SMARCA1 (SNF2 related chromatin remodeling ATPase 1)

Gene

• Entrez ID: 6594
• Gene name: SNF2 related chromatin remodeling ATPase 1
• Gene symbol: SMARCA1
• Synonyms: ISWI, NURF140, SNF2L, SNF2L1, SNF2LB, SNF2LT, SWI, SWI2, hSNF2L
• 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

SNPs

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

miRNA

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

Transcription factors

Transcription factor	Regulation	Reference
SP1	Unknown	18243132

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000733	Process	DNA strand renaturation	IEA
GO:0003677	Function	DNA binding	IBA	21873635
GO:0004386	Function	Helicase activity	IEA
GO:0005515	Function	Protein binding	IPI	14609955, 15640247, 26030138
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	14609955
GO:0005654	Component	Nucleoplasm	IDA
GO:0006338	Process	Chromatin remodeling	IDA	14609955
GO:0007420	Process	Brain development	IMP	14609955
GO:0008094	Function	DNA-dependent ATPase activity	IDA	14609955
GO:0008134	Function	Transcription factor binding	IPI	27141965
GO:0016589	Component	NURF complex	IDA	20850016
GO:0030182	Process	Neuron differentiation	ISS
GO:0031491	Function	Nucleosome binding	IEA
GO:0036310	Function	Annealing helicase activity	IDA	22705370
GO:0043044	Process	ATP-dependent chromatin remodeling	IDA	15640247
GO:0043231	Component	Intracellular membrane-bounded organelle	IDA
GO:0045893	Process	Positive regulation of transcription, DNA-templated	IMP	14609955
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	14609955
GO:0070615	Function	Nucleosome-dependent ATPase activity	IDA	15640247
GO:0090537	Component	CERF complex	IDA	15640247

Other IDs

• MIM: 300012
• HGNC: 11097
• e!Ensembl: ENSG00000102038

Protein

• UniProt ID: 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

• Sequence:

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

• Sequence length: 1054

Pathways

KEGG:

ATP-dependent chromatin remodeling

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Coffin-siris syndrome	Coffin-Siris syndrome	rs797045262, rs387906846, rs387906857, rs387907140, rs876657379, rs387907141, rs876657380, rs748363079, rs387907142, rs876657381, rs387907143, rs387907144, rs876657382, rs786205584, rs794727977, rs796052242, rs796052240, rs772995852, rs796052241, rs753933273, rs797045272, rs797045277, rs797045278, rs797045279, rs797045280, rs797045281, rs797045282, rs797045283, rs869312697, rs869312712, rs878854600, rs879253746, rs886040958, rs750447037, rs35441529, rs886041878, rs886041706, rs886044620, rs1057518045, rs1057517825, rs1057518951, rs1057519009, rs1057518984, rs1057518648, rs1057518691, rs1554294674, rs1064793482, rs1085307818, rs1085307695, rs1131691706, rs1131692263, rs1028186690, rs1553153771, rs1555155026, rs1554248236, rs1554265319, rs1554301230, rs1554231836, rs1554231845, rs1554234341, rs1554237269, rs1554265275, rs1554270809, rs1554294698, rs1404726383, rs758120346, rs1555031372, rs1554231278, rs1555155252, rs1555139310, rs1553152590, rs1554298232, rs1554238072, rs773740590, rs1554237992, rs1554237658, rs1554233122, rs1554236040, rs1554256703, rs201653711, rs1554238035, rs1554237785, rs1554232959, rs1555031500, rs1555032051, rs1555032044, rs1555032074, rs1555154946, rs1334099693, rs1555605795, rs1554265271, rs1562328526, rs1562331655, rs772973856, rs1554235834, rs1562347066, rs1562355401, rs377021700, rs1451259945, rs1562345819, rs1554294593, rs1562350940, rs1554231904, rs1565642121, rs1565903353, rs1206884190, rs1565903367, rs1565917836, rs1565896447, rs1562354784, rs1464282327, rs1582601669, rs1582601747, rs1583469292, rs1426841589, rs1582908829, rs1583280025, rs1583368813, rs1583513256, rs1583516082, rs1583438967, rs1554232919, rs1583280152, rs1583451360, rs1289067120, rs1583451146, rs1583502875, rs1554248082, rs1583491381, rs1583491515, rs1583518354, rs1592145571, rs754167205, rs1592118927, rs1592324196, rs1592121202, rs1592289150, rs1592294569, rs1592295890, rs1592295914, rs372368908, rs943407609, rs1417035592, rs1794276185, rs1554265316, rs1554232925	26740508, 26539891
Prostate cancer	Malignant neoplasm of prostate	rs121909139, rs121909140, rs121909141, rs121909142, rs121909143, rs606231169, rs606231170, rs137852584, rs137852578, rs137852580, rs137852581, rs137852582	29610475

Unknown
Disease name	Disease term	dbSNP ID	References
Prostatic neoplasms	Prostatic Neoplasms		29610475