Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10943
Gene name	MSL complex subunit 3
Gene symbol	MSL3
Synonyms (NCBI Gene)	MRSXBAMRXS36MRXSBAMSL3L1
Chromosome	X
Chromosome location	Xp22.2
Summary	This gene encodes a nuclear protein that is similar to the product of the Drosophila male-specific lethal-3 gene. The Drosophila protein plays a critical role in a dosage-compensation pathway, which equalizes X-linked gene expression in males and females.

Show/Hide all (13)

SNP ID	Visualize variation	Clinical significance	Consequence
rs768515139	C>-,CC	Pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant
rs1555906707	T>C	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs1555906768	C>T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs1555906781	TG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555907215	C>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1555907620	C>T	Pathogenic, likely-pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant
rs1555907623	ATTGTTTG>-	Pathogenic, likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1555907626	G>T	Pathogenic, likely-pathogenic	Genic downstream transcript variant, splice donor variant
rs1555907653	->C	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1555907864	GC>A	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1601769604	AGAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs1601769873	AA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1601774648	G>A	Likely-pathogenic	Splice donor variant, genic downstream transcript variant

112

Show/Hide all (112)

miRTarBase ID	miRNA	Experiments	Reference
MIRT049772	hsa-miR-92a-3p	qRT-PCR	23622248
MIRT051352	hsa-let-7f-5p	CLASH	23622248
MIRT051183	hsa-miR-16-5p	CLASH	23622248
MIRT050657	hsa-miR-18a-5p	CLASH	23622248
MIRT050069	hsa-miR-26a-5p	CLASH	23622248
MIRT049772	hsa-miR-92a-3p	CLASH	23622248
MIRT048163	hsa-miR-196a-5p	CLASH	23622248
MIRT048029	hsa-miR-148a-3p	CLASH	23622248
MIRT047555	hsa-miR-10a-5p	CLASH	23622248
MIRT047419	hsa-miR-10b-5p	CLASH	23622248
MIRT045319	hsa-miR-185-5p	CLASH	23622248
MIRT045135	hsa-miR-186-5p	CLASH	23622248
MIRT042164	hsa-miR-484	CLASH	23622248
MIRT039372	hsa-miR-421	CLASH	23622248
MIRT1161688	hsa-miR-4659a-5p	CLIP-seq
MIRT1161689	hsa-miR-4659b-5p	CLIP-seq
MIRT1161690	hsa-miR-4776-3p	CLIP-seq
MIRT1161691	hsa-miR-103a	CLIP-seq
MIRT1161692	hsa-miR-107	CLIP-seq
MIRT1161693	hsa-miR-122	CLIP-seq
MIRT1161694	hsa-miR-1228	CLIP-seq
MIRT1161695	hsa-miR-129-5p	CLIP-seq
MIRT1161696	hsa-miR-203	CLIP-seq
MIRT1161697	hsa-miR-2277-3p	CLIP-seq
MIRT1161698	hsa-miR-3145-3p	CLIP-seq
MIRT1161699	hsa-miR-3184	CLIP-seq
MIRT1161700	hsa-miR-3189-5p	CLIP-seq
MIRT1161701	hsa-miR-3198	CLIP-seq
MIRT1161702	hsa-miR-3647-3p	CLIP-seq
MIRT1161703	hsa-miR-365	CLIP-seq
MIRT1161704	hsa-miR-370	CLIP-seq
MIRT1161705	hsa-miR-423-5p	CLIP-seq
MIRT1161706	hsa-miR-4309	CLIP-seq
