | 69.397 | 0.34584 | 1335 | ||
Synonymous | 0.672 | 63 | 70.2 | 0.898 | 0.00000554 | 942 |
Loss of Function | 3.80 | 0 | 16.8 | 0.00 | 0.00000113 | 351 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in chromatin remodeling and transcriptional regulation. May have a role in X inactivation. Component of the MSL complex which is responsible for the majority of histone H4 acetylation at 'Lys-16' which is implicated in the formation of higher-order chromatin structure. Specifically recognizes histone H4 monomethylated at 'Lys-20' (H4K20Me1) in a DNA-dependent manner and is proposed to be involved in chromosomal targeting of the MSL complex. {ECO:0000269|PubMed:16227571, ECO:0000269|PubMed:20018852, ECO:0000269|PubMed:20657587, ECO:0000269|PubMed:20943666, ECO:0000269|PubMed:21217699, ECO:0000269|PubMed:22547026}.;
- Pathway
- Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.0976
Intolerance Scores
- loftool
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.32
Haploinsufficiency Scores
- pHI
- 0.241
- hipred
- Y
- hipred_score
- 0.746
- ghis
- 0.528
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.872
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Msl3
- Phenotype
Gene ontology
- Biological process
- chromatin silencing;histone acetylation;histone deacetylation;histone H4 acetylation;histone H2A acetylation;histone H4-K16 acetylation
- Cellular component
- histone acetyltransferase complex;nucleoplasm;NuA4 histone acetyltransferase complex;MSL complex
- Molecular function
- DNA binding;methylated histone binding