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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6594
Gene name	SNF2 related chromatin remodeling ATPase 1
Gene symbol	SMARCA1
Synonyms (NCBI Gene)	ISWINURF140SNF2LSNF2L1SNF2LBSNF2LTSWISWI2hSNF2L
Chromosome	X
Chromosome location	Xq25-q26.1
Summary	This gene encodes a member of the SWI/SNF family of proteins. The encoded protein is an ATPase which is expressed in diverse tissues and contributes to the chromatin remodeling complex that is involved in transcription. The protein may also play a role in

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SNP ID	Visualize variation	Clinical significance	Consequence
rs1060499736	G>A	Likely-pathogenic	Coding sequence variant, stop gained

102

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miRTarBase ID	miRNA	Experiments	Reference
MIRT019340	hsa-miR-148b-3p	Microarray	17612493
MIRT021323	hsa-miR-9-5p	Microarray	17612493
MIRT023690	hsa-miR-1-3p	Proteomics	18668040
MIRT028492	hsa-miR-30a-5p	Proteomics	18668040
MIRT032345	hsa-let-7b-5p	Proteomics	18668040
MIRT1371405	hsa-miR-3136-3p	CLIP-seq
MIRT1371406	hsa-miR-4694-3p	CLIP-seq
MIRT1371407	hsa-miR-522	CLIP-seq
MIRT2110175	hsa-miR-1248	CLIP-seq
MIRT2110176	hsa-miR-144	CLIP-seq
MIRT1371405	hsa-miR-3136-3p	CLIP-seq
MIRT2110177	hsa-miR-3180-5p	CLIP-seq
MIRT2333769	hsa-miR-3124-3p	CLIP-seq
MIRT1371405	hsa-miR-3136-3p	CLIP-seq
MIRT2628013	hsa-miR-101	CLIP-seq
MIRT2628014	hsa-miR-1179	CLIP-seq
MIRT2628015	hsa-miR-1290	CLIP-seq
MIRT2628016	hsa-miR-1292	CLIP-seq
MIRT2628017	hsa-miR-142-5p	CLIP-seq
MIRT2110176	hsa-miR-144	CLIP-seq
MIRT2628018	hsa-miR-203	CLIP-seq
MIRT2628019	hsa-miR-2117	CLIP-seq
MIRT2628020	hsa-miR-28-3p	CLIP-seq
MIRT2628021	hsa-miR-3163	CLIP-seq
MIRT2628022	hsa-miR-320a	CLIP-seq
MIRT2628023	hsa-miR-320b	CLIP-seq
MIRT2628024	hsa-miR-320c	CLIP-seq
MIRT2628025	hsa-miR-320d	CLIP-seq
MIRT2628026	hsa-miR-330-3p	CLIP-seq
MIRT2628027	hsa-miR-340	CLIP-seq
MIRT2628028	hsa-miR-3617	CLIP-seq
MIRT2628029	hsa-miR-369-3p	CLIP-seq
MIRT2628030	hsa-miR-374c	CLIP-seq
MIRT2628031	hsa-miR-3927	CLIP-seq
MIRT2628032	hsa-miR-410	CLIP-seq
MIRT2628033	hsa-miR-4274	CLIP-seq
MIRT2628034	hsa-miR-4422	CLIP-seq
MIRT2628035	hsa-miR-4426	CLIP-seq
MIRT2628036	hsa-miR-4429	CLIP-seq
MIRT2628037	hsa-miR-4471	CLIP-seq
MIRT2628038	hsa-miR-4519	CLIP-seq
MIRT2628039	hsa-miR-4643	CLIP-seq
MIRT2628040	hsa-miR-4647	CLIP-seq
MIRT2628041	hsa-miR-4650-3p	CLIP-seq
MIRT2628042	hsa-miR-466	CLIP-seq
MIRT2628043	hsa-miR-4662b	CLIP-seq
MIRT2628044	hsa-miR-4696	CLIP-seq
MIRT2628045	hsa-miR-4699-5p	CLIP-seq
MIRT2628046	hsa-miR-4709-3p	CLIP-seq
MIRT2628047	hsa-miR-4731-3p	CLIP-seq
MIRT2628048	hsa-miR-4753-3p	CLIP-seq
MIRT2628049	hsa-miR-4789-3p	CLIP-seq
MIRT2628050	hsa-miR-4801	CLIP-seq
MIRT2628051	hsa-miR-494	CLIP-seq
MIRT2628052	hsa-miR-503	CLIP-seq
MIRT2628053	hsa-miR-607	CLIP-seq
MIRT2628054	hsa-miR-641	CLIP-seq
MIRT2628055	hsa-miR-651	CLIP-seq
MIRT2628056	hsa-miR-655	CLIP-seq
MIRT2628021	hsa-miR-3163	CLIP-seq
MIRT2628021	hsa-miR-3163	CLIP-seq
MIRT2628013	hsa-miR-101	CLIP-seq
MIRT2628014	hsa-miR-1179	CLIP-seq
MIRT2628015	hsa-miR-1290	CLIP-seq
MIRT2628016	hsa-miR-1292	CLIP-seq
MIRT2628017	hsa-miR-142-5p	CLIP-seq
MIRT2110176	hsa-miR-144	CLIP-seq
MIRT2628018	hsa-miR-203	CLIP-seq
MIRT2628019	hsa-miR-2117	CLIP-seq
MIRT2628020	hsa-miR-28-3p	CLIP-seq
MIRT2628021	hsa-miR-3163	CLIP-seq
MIRT2628022	hsa-miR-320a	CLIP-seq
MIRT2628023	hsa-miR-320b	CLIP-seq
MIRT2628024	hsa-miR-320c	CLIP-seq
MIRT2628025	hsa-miR-320d	CLIP-seq
MIRT2628026	hsa-miR-330-3p	CLIP-seq
MIRT2628027	hsa-miR-340	CLIP-seq
MIRT2628028	hsa-miR-3617	CLIP-seq
MIRT2628029	hsa-miR-369-3p	CLIP-seq
MIRT2628030	hsa-miR-374c	CLIP-seq
MIRT2628031	hsa-miR-3927	CLIP-seq
MIRT2628034	hsa-miR-4422	CLIP-seq
MIRT2628035	hsa-miR-4426	CLIP-seq
MIRT2628036	hsa-miR-4429	CLIP-seq
MIRT2628037	hsa-miR-4471	CLIP-seq
MIRT2628039	hsa-miR-4643	CLIP-seq
MIRT2628040	hsa-miR-4647	CLIP-seq
MIRT2628041	hsa-miR-4650-3p	CLIP-seq
MIRT2628042	hsa-miR-466	CLIP-seq
MIRT2628043	hsa-miR-4662b	CLIP-seq
MIRT2628045	hsa-miR-4699-5p	CLIP-seq
MIRT2628046	hsa-miR-4709-3p	CLIP-seq
MIRT2628047	hsa-miR-4731-3p	CLIP-seq
MIRT2628048	hsa-miR-4753-3p	CLIP-seq
MIRT2628049	hsa-miR-4789-3p	CLIP-seq
MIRT2628050	hsa-miR-4801	CLIP-seq
MIRT2628051	hsa-miR-494	CLIP-seq
MIRT2628052	hsa-miR-503	CLIP-seq
MIRT2691411	hsa-miR-548aa	CLIP-seq
MIRT2628053	hsa-miR-607	CLIP-seq
MIRT2628054	hsa-miR-641	CLIP-seq
MIRT2628056	hsa-miR-655	CLIP-seq

