SMARCAL1 (SNF2 related chromatin remodeling annealing helicase 1)

Gene

• Entrez ID: 50485
• Gene name: SNF2 related chromatin remodeling annealing helicase 1
• Gene symbol: SMARCAL1
• Synonyms: HARP, HHARP
• Chromosome: 2
• Chromosome location: 2q35
• Summary: The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. T

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs2066514	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs119473033	G>T	Pathogenic	Stop gained, coding sequence variant
rs119473034	C>T	Pathogenic	Stop gained, coding sequence variant
rs119473035	C>T	Pathogenic	Stop gained, coding sequence variant
rs119473036	T>A,C	Pathogenic	Coding sequence variant, missense variant
rs119473037	C>T	Pathogenic	Coding sequence variant, missense variant
rs119473038	C>T	Pathogenic	Coding sequence variant, missense variant
rs139445683	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs139872089	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs139949668	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs145908212	G>A,C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs148752234	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs149425324	C>A,G,T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, stop gained
rs188833040	C>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs200644381	C>G,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs200666300	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs201601053	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs202031614	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs267607071	G>A	Pathogenic	Coding sequence variant, missense variant
rs535448005	->C	Pathogenic	Coding sequence variant, frameshift variant
rs748106387	C>A,T	Pathogenic	Stop gained, synonymous variant, coding sequence variant
rs761546902	A>G	Pathogenic	Splice acceptor variant
rs766291662	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs775057827	T>C	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs780778758	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs781023326	TT>-	Pathogenic	Frameshift variant, coding sequence variant
rs864309531	G>T	Pathogenic	Coding sequence variant, stop gained
rs1057524680	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1057524681	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1553526162	->CTGGGG	Likely-pathogenic	Coding sequence variant, inframe insertion
rs1553526228	C>T	Pathogenic	Stop gained, coding sequence variant
rs1553526733	GG>TT	Likely-pathogenic	Coding sequence variant, missense variant
rs1553535161	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1559138455	G>A	Pathogenic	Splice donor variant
rs1574443133	CA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1574443257	TC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1574450161	AAGT>-	Likely-pathogenic	Coding sequence variant, splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT038478	hsa-miR-296-3p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000733	Process	DNA strand renaturation	IEA
GO:0005515	Function	Protein binding	IPI	19793862, 19793863, 24126761, 24910198, 24981860
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	18974355
GO:0005654	Component	Nucleoplasm	IDA
GO:0005662	Component	DNA replication factor A complex	IBA	21873635
GO:0005662	Component	DNA replication factor A complex	IDA	19793862, 19793863
GO:0006259	Process	DNA metabolic process	IMP	18974355
GO:0006281	Process	DNA repair	IBA	21873635
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IMP	26089390
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IMP	18974355
GO:0006974	Process	Cellular response to DNA damage stimulus	IMP	19793862
GO:0008094	Function	DNA-dependent ATPase activity	IMP	18974355
GO:0031297	Process	Replication fork processing	IBA	21873635
GO:0031297	Process	Replication fork processing	IMP	19793862
GO:0031297	Process	Replication fork processing	TAS	27918544
GO:0032508	Process	DNA duplex unwinding	IEA
GO:0035861	Component	Site of double-strand break	IDA	19793862, 19793863
GO:0036310	Function	Annealing helicase activity	IDA	22705370
GO:0036310	Function	Annealing helicase activity	IMP	18974355
GO:0043596	Component	Nuclear replication fork	IBA	21873635
GO:0048478	Process	Replication fork protection	IBA	21873635
GO:0090656	Process	T-circle formation	TAS	27918544

Other IDs

• MIM: 606622
• HGNC: 11102
• e!Ensembl: ENSG00000138375

Protein

• UniProt ID: Q9NZC9
• Protein name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 (EC 3.6.4.-) (HepA-related protein) (hHARP) (Sucrose nonfermenting protein 2-like 1)
• Protein function: ATP-dependent annealing helicase that binds selectively to fork DNA relative to ssDNA or dsDNA and catalyzes the rewinding of the stably unwound DNA. Rewinds single-stranded DNA bubbles that are stably bound by replication protein A (RPA). Acts
• PDB: 4MQV
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07443	HARP	248 → 302	HepA-related protein (HARP)	Family
  PF07443	HARP	343 → 397	HepA-related protein (HARP)	Family
  PF00176	SNF2_N	447 → 729	SNF2 family N-terminal domain	Family
  PF00271	Helicase_C	712 → 822	Helicase conserved C-terminal domain	Family

