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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	50485
Gene name Gene Name - the full gene name approved by the HGNC.	SNF2 related chromatin remodeling annealing helicase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SMARCAL1
Synonyms (NCBI Gene) Gene synonyms aliases	HARP, HHARP
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q35
Summary Summary of gene provided in NCBI Entrez Gene.	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

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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

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

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

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Immunodeficiency	Inherited Immunodeficiency Diseases	rs1574450161, rs200666300	N/A
Nephrotic Syndrome	nephrotic syndrome	rs119473033	N/A
Schimke Immuno-Osseous Dysplasia	schimke immuno-osseous dysplasia	rs119473033, rs1553526228, rs200666300, rs1553526162, rs119473034, rs775057827, rs1574450161, rs119473035, rs761546902, rs1693577284, rs119473036, rs766291662, rs1694062061, rs119473037, rs781023326 View all (11 more)	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
focal segmental glomerulosclerosis	Focal segmental glomerulosclerosis	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (38)

Disease Name	Relationship Type	References
Associations from Text Mining Disease 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)