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.	3070
Gene name Gene Name - the full gene name approved by the HGNC.	Helicase, lymphoid specific
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	HELLS
Synonyms (NCBI Gene) Gene synonyms aliases	ICF4, LSH, Nbla10143, PASG, SALNR, SMARCA6
Disease Acronyms (UniProt) Disease acronyms from UniProt database	ICF4
Chromosome Chromosome number	10
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	10q23.33
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a lymphoid-specific helicase. Other helicases function in processes involving DNA strand separation, including replication, repair, recombination, and transcription. This protein is thought to be involved with cellular proliferation and

Show/Hide all(6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs140316223	T>A	Pathogenic	Splice donor variant, genic upstream transcript variant
rs879253733	A>G	Pathogenic	Coding sequence variant, missense variant
rs879253734	GTCT>-	Pathogenic	Coding sequence variant, frameshift variant
rs879253735	A>T	Pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs879253736	->TGAGGAAA	Pathogenic	Stop gained, coding sequence variant, intron variant, initiator codon variant, genic upstream transcript variant, 5 prime UTR variant
rs879253737	GTT>-	Pathogenic	Coding sequence variant, inframe deletion

Show/Hide all(121)

miRTarBase ID	miRNA	Experiments	Reference
MIRT004361	hsa-miR-7-5p	Luciferase reporter assay	18823940
MIRT016323	hsa-miR-193b-3p	Microarray	20304954
MIRT022243	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT032248	hsa-let-7b-5p	Proteomics	18668040
MIRT039720	hsa-miR-615-3p	CLASH	23622248
MIRT039180	hsa-miR-769-5p	CLASH	23622248
MIRT036852	hsa-miR-877-3p	CLASH	23622248
MIRT716951	hsa-miR-205-3p	HITS-CLIP	19536157
MIRT716950	hsa-miR-138-2-3p	HITS-CLIP	19536157
MIRT716949	hsa-miR-6895-3p	HITS-CLIP	19536157
MIRT716948	hsa-miR-607	HITS-CLIP	19536157
MIRT735550	hsa-miR-451a	Luciferase reporter assay, Western blotting, qRT-PCR	33460027
MIRT716951	hsa-miR-205-3p	HITS-CLIP	19536157
MIRT716950	hsa-miR-138-2-3p	HITS-CLIP	19536157
MIRT716949	hsa-miR-6895-3p	HITS-CLIP	19536157
MIRT716948	hsa-miR-607	HITS-CLIP	19536157
MIRT1043840	hsa-miR-1246	CLIP-seq
MIRT1043841	hsa-miR-1299	CLIP-seq
MIRT1043842	hsa-miR-140-5p	CLIP-seq
MIRT1043843	hsa-miR-2116	CLIP-seq
MIRT1043844	hsa-miR-24	CLIP-seq
MIRT1043845	hsa-miR-28-3p	CLIP-seq
MIRT1043846	hsa-miR-3138	CLIP-seq
MIRT1043847	hsa-miR-323b-3p	CLIP-seq
MIRT1043848	hsa-miR-34b	CLIP-seq
MIRT1043849	hsa-miR-34c-3p	CLIP-seq
MIRT1043850	hsa-miR-3613-3p	CLIP-seq
MIRT1043851	hsa-miR-3616-5p	CLIP-seq
MIRT1043852	hsa-miR-3647-3p	CLIP-seq
MIRT1043853	hsa-miR-3647-5p	CLIP-seq
MIRT1043854	hsa-miR-3682-5p	CLIP-seq
MIRT1043855	hsa-miR-3692	CLIP-seq
MIRT1043856	hsa-miR-369-3p	CLIP-seq
MIRT1043857	hsa-miR-3713	CLIP-seq
MIRT1043858	hsa-miR-371-5p	CLIP-seq
MIRT1043859	hsa-miR-371b-5p	CLIP-seq
MIRT1043860	hsa-miR-374a	CLIP-seq
MIRT1043861	hsa-miR-374b	CLIP-seq
MIRT1043862	hsa-miR-375	CLIP-seq
MIRT1043863	hsa-miR-3923	CLIP-seq
MIRT1043864	hsa-miR-4264	CLIP-seq
MIRT1043865	hsa-miR-4273	CLIP-seq
MIRT1043866	hsa-miR-4495	CLIP-seq
MIRT1043867	hsa-miR-4511	CLIP-seq
MIRT1043868	hsa-miR-4517	CLIP-seq
MIRT1043869	hsa-miR-4643	CLIP-seq
MIRT1043870	hsa-miR-466	CLIP-seq
MIRT1043871	hsa-miR-4666-5p	CLIP-seq
MIRT1043872	hsa-miR-4677-5p	CLIP-seq
MIRT1043873	hsa-miR-4789-3p	CLIP-seq
MIRT1043874	hsa-miR-4795-5p	CLIP-seq
MIRT1043875	hsa-miR-505	CLIP-seq
MIRT1043876	hsa-miR-510	CLIP-seq
MIRT1043877	hsa-miR-512-5p	CLIP-seq
MIRT1043878	hsa-miR-548b-3p	CLIP-seq
MIRT1043879	hsa-miR-568	CLIP-seq
MIRT1043880	hsa-miR-573	CLIP-seq
MIRT1043881	hsa-miR-576-3p	CLIP-seq
MIRT1043882	hsa-miR-622	CLIP-seq
MIRT1043883	hsa-miR-7	CLIP-seq
MIRT1043884	hsa-miR-875-3p	CLIP-seq
MIRT1043885	hsa-miR-889	CLIP-seq
MIRT1043843	hsa-miR-2116	CLIP-seq
MIRT1043844	hsa-miR-24	CLIP-seq
MIRT1043846	hsa-miR-3138	CLIP-seq
MIRT1043850	hsa-miR-3613-3p	CLIP-seq
MIRT1043851	hsa-miR-3616-5p	CLIP-seq
MIRT1043852	hsa-miR-3647-3p	CLIP-seq
MIRT1043853	hsa-miR-3647-5p	CLIP-seq
MIRT1043854	hsa-miR-3682-5p	CLIP-seq
MIRT1043857	hsa-miR-3713	CLIP-seq
MIRT1043858	hsa-miR-371-5p	CLIP-seq
MIRT1043859	hsa-miR-371b-5p	CLIP-seq
MIRT1043862	hsa-miR-375	CLIP-seq
MIRT1043864	hsa-miR-4264	CLIP-seq
MIRT1043865	hsa-miR-4273	CLIP-seq
MIRT1043872	hsa-miR-4677-5p	CLIP-seq
MIRT2009446	hsa-miR-4733-5p	CLIP-seq
MIRT1043874	hsa-miR-4795-5p	CLIP-seq
MIRT1043876	hsa-miR-510	CLIP-seq
MIRT1043877	hsa-miR-512-5p	CLIP-seq
MIRT1043880	hsa-miR-573	CLIP-seq
MIRT1043882	hsa-miR-622	CLIP-seq
MIRT1043840	hsa-miR-1246	CLIP-seq
MIRT1043842	hsa-miR-140-5p	CLIP-seq
MIRT1043843	hsa-miR-2116	CLIP-seq
MIRT2241822	hsa-miR-216b	CLIP-seq
MIRT2241823	hsa-miR-217	CLIP-seq
MIRT1043844	hsa-miR-24	CLIP-seq
MIRT1043846	hsa-miR-3138	CLIP-seq
MIRT1043847	hsa-miR-323b-3p	CLIP-seq
MIRT2241824	hsa-miR-3545-3p	CLIP-seq
MIRT1043851	hsa-miR-3616-5p	CLIP-seq
MIRT1043853	hsa-miR-3647-5p	CLIP-seq
MIRT1043854	hsa-miR-3682-5p	CLIP-seq
MIRT1043857	hsa-miR-3713	CLIP-seq
MIRT1043858	hsa-miR-371-5p	CLIP-seq
MIRT1043859	hsa-miR-371b-5p	CLIP-seq
MIRT1043862	hsa-miR-375	CLIP-seq
MIRT1043864	hsa-miR-4264	CLIP-seq
MIRT1043865	hsa-miR-4273	CLIP-seq
MIRT1043868	hsa-miR-4517	CLIP-seq
MIRT2241825	hsa-miR-4641	CLIP-seq
MIRT1043869	hsa-miR-4643	CLIP-seq
MIRT1043870	hsa-miR-466	CLIP-seq
MIRT1043872	hsa-miR-4677-5p	CLIP-seq
MIRT2009446	hsa-miR-4733-5p	CLIP-seq
MIRT1043873	hsa-miR-4789-3p	CLIP-seq
MIRT1043874	hsa-miR-4795-5p	CLIP-seq
MIRT1043876	hsa-miR-510	CLIP-seq
MIRT1043877	hsa-miR-512-5p	CLIP-seq
MIRT1043880	hsa-miR-573	CLIP-seq
MIRT1043882	hsa-miR-622	CLIP-seq
MIRT1043885	hsa-miR-889	CLIP-seq
MIRT1043841	hsa-miR-1299	CLIP-seq
MIRT1043842	hsa-miR-140-5p	CLIP-seq
MIRT1043855	hsa-miR-3692	CLIP-seq
MIRT1043874	hsa-miR-4795-5p	CLIP-seq
MIRT1043879	hsa-miR-568	CLIP-seq
MIRT1043883	hsa-miR-7	CLIP-seq
MIRT1043884	hsa-miR-875-3p	CLIP-seq