• Sequence:

  MSLPLTEEQRKKIEENRQKALARRAEKLLAEQHQRTSSGTSIAGNPFQAKQGPSQNFPRE
  SCKPVSHGVIFKQQNLSSSSNADQRPHDSHSFQAKGIWKKPEEMPTACPGHSPRSQMALT
  GISPPLAQSPPEVPKQQLLSYELGQGHAQASPEIRFTPFANPTHKPLAKPKSSQETPAHS
  SGQPPRDAKLEAKTAKASPSGQNISYIHSSSESVTPRTEGRLQQKSGSSVQKGVNSQKGK
  CVRNGDRFQVLIGYNAELIAVFKTLPSKNYDPDTKTWNFSMNDYSALMKAAQSLPTVNLQ
  PLEWAYGSSESPSTSSEGQAGLPSAPSLSFVKGRCMLISRAYFEADISYSQDLIALFKQM
  DSRRYDVKTRKWSFLLEEHSKLIAKVRCLPQVQLDPLPTTLTLAFASQLKKTSLSLTPDV
  PEADLSEVDPKLVSNLMPFQRAGVNFAIAKGGRLLLADDMGLGKTIQAICIAAFYRKEWP
  LLVVVPSSVRFTWEQAFLRWLPSLSPDCINVVVTGKDRLTAGLINIVSFDLLSKLEKQLK
  TPFKVVIIDESHFLKNSRTARCRAAMPVLKVAKRVILLSGTPAMSRPAELYTQIIAVKPT
  FFPQFHAFGLRYCDAKRMPWGWDYSGSSNLGELKLLLEEAVMLRRLKSDVLSQLPAKQRK
  IVVIAPGRINARTRAALDAAAKEMTTKDKTKQQQKDALILFFNRTAEAKIPSVIEYILDL
  LESGREKFLVFAHHKVVLDAITQELERKHVQHIRIDGSTSSAEREDLCQQFQLSERHAVA
  VLSITAANMGLTFSSADLVVFAELFWNPGVLIQAEDRVHRIGQTSSVGIHYLVAKGTADD
  YLWPLIQEKIKVLAEAGLSETNFSEMTESTDYLYKDPKQQKIYDLFQKSFEKEGSDMELL
  EAAESFDPGSASGTSGSSSQNMGDTLDESSLTASPQKKRRFEFFDNWDSFTSPL