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Transcription factor	Regulation	Reference
SP1	Unknown	18243132

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IBA
GO:0003677	Function	DNA binding	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IBA
GO:0004386	Function	Helicase activity	IEA
GO:0004386	Function	Helicase activity	TAS	1408766
GO:0005515	Function	Protein binding	IPI	14609955, 15640247, 26030138, 30021884, 35271311
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	14609955
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	14609955
GO:0005654	Component	Nucleoplasm	IDA
GO:0005694	Component	Chromosome	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IDA	14609955, 15640247
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IDA	14609955
GO:0007420	Process	Brain development	IMP	14609955
GO:0007420	Process	Brain development	NAS	14609955
GO:0008094	Function	ATP-dependent activity, acting on DNA	IDA	14609955
GO:0016589	Component	NURF complex	IDA	20850016
GO:0016589	Component	NURF complex	IEA
GO:0016589	Component	NURF complex	IPI	14609955
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030182	Process	Neuron differentiation	ISS
GO:0031491	Function	Nucleosome binding	IEA
GO:0031507	Process	Heterochromatin formation	IBA
GO:0036310	Function	ATP-dependent DNA/DNA annealing activity	IDA	22705370
GO:0045893	Process	Positive regulation of DNA-templated transcription	IMP	14609955
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	14609955
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IPI	27141965
GO:0090537	Component	CERF complex	IDA	15640247
GO:0090537	Component	CERF complex	IPI	15640247
GO:0140658	Function	ATP-dependent chromatin remodeler activity	IDA	15640247
GO:0140658	Function	ATP-dependent chromatin remodeler activity	IDA	15640247
GO:0140658	Function	ATP-dependent chromatin remodeler activity	IEA
GO:0140750	Function	Nucleosome array spacer activity	IBA
GO:1904949	Component	ATPase complex	IDA	14609955

MIM	HGNC	e!Ensembl
300012	11097	ENSG00000102038

P28370

Protein name

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 1 (SMARCA1) (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin A1) (EC 3.6.4.-) (Global transcription activator SNF2L1) (Nucleosome-remodeli