MIRT1161707	hsa-miR-4514	CLIP-seq
MIRT1161708	hsa-miR-4520a-3p	CLIP-seq
MIRT1161709	hsa-miR-4520b-3p	CLIP-seq
MIRT1161710	hsa-miR-4529-3p	CLIP-seq
MIRT1161711	hsa-miR-4692	CLIP-seq
MIRT1161712	hsa-miR-4705	CLIP-seq
MIRT1161713	hsa-miR-4711-3p	CLIP-seq
MIRT1161714	hsa-miR-4729	CLIP-seq
MIRT1161715	hsa-miR-4738-3p	CLIP-seq
MIRT1161716	hsa-miR-4758-3p	CLIP-seq
MIRT1161717	hsa-miR-4766-5p	CLIP-seq
MIRT1161718	hsa-miR-4794	CLIP-seq
MIRT1161719	hsa-miR-566	CLIP-seq
MIRT1161720	hsa-miR-654-3p	CLIP-seq
MIRT2046406	hsa-miR-27a	CLIP-seq
MIRT2046407	hsa-miR-27b	CLIP-seq
MIRT2046408	hsa-miR-409-3p	CLIP-seq
MIRT2046409	hsa-miR-4760-5p	CLIP-seq
MIRT2046410	hsa-miR-513a-5p	CLIP-seq
MIRT2275487	hsa-miR-1225-3p	CLIP-seq
MIRT2275488	hsa-miR-4323	CLIP-seq
MIRT2275489	hsa-miR-4761-5p	CLIP-seq
MIRT2574357	hsa-miR-1208	CLIP-seq
MIRT2574358	hsa-miR-1273g	CLIP-seq
MIRT1161696	hsa-miR-203	CLIP-seq
MIRT2574359	hsa-miR-3140-3p	CLIP-seq
MIRT2574360	hsa-miR-3672	CLIP-seq
MIRT2574361	hsa-miR-3973	CLIP-seq
MIRT2574362	hsa-miR-423-3p	CLIP-seq
MIRT2574363	hsa-miR-4420	CLIP-seq
MIRT1161708	hsa-miR-4520a-3p	CLIP-seq
MIRT1161709	hsa-miR-4520b-3p	CLIP-seq
MIRT1161710	hsa-miR-4529-3p	CLIP-seq
MIRT2574364	hsa-miR-4638-5p	CLIP-seq
MIRT1161688	hsa-miR-4659a-5p	CLIP-seq
MIRT1161689	hsa-miR-4659b-5p	CLIP-seq
MIRT1161690	hsa-miR-4776-3p	CLIP-seq
MIRT2574365	hsa-miR-4797-5p	CLIP-seq
MIRT2574366	hsa-miR-502-5p	CLIP-seq
MIRT2574367	hsa-miR-518a-5p	CLIP-seq
MIRT2574368	hsa-miR-527	CLIP-seq
MIRT2574369	hsa-miR-548a-5p	CLIP-seq
MIRT2574370	hsa-miR-548ab	CLIP-seq
MIRT2574371	hsa-miR-548ak	CLIP-seq
MIRT2574372	hsa-miR-548b-5p	CLIP-seq
MIRT2574373	hsa-miR-548c-5p	CLIP-seq
MIRT2574374	hsa-miR-548d-5p	CLIP-seq
MIRT2574375	hsa-miR-548h	CLIP-seq
MIRT2574376	hsa-miR-548i	CLIP-seq
MIRT2574377	hsa-miR-548j	CLIP-seq
MIRT2574378	hsa-miR-548w	CLIP-seq
MIRT2574379	hsa-miR-548y	CLIP-seq
MIRT2574380	hsa-miR-559	CLIP-seq
MIRT2574357	hsa-miR-1208	CLIP-seq
MIRT2275487	hsa-miR-1225-3p	CLIP-seq
MIRT2574358	hsa-miR-1273g	CLIP-seq
MIRT1161696	hsa-miR-203	CLIP-seq
MIRT2574359	hsa-miR-3140-3p	CLIP-seq
MIRT2685386	hsa-miR-3613-3p	CLIP-seq
MIRT2574360	hsa-miR-3672	CLIP-seq
MIRT2685387	hsa-miR-3945	CLIP-seq
MIRT2574362	hsa-miR-423-3p	CLIP-seq
MIRT2685388	hsa-miR-4253	CLIP-seq
MIRT2275488	hsa-miR-4323	CLIP-seq
MIRT2574363	hsa-miR-4420	CLIP-seq
MIRT1161708	hsa-miR-4520a-3p	CLIP-seq
MIRT1161709	hsa-miR-4520b-3p	CLIP-seq
MIRT1161710	hsa-miR-4529-3p	CLIP-seq
MIRT2574364	hsa-miR-4638-5p	CLIP-seq
MIRT1161688	hsa-miR-4659a-5p	CLIP-seq
MIRT1161689	hsa-miR-4659b-5p	CLIP-seq
MIRT2275489	hsa-miR-4761-5p	CLIP-seq
MIRT1161690	hsa-miR-4776-3p	CLIP-seq
MIRT2574365	hsa-miR-4797-5p	CLIP-seq
MIRT2574366	hsa-miR-502-5p	CLIP-seq
MIRT2574367	hsa-miR-518a-5p	CLIP-seq
MIRT2574368	hsa-miR-527	CLIP-seq
MIRT2685389	hsa-miR-541	CLIP-seq
MIRT2685390	hsa-miR-654-5p	CLIP-seq