• Sequence length: 954

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Anemia	Anemia	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Atrioventricular septal defect	Atrioventricular Septal Defect	rs121912626, rs121912627, rs137852683, rs137852686, rs104894073, rs1598737972, rs1057518960, rs774018674, rs1575650682, rs1598737976, rs1188358849, rs2033057699
Breast cancer	Malignant neoplasm of breast	rs587776547, rs1137887, rs137853007, rs587776650, rs80359351, rs80359714, rs121917783, rs104886456, rs121964878, rs80359874, rs80357868, rs80357508, rs387906843, rs80357569, rs80358158, rs80357524, rs80357115, rs80357945, rs80357729, rs80357609, rs80357259, rs80357981, rs80358063, rs80357389, rs80356862, rs80359876, rs80357580, rs80358053, rs80358089, rs80187739, rs397507241, rs80358069, rs80357590, rs80357284, rs80357941, rs80359261, rs80359272, rs80359276, rs276174813, rs80358474, rs80359316, rs1555282969, rs80359388, rs80359499, rs80359505, rs80359520, rs80359526, rs80359533, rs56253082, rs80358824, rs80359554, rs80359636, rs80359651, rs80359659, rs80359011, rs80359012, rs80359013, rs80359718, rs397507410, rs81002812, rs80359730, rs80359152, rs80359159, rs397507419, rs28897759, rs80359211, rs80359775, rs397514577, rs397507584, rs80358435, rs80358456, rs80359340, rs80359343, rs80359365, rs80358579, rs397507670, rs80358593, rs80359406, rs80359444, rs80359454, rs276174853, rs276174854, rs80359483, rs80359537, rs80358815, rs80358843, rs80359558, rs80359560, rs80359594, rs80358893, rs28897743, rs397507900, rs397507906, rs397507918, rs80358971, rs80358981, rs397507941, rs80359030, rs80359035, rs41293511, rs397507396, rs81002806, rs80359112, rs397508006, rs81002893, rs45580035, rs80359760, rs397508051, rs80359772, rs4987049, rs80359777, rs80357770, rs397508867, rs62625303, rs397508874, rs80357506, rs80357287, rs273898674, rs80358042, rs80358083, rs80357058, rs41286296, rs80357960, rs80356945, rs80357223, rs386134270, rs80358116, rs80357856, rs80357424, rs397509050, rs80357485, rs80357966, rs397509067, rs80357310, rs80356866, rs80357260, rs80357437, rs80358023, rs80358086, rs80357133, rs80356993, rs80357997, rs80357239, rs80357227, rs397509243, rs80356969, rs80356959, rs63750617, rs63751319, rs587779315, rs200640585, rs398122546, rs80357543, rs398122687, rs80359328, rs398122779, rs398122783, rs62517194, rs80358029, rs515726060, rs180177103, rs180177111, rs180177133, rs587776527, rs180177135, rs180177136, rs515726117, rs587779813, rs587779909, rs587780024, rs587780100, rs28909982, rs121908698, rs180177100, rs587780210, rs587780240, rs587780639, rs587781269, rs587781353, rs587781471, rs587781658, rs587781697, rs587781730, rs587781894, rs587781948, rs587782005, rs587782011, rs200928781, rs587781558, rs370228071, rs587782245, rs587782401, rs180177110, rs587782504, rs72552322, rs587782531, rs587782620, rs587782680, rs587782774, rs587782818, rs730881411, rs730881389, rs564652222, rs397507768, rs587776419, rs730881868, rs730881940, rs56383036, rs758972589, rs201089102, rs730881348, rs786202608, rs786201886, rs786203318, rs786203775, rs786203714, rs786202033, rs750621215, rs786203884, rs786203650, rs772821016, rs863224521, rs864622223, rs864622655, rs375699023, rs876659572, rs768362387, rs876659535, rs876658957, rs483353072, rs876659435, rs267608041, rs876661113, rs730881369, rs878853535, rs772228129, rs878855122, rs760551339, rs80359596, rs397509222, rs886039630, rs886039683, rs886040828, rs587781799, rs886040374, rs886040649, rs397507967, rs878854957, rs886040043, rs1057517589, rs1060502769, rs866380588, rs863224765, rs1064793243, rs747563556, rs1555074976, rs1064795885, rs753961188, rs1064794708, rs869312772, rs1064793887, rs1131690820, rs1135401928, rs1135401868, rs1135401859, rs1553370324, rs397507630, rs1555283160, rs1555283251, rs1555283262, rs1555283361, rs1555286298, rs1555288462, rs886040950, rs1555289566, rs776323117, rs80357123, rs1555579627, rs1555580697, rs80358054, rs1555593302, rs1328985852, rs763470424, rs1555139694, rs878854697, rs1555461217, rs1555461765, rs774684620, rs766416564, rs1554558613, rs1305740166, rs1555461460, rs1555461407, rs1555461586, rs1555567202, rs1555607022, rs1555069815, rs1442299125, rs1474786480, rs1555084947, rs1555457867, rs141087784, rs1482641121, rs1564830522, rs1565469955, rs1565503137, rs864622613, rs755263466, rs757679199, rs1593903166, rs1597801649, rs1603293306, rs879253880, rs80358754, rs1597062038, rs45494092, rs1603275367, rs887358871, rs1597091518, rs1966967065, rs1064793049, rs2082872908, rs2085078278, rs2072475243
Cafe-au-lait spot	Cafe au lait spots, multiple	rs1057518792, rs1555613206, rs1555608663
