MSL1

protein-coding

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

Gene summary

Enables protein-macromolecule adaptor activity. Involved in positive regulation of DNA-templated transcription. Located in nuclear speck. Part of MSL complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001365919.1

Inheritance

—

ClinVar variants

U:42

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:40,121,971-40,136,917

External References & Databases

Ensembl (ENSG00000188895)

Transcript & Mutation Effects

hg38 • Region Span ~14.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MSL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001365919.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	42	0	0	42

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001365919.1	RefSeq	NP_001352848.1	9	MANE Select
ENST00000398532.9	Ensembl	ENSP00000381543.3	9	MANE Select
NM_001012241.2	RefSeq	NP_001012241.1	8	Standard
NM_001365920.1	RefSeq	NP_001352849.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization

Biological Process

histone H4-K16 acetylation

Molecular Function

chromatin binding

Cellular Component

nucleoplasm
MSL complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000579565
Coding exons: 8
Length: 14492
Individuals with no LoFs: 124476
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124477
p: 0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.77	115	182	0.631	0.00000967	2247
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.236
RVIS EVS: -0.05
RVIS percentile EVS: 49.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.803

Gene Damage Prediction

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