MSL2
Basic information
Region (hg38): 3:136148917-136197241
Previous symbols: [ "RNF184", "MSL2L1" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Strong), mode of inheritance: AD
- Karayol-Borroto-Haghshenas neurodevelopmental syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Karayol-Borroto-Haghshenas neurodevelopmental syndrome | AD | 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; Ophthalmologic | 38815585 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (47 variants)
- not_provided (27 variants)
- Karayol-Borroto-Haghshenas_neurodevelopmental_syndrome (8 variants)
- Syndromic_neurodevelopmental_disorder (3 variants)
- Autism (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSL2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018133.4. 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 | 0 | |||||
missense | 55 | 60 | ||||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 15 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 5 | 7 | 66 | 4 | 0 |
Highest pathogenic variant AF is 0.0000012393663
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MSL2 | protein_coding | protein_coding | ENST00000309993 | 2 | 48320 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.624 | 0.376 | 125737 | 0 | 4 | 125741 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.00 | 210 | 309 | 0.679 | 0.0000166 | 3789 |
Missense in Polyphen | 38 | 96.425 | 0.39409 | 1227 | ||
Synonymous | -2.27 | 146 | 115 | 1.27 | 0.00000619 | 1164 |
Loss of Function | 3.03 | 3 | 16.1 | 0.186 | 9.73e-7 | 226 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000176 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of histone acetyltransferase complex responsible for the majority of histone H4 acetylation at lysine 16 which is implicated in the formation of higher-order chromatin structure. Acts as an E3 ubiquitin ligase that promotes monoubiquitination of histone H2B at 'Lys-35' (H2BK34Ub), but not that of H2A. This activity is greatly enhanced by heterodimerization with MSL1. H2B ubiquitination in turn stimulates histine H3 methylation at 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) and leads to gene activation, including that of HOXA9 and MEIS1. {ECO:0000269|PubMed:21726816}.;
- Pathway
- Chromatin modifying enzymes;TCR;HATs acetylate histones;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.00717
- rvis_EVS
- -0.53
- rvis_percentile_EVS
- 20.7
Haploinsufficiency Scores
- pHI
- 0.972
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Msl2
- Phenotype
Gene ontology
- Biological process
- protein ubiquitination;histone H4-K16 acetylation
- Cellular component
- nucleoplasm;MSL complex
- Molecular function
- metal ion binding;ubiquitin protein ligase activity