Show/Hide all (19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IDA	20657587
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	30224647, 32814053
GO:0005634	Component	Nucleus	IDA	16227571, 30224647
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006325	Process	Chromatin organization	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IMP	30224647
GO:0035267	Component	NuA4 histone acetyltransferase complex	IBA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IDA	11742995, 11965546, 22547026
GO:0045893	Process	Positive regulation of DNA-templated transcription	IDA	20657587
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	ISO
GO:0072487	Component	MSL complex	IBA
GO:0072487	Component	MSL complex	IDA	20018852, 30224647, 33837287
GO:0072487	Component	MSL complex	IEA
GO:0140046	Function	Histone H4K16ac reader activity	IDA	20657587
GO:0140566	Function	Histone reader activity	IDA	20657587

MIM	HGNC	e!Ensembl
300609	7370	ENSG00000005302

Q8N5Y2

Protein name

MSL complex subunit 3 (Male-specific lethal 3 homolog) (Male-specific lethal-3 homolog 1) (Male-specific lethal-3 protein-like 1) (MSL3-like 1)

Protein function

Non-catalytic component of the MSL histone acetyltransferase complex, a multiprotein complex that mediates the majority of histone H4 acetylation at 'Lys-16' (H4K16ac), an epigenetic mark that prevents chromatin compaction (PubMed:16227571, PubM

PDB

2Y0N , 3OA6 , 3OB9

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF11717	Tudor-knot	11 → 74	RNA binding activity-knot of a chromodomain	Family
PF05712	MRG	151 → 506	MRG	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in many tissues including liver, pancreas, heart, lung, kidney, skeletal muscle, brain, and placenta, with highest expression in skeletal muscle and heart. {ECO:0000269|PubMed:10395802}.

Sequence

MSASEGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWN
RSWDRWAAEDHVLRDTDENRRLQRKLARKAVARLRSTGRKKKRCRLPGVDSVLKGLPTEE
KDENDENSLSSSSDCSENKDEEISEESDIEEKTEVKEEPELQTRREMEERTITIEIPEVL
KKQLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSANERPRHHHVMPHANM
NVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATS
TNRSQEELSPSPPLLNPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDR
LSESSASPQPKRRQQDTSASMPKLFLHLEKKTPVHSRSSSPIPLTPSKEGSAVFAGFEGR
RTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGKMSFSEKNLKAL
LKHFDLFLRFLAEYHDDFFPESAYVAACEAHYSTKNPRAIY

Sequence length

521

Interactions

View interactions

	Reactome
			HATs acetylate histones

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Basilicata-Akhtar syndrome	Pathogenic; Likely pathogenic	rs2147244828, rs2147245787, rs2147250167, rs2147244798, rs1601769604, rs2518435267, rs2518420699, rs2518426396, rs2518423160, rs1555906707, rs1555906768, rs1555907620, rs1555907623, rs1555907626, rs1601774648 View all (3 more)	RCV001376014 RCV001706792 RCV001775424 RCV002274288 RCV002286463 View all (13 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Global developmental delay	Pathogenic	rs1601769604	RCV001027676	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic; Pathogenic	rs1555906707, rs1555906768, rs1555906781, rs1555907620, rs1555907623, rs1555907626, rs1555907653, rs1555907864	RCV000656439 RCV000656438 RCV000656441 RCV000656440 RCV000656437 RCV000656436 RCV000656443 RCV000656442 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental abnormality	Pathogenic	rs2053176048	RCV001264670	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nonpapillary renal cell carcinoma	Likely pathogenic	rs2518423160	RCV005933659	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ovarian serous cystadenocarcinoma	Pathogenic	rs2053176048	RCV005909297	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Pathogenic	rs2147247578	RCV005919025	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
X-linked neurodevelopmental delay, dysmorphism, and progressive neurological disorder	Pathogenic	rs2147247578	RCV001580274	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL DISABILITIES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MSL3-related disorder	Benign; Likely benign; Uncertain significance; not provided	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (10)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Child Development Deviations	Development Disorder	CTD_human_DG	30224647		★★★★★ ★☆☆☆☆ Found in Text Mining only
Child Development Disorders, Specific	Development Disorder	CTD_human_DG	30224647		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	38274809	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	CTD_human_DG	30224647		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Developmental disability	Pubtator	33173220	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	15988010, 16227571, 20657587, 20943666, 24898753, 25900149, 28135719		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gait Disorders, Neurologic	Gait disturbance	CTD_human_DG	30224647		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	30224647		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual Disability	Intellectual developmental disorder	Pubtator	33173220	Associate	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	31578411	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

MSL3 (MSL complex subunit 3)