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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	50485
Gene name	SNF2 related chromatin remodeling annealing helicase 1
Gene symbol	SMARCAL1
Synonyms (NCBI Gene)	HARPHHARP
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

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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

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

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	19793862, 19793863, 24126761, 24910198, 24981860
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	18974355
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005662	Component	DNA replication factor A complex	IDA	19793862, 19793863
GO:0006281	Process	DNA repair	IBA
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	DNA damage response	IMP	19793862
GO:0008094	Function	ATP-dependent activity, acting on DNA	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0031297	Process	Replication fork processing	IBA
GO:0031297	Process	Replication fork processing	IMP	19793862
GO:0031297	Process	Replication fork processing	TAS	27918544
GO:0035861	Component	Site of double-strand break	IDA	19793862, 19793863
GO:0036310	Function	ATP-dependent DNA/DNA annealing activity	IDA	22705370
GO:0036310	Function	ATP-dependent DNA/DNA annealing activity	IMP	18974355
GO:0043596	Component	Nuclear replication fork	IBA
GO:0090656	Process	T-circle formation	TAS	27918544

MIM	HGNC	e!Ensembl
606622	11102	ENSG00000138375

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

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed, with high levels in testis. {ECO:0000269|PubMed:10857751, ECO:0000269|PubMed:11799392}.

Sequence

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

Sequence length

954

Interactions

View interactions

1164

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Atypical hemolytic-uremic syndrome	Likely pathogenic	rs1694866812	RCV001328269
Familial cancer of breast	Pathogenic	rs761546902	RCV005901603
Glioma susceptibility 1	Likely pathogenic	rs1694789584	RCV005912425
Inherited Immunodeficiency Diseases	Likely pathogenic; Pathogenic	rs200666300, rs1574450161	RCV001027621 RCV001027619
Nephrotic syndrome	Likely pathogenic; Pathogenic	rs1694331040, rs2106050388, rs2106055226, rs119473033	RCV001849878 RCV001849880 RCV001849881 RCV001849255
Pilocytic astrocytoma	Pathogenic	rs2469012609	RCV006254360
Schimke immuno-osseous dysplasia	Pathogenic; Likely pathogenic	rs2106020733, rs2106040403, rs1271242899, rs2106015063, rs2106015104, rs758888999, rs956223874, rs2106029249, rs1226835488, rs1694059874, rs762716070, rs2106086566, rs1281345070, rs2106055226, rs772028268 View all (107 more)	RCV001374719 RCV001377657 RCV001387850 RCV001384141 RCV001387391 RCV001386132 RCV001386133 RCV001380885 RCV001380762 RCV001380684 RCV001386134 RCV001382139 RCV001783781 RCV004587222 RCV002036489 RCV001864203 RCV001864978 RCV001999806 RCV001904405 RCV001950832 RCV001949297 RCV001977049 RCV001909776 RCV002037907 RCV001941590 RCV001949493 RCV001956344 RCV001956204 RCV001940401 RCV001962355 RCV001928145 RCV002240144 RCV000004388 RCV000004389 RCV000004390 RCV000004391 RCV000004392 RCV000004395 RCV002651604 RCV002648045 RCV002601580 RCV002635286 RCV002645828 RCV002715760 RCV002824111 RCV002824156 RCV002820547 RCV002811899 RCV002861536 RCV002857027 RCV002889589 RCV002881338 RCV002932737 RCV000202608 RCV003046195 RCV003034014 RCV003053726 RCV003057626 RCV003057113 RCV003134139 RCV003156047 RCV003503543 RCV003502945 RCV003504340 RCV003504521 RCV003504522 RCV003504523 RCV003504524 RCV003504525 RCV003502247 RCV003502332 RCV003503249 RCV003502435 RCV003504032 RCV003503313 RCV003503297 RCV003503382 RCV003503419 RCV003611740 RCV003611953 RCV003612595 RCV003612619 RCV003612650 RCV003612717 RCV003613038 RCV003612943 RCV003613169 RCV003613389 RCV003613245 RCV003613503 RCV003611232 RCV003612238 RCV003612379 RCV003858109 RCV003890762 RCV001196355 RCV000524685 RCV000590927 RCV002498879 RCV000625629 RCV000797448 RCV000700786 RCV001035667 RCV000735766 RCV000795753 RCV000804838 RCV000991373 RCV001040718 RCV001862410 RCV001062876 RCV001054627 RCV001035735 RCV001089943 RCV001207503 RCV001216644 RCV001210892 RCV001205385 RCV001209657 RCV001205978 RCV001205193 RCV001242020 RCV003502592 RCV001280866
See cases	Likely pathogenic; Pathogenic	rs956223874, rs1553526162	RCV002252678 RCV004584219
SMARCAL1-related disorder	Pathogenic	rs1265248594, rs761546902	RCV003941201 RCV003420206

