MSL1

MSL complex subunit 1, the group of MSL histone acetyltransferase complex

Basic information

Region (hg38): 17:40121971-40136917

Links

ENSG00000188895 ∙ NCBI:339287 ∙ OMIM:614801 ∙ HGNC:27905 ∙ Uniprot:Q68DK7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MSL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSL1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in MSL1

This is a list of pathogenic ClinVar variants found in the MSL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-40126289-A-G		not specified	Uncertain significance (Aug 20, 2024)
17-40126319-T-C		not specified	Uncertain significance (Jun 24, 2022)
17-40126388-G-C		not specified	Uncertain significance (Oct 20, 2021)
17-40129265-C-T		not specified	Uncertain significance (May 31, 2023)
17-40129280-C-T		not specified	Uncertain significance (Jun 16, 2023)
17-40129424-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-40129502-C-T		not specified	Uncertain significance (Feb 14, 2023)
17-40129515-A-T		not specified	Uncertain significance (Oct 22, 2024)
17-40129586-C-A		not specified	Uncertain significance (Oct 11, 2024)
17-40131557-G-A		not specified	Uncertain significance (Oct 01, 2024)
17-40133050-T-G		not specified	Uncertain significance (Aug 09, 2021)
17-40133103-G-T		not specified	Uncertain significance (Feb 28, 2024)
17-40133848-C-G		not specified	Uncertain significance (Jun 07, 2024)
17-40133863-T-C		not specified	Uncertain significance (Jun 07, 2024)
17-40134279-G-T		not specified	Uncertain significance (Aug 05, 2024)
17-40134293-C-T		not specified	Uncertain significance (Jan 09, 2024)
17-40134314-G-A		not specified	Uncertain significance (Nov 27, 2023)
17-40134337-A-C		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSL1	protein_coding	protein_coding	ENST00000579565	8	14492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00110	124476	0	1	124477	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	115	182	0.631	0.00000967	2247
Missense in Polyphen		38	87.547	0.43405		1086
Synonymous	0.448	64	68.7	0.931	0.00000360	665
Loss of Function	4.12	0	19.8	0.00	0.00000110	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000647
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: dbNSFP

• Function: FUNCTION: Component of histone acetyltransferase complex responsible for the majority of histone H4 acetylation at 'Lys-16' (H4K16ac) which is implicated in the formation of higher-order chromatin structure. Greatly enhances MSL2 E3 ubiquitin ligase activity, promoting monoubiquitination of histone H2B at 'Lys-34' (H2BK34Ub). This modification in turn stimulates histone H3 methylation at 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) and leads to gene activation, including that of HOXA9 and MEIS1. In the MSL complex, acts as a scaffold to tether MSL3 and KAT8 together for enzymatic activity regulation. {ECO:0000269|PubMed:16227571, ECO:0000269|PubMed:21726816, ECO:0000269|PubMed:22547026}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.236
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.662
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.803

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Msl1

Gene ontology

• Biological process: histone H4-K16 acetylation
• Cellular component: nucleoplasm;MSL complex
• Molecular function: chromatin binding