Protein function

[Isoform 1]: ATPase that possesses intrinsic ATP-dependent chromatin-remodeling activity (PubMed:14609955, PubMed:15310751, PubMed:15640247, PubMed:28801535). ATPase activity is substrate-dependent, and is increased when nucleosomes are the subs

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13892	DBINO	43 → 116	DNA-binding domain	Domain
PF00176	SNF2_N	186 → 466	SNF2 family N-terminal domain	Family
PF00271	Helicase_C	486 → 612	Helicase conserved C-terminal domain	Family
PF09110	HAND	758 → 856	HAND	Domain
PF09111	SLIDE	913 → 1027	SLIDE	Domain

Tissue specificity

TISSUE SPECIFICITY: [Isoform 1]: Expressed in lung, breast, kidney, ovary, skeletal muscle and brain. {ECO:0000269|PubMed:15310751}.; TISSUE SPECIFICITY: [Isoform 2]: Mainly expressed in non-neuronal tissues such as lung, breast, kidney, and ovary. {ECO:0

Sequence

MEQDTAAVAATVAAADATATIVVIEDEQPGPSTSQEEGAAAAATEATAATEKGEKKKEKN
VSSFQLKLAAKAPKSEKEMDPEYEEKMKADRAKRFEFLLKQTELFAHFIQPSAQKSPTSP
LNMKLGRPRIKKDEKQSLISAGDYRHRRTEQEEDEELLSESRKTSNVCIRFEVSPSYVKG
GPLRDYQIRGLNWLISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVP
KSTLHNWMNEFKRWVPSLRVICFVGDKDARAAFIRDEMMPGEWDVCVTSYEMVIKEKSVF
KKFHWRYLVIDEAHRIKNEKSKLSEIVREFKSTNRLLLTGTPLQNNLHELWALLNFLLPD
VFNSADDFDSWFDTKNCLGDQKLVERLHAVLKPFLLRRIKTDVEKSLPPKKEIKIYLGLS
KMQREWYTKILMKDIDVLNSSGKMDKMRLLNILMQLRKCCNHPYLFDGAEPGPPYTTDEH
IVSNSGKMVVLDKLLAKLKEQGSRVLIFSQMTRLLDILEDYCMWRGYEYCRLDGQTPHEE
REDKFLEVEFLGQREAIEAFNAPNSSKFIFMLSTRAGGLGINLASADVVILYDSDWNPQV
DLQAMDRAHRIGQKKPVRVFRLITDNTVEERIVERAEIKLRLDSIVIQQGRLIDQQSNKL
AKEEMLQMIRHGATHVFASKESELTDEDITTILERGEKKTAEMNERLQKMGESSLRNFRM
DIEQSLYKFEGEDYREKQKLGMVEWIEPPKRERKANYAVDAYFREALRVSEPKIPKAPRP
PKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRNPDIPNPALAQREEQKKIDGAEP
LTPEETEEKEKLLTQGFTNWTKRDFNQFIKANEKYGRDDIDNIAREVEGKSPEEVMEYSA
VFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDAKIARYKAPFHQLRIQYGTSKGK
NYTEEEDRFLICMLHKMGFDRENVYEELRQCVRNAPQFRFDWFIKSRTAMEFQRRCNTLI
SLIEKENMEIEERERAEKKKRATKTPMVKFSAFS

Sequence length

1054

Interactions

View interactions

	KEGG
	ATP-dependent chromatin remodeling

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal brain morphology	Likely pathogenic	rs1060499736	RCV000454288
Non-syndromic X-linked intellectual disability	Likely pathogenic	rs2521753491, rs2521764639	RCV004584578 RCV004584579

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Neurodevelopmental disorder	Uncertain significance; Conflicting classifications of pathogenicity	rs766401027, rs1934884804	RCV005416040 RCV005416043
Nonpapillary renal cell carcinoma	Uncertain significance	rs1933921672	RCV005914901
See cases	Uncertain significance	rs1933921672	RCV001542451
SMARCA1-related disorder	Uncertain significance	rs1934886114	RCV003414408
X-linked intellectual disability	Uncertain significance	rs2521387318	RCV003148171

Show/Hide Text Mining Associations (14)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma	Associate	36126083
Adenocarcinoma of Lung	Associate	36126083
Carcinoma Squamous Cell	Associate	36126083
Central Nervous System Vascular Malformations	Associate	26539891
Colonic Neoplasms	Associate	36126083
Developmental Disabilities	Associate	26740508
Ectrodactyly	Associate	22577152
Endometrial Neoplasms	Associate	36126083
Mental Retardation X Linked	Associate	18302774
Neoplasms	Associate	22577152, 27869826, 34315468, 36126083
Oculocerebrorenal Syndrome	Associate	31376231
Precancerous Conditions	Associate	36126083
Rett Syndrome	Associate	26740508
Squamous Cell Carcinoma of Head and Neck	Associate	36126083

SMARCA1 (SNF2 related chromatin remodeling ATPase 1)