Show/Hide Unknown Diseases (21)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Adrenocortical carcinoma, hereditary	Conflicting classifications of pathogenicity	rs2066514	RCV005896746
Cervical cancer	Benign	rs3816784	RCV005917410
Cholangiocarcinoma	Benign	rs3816784, rs2066527	RCV005917414 RCV005892910
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	rs2066527	RCV005892911
Colorectal cancer	Benign	rs2066527	RCV005892908
Familial pancreatic carcinoma	Benign	rs2066527	RCV005892906
Focal segmental glomerulosclerosis	Conflicting classifications of pathogenicity; Benign; Likely benign	rs150148936, rs776290743, rs2066522, rs2066518, rs35907255, rs2066526, rs145908212, rs58848916, rs200644381, rs372995559	RCV002294642 RCV002294659 RCV002294068 RCV002294070 RCV002294172 RCV002294171 RCV002294217 RCV002294344 RCV004773137 RCV002294430
Gastric cancer	Benign	rs3816784	RCV005917411
Hepatocellular carcinoma	Benign	rs2066527	RCV005892902
Kidney disorder	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs780104716, rs11555797, rs2066513, rs2066520, rs199805770, rs2271336, rs35087810	RCV002294683 RCV002294066 RCV002294067 RCV002294215 RCV002294289 RCV002294345 RCV002294429
Lung cancer	Benign; Likely benign	rs3816784, rs205980, rs149510554	RCV005917415 RCV005920076 RCV005900179
Malignant lymphoma, large B-cell, diffuse	Benign	rs205980, rs2066527	RCV005920074 RCV005892907
Malignant tumor of esophagus	Benign	rs3816784	RCV005917409
Melanoma	Uncertain significance	rs145264115	RCV005898665
Nonpapillary renal cell carcinoma	Benign	rs2066527	RCV005892903
Ovarian cancer	Benign	rs2066527	RCV005892904
Ovarian serous cystadenocarcinoma	Benign	rs3816784	RCV005917412
Thymoma	Benign; Conflicting classifications of pathogenicity	rs3816784, rs2066514	RCV005917413 RCV005896747
Uterine carcinosarcoma	Benign	rs205980, rs2066527	RCV005920075 RCV005892909
Uterine corpus endometrial carcinoma	Conflicting classifications of pathogenicity	rs145908212	RCV005895786
Uveal melanoma	Benign	rs2066527	RCV005892905

Show/Hide Text Mining Associations (38)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	33221751
Alternating hemiplegia of childhood	Associate	34103668, 36689342
Amelogenesis imperfecta local hypoplastic form	Associate	22699664
Anodontia	Associate	22699664
Arterial Occlusive Diseases	Stimulate	31474762
Arteriosclerosis	Associate	22998683
Atherosclerosis	Associate	16840568
Bone Diseases	Associate	38218042
Carcinogenesis	Associate	36689342
Carcinoma	Associate	23630135
Carcinoma Large Cell	Associate	31474762
Cerebrovascular Disorders	Stimulate	31474762
Dementia	Associate	16840568
Dementia Multi Infarct	Associate	21327070
Emphysema	Associate	22998683
Epiphyseal Dysplasia of Femoral Head Myopia and Deafness	Associate	20013129
Esophageal Squamous Cell Carcinoma	Associate	26812616
Glioblastoma	Associate	29802247, 36689342
Glioblastoma	Inhibit	34103668
Glioma	Associate	36689342
Glomerulosclerosis Focal Segmental	Associate	29138824
Growth Disorders	Associate	21327070
Heart Diseases	Associate	16840568
Hypertension Pulmonary	Associate	16840568
Immune System Diseases	Associate	21327070, 33203071
Kidney Diseases	Associate	28796785, 32393263
Kidney Neoplasms	Associate	33203071
Lymphoma	Associate	30610086
Lymphopenia	Associate	33203071
Moyamoya disease 1	Associate	31474762
Neoplasms	Associate	34103668, 34315468, 36689342, 37890990
Nephroma Mesoblastic	Associate	33203071
Nephrotic Syndrome	Associate	16050398, 28796785, 29127259
Osteochondrodysplasias	Associate	20013129
Osteosarcoma	Associate	36689342
Renal Insufficiency	Associate	21327070
Schimke immunoosseous dysplasia	Associate	16840568, 18974355, 19793861, 19793862, 20013129, 21327070, 22279047, 22699664, 22704558, 22998683, 23630135, 24565939, 24589093, 25943327, 26195148 View all (8 more)
X Linked Combined Immunodeficiency Diseases	Associate	33203071

SMARCAL1 (SNF2 related chromatin remodeling annealing helicase 1)