MSL2

MSL complex subunit 2, the group of Ring finger proteins|MSL histone acetyltransferase complex

Basic information

Region (hg38): 3:136148917-136197241

Previous symbols: [ "RNF184", "MSL2L1" ]

Links

ENSG00000174579NCBI:55167OMIM:614802HGNC:25544Uniprot:Q9HCI7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • complex neurodevelopmental disorder (Strong), mode of inheritance: AD
  • Karayol-Borroto-Haghshenas neurodevelopmental syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Karayol-Borroto-Haghshenas neurodevelopmental syndromeADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic; Ophthalmologic38815585

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MSL2 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
1
clinvar
55
clinvar
4
clinvar
60
nonsense
3
clinvar
1
clinvar
3
clinvar
7
start loss
0
frameshift
1
clinvar
6
clinvar
8
clinvar
15
splice donor/acceptor (+/-2bp)
0
Total 5 7 66 4 0

Highest pathogenic variant AF is 0.0000012393663

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MSL2protein_codingprotein_codingENST00000309993 248320
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6240.376125737041257410.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.002103090.6790.00001663789
Missense in Polyphen3896.4250.394091227
Synonymous-2.271461151.270.000006191164
Loss of Function3.03316.10.1869.73e-7226

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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