Hypertension	Hypertensive disease	rs13306026, rs13333226
Myopia	Myopia	rs387907109, rs146936371, rs587776903, rs786205127, rs398122836, rs199624584, rs587777625, rs786205216, rs758872875, rs764211125, rs1135402746, rs765658563, rs1555941129, rs1555941116, rs199923805, rs782555528, rs1554862601, rs1586620121, rs1387950081, rs2051026773, rs1422332023
Nephrotic syndrome	Nephrotic Syndrome	rs876657369, rs121912601, rs121912602, rs876657370, rs121912603, rs121912604, rs121912605, rs121907900, rs121907901, rs28941778, rs587776576, rs28942089, rs587776577, rs28941777, rs121907910, rs1568296260, rs119473033, rs74315342, rs74315343, rs74315345, rs74315346, rs74315347, rs74315348, rs121434394, rs267606919, rs121912488, rs267606953, rs267606954, rs267606955, rs104886210, rs1591732280, rs1591750243, rs140511594, rs140781106, rs147972030, rs587776969, rs386833863, rs386833880, rs386833882, rs386833892, rs386833895, rs386833909, rs386833911, rs386833920, rs386833935, rs386833947, rs1555763603, rs398122978, rs398122979, rs398122980, rs369573693, rs398122981, rs398122982, rs398122983, rs200482683, rs730882194, rs180177201, rs587777552, rs587777553, rs775170915, rs749740335, rs12568913, rs530318579, rs786204583, rs786204708, rs786204632, rs138656762, rs797044992, rs797044994, rs797044995, rs864321632, rs864321687, rs864321688, rs864321633, rs869025495, rs869025541, rs869312747, rs145473779, rs757674160, rs869320695, rs138909849, rs869312984, rs1057516900, rs763818901, rs199506378, rs1057517164, rs1057516523, rs1057516414, rs778055996, rs1057516395, rs1057516747, rs1057516880, rs1057516680, rs778217926, rs1057519347, rs764587648, rs1060499703, rs121907903, rs769259446, rs1131692252, rs1131692253, rs1131692254, rs1131692255, rs1131692256, rs746887949, rs1131692235, rs1135402911, rs1135402912, rs1135402913, rs1554946480, rs1555331969, rs773173317, rs1555816634, rs775006954, rs1320543506, rs534522842, rs1272948499, rs1191455921, rs1291398331, rs1554939785, rs776016942, rs1031744496, rs748812981, rs755972674, rs1553312833, rs967339926, rs1462028977, rs1212702104, rs1167223941, rs762631237, rs1553316575, rs1553315173, rs1553316648, rs1553316611, rs780761368, rs368572297, rs1568070817, rs1321552081, rs1558108130, rs1558091788, rs1565707103, rs1558355124, rs1564622701, rs1351580598, rs1589475328, rs1589413498, rs1572255744, rs1572262824, rs761410195, rs1602413491, rs1590326226, rs375998390, rs570583897, rs369363545, rs201488687, rs1334894971, rs763782471, rs138047529, rs895782232, rs1572255047, rs1589433172, rs1589509476, rs1572277600, rs1572282458, rs1584675898, rs759043857, rs1853443391	18805831, 24589093, 11799392
Neutropenia	Neutropenia	rs879253882
Renal insufficiency	Renal Insufficiency	rs1596536873
Schimke immuno-osseous dysplasia	Schimke immuno-osseous dysplasia	rs119473033, rs119473034, rs119473035, rs119473036, rs119473037, rs267607071, rs864309531, rs748106387, rs149425324, rs1553535161, rs1553526228, rs1553526162, rs775057827, rs761546902, rs766291662, rs781023326, rs1559138455, rs1574443133, rs535448005, rs1574443257, rs200666300, rs1574450161, rs1693577284, rs1694062061, rs1694789584, rs1693554666
Skeletal dysplasia	Skeletal dysplasia	rs121912632, rs121912633, rs121912634, rs121912636, rs121912637, rs267607147, rs387906324, rs267607150, rs397514473, rs398123438, rs515726153, rs515726154, rs515726162, rs515726163, rs515726172, rs757011098
Spondyloepiphyseal dysplasia	Spondyloepiphyseal Dysplasia	rs72555367, rs121908950, rs121908951, rs121908952, rs104893637, rs104893639, rs387906534, rs121913568, rs606231241, rs606231242, rs786200933, rs606231243, rs786200934, rs397515546, rs797045099, rs869312907, rs886041895, rs760093841, rs374379931, rs1471554906, rs1567185220, rs1567186585, rs1592198747, rs1239366051, rs1592197682

Unknown
Disease name	Disease term	dbSNP ID	References
Arteriosclerosis	Arteriosclerosis
Astigmatism	Astigmatism
Congenital cataract	Congenital cataract
Congenital microcephaly	Congenital microcephaly
Glomerulosclerosis	Focal glomerulosclerosis
Lymphopenia	Lymphopenia
Malignant neoplasm	Malignant Neoplasms		29299148
Melanocytic nevus	Melanocytic nevus
Microdontia	Microdontia (disorder)
Motor delay	Clumsiness - motor delay
Osteopenia	Osteopenia
Renal glomerular disease	Renal glomerular disease
Spondyloepiphyseal dysplasia nephrotic syndrome	Schimke immunoosseous dysplasia		17089404, 15523612, 22998683, 19127206, 15880370, 16237566, 11799392, 9674900, 25748404, 16840568, 26089390, 23671665, 28796785, 19793862, 26499378, 18974355, 24589093, 18805831, 21914180, 19793864
Transient ischemic attack	Transient Ischemic Attack