Show/Hide all(20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000775	Component	Chromosome, centromeric region	ISS
GO:0003682	Function	Chromatin binding	IBA	21873635
GO:0004386	Function	Helicase activity	IEA
GO:0005515	Function	Protein binding	IPI	22157815
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005721	Component	Pericentric heterochromatin	IBA	21873635
GO:0005721	Component	Pericentric heterochromatin	ISS
GO:0006306	Process	DNA methylation	IBA	21873635
GO:0006346	Process	DNA methylation-dependent heterochromatin assembly	IBA	21873635
GO:0006346	Process	DNA methylation-dependent heterochromatin assembly	ISS
GO:0007049	Process	Cell cycle	IEA
GO:0007275	Process	Multicellular organism development	ISS
GO:0010216	Process	Maintenance of DNA methylation	IBA	21873635
GO:0010216	Process	Maintenance of DNA methylation	ISS
GO:0031508	Process	Pericentric heterochromatin assembly	IBA	21873635
GO:0031508	Process	Pericentric heterochromatin assembly	ISS
GO:0046651	Process	Lymphocyte proliferation	IBA	21873635
GO:0046651	Process	Lymphocyte proliferation	ISS
GO:0051301	Process	Cell division	IEA

MIM	HGNC	e!Ensembl
603946	4861	ENSG00000119969

Protein

UniProt ID

Q9NRZ9

Protein name

Lymphoid-specific helicase (EC 3.6.4.-) (Proliferation-associated SNF2-like protein) (SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin subfamily A member 6)

Protein function

Plays an essential role in normal development and survival. Involved in regulation of the expansion or survival of lymphoid cells. Required for de novo or maintenance DNA methylation. May control silencing of the imprinted CDKN1C gene through DN

PDB

8SKZ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00176	SNF2_N	226 → 577	SNF2 family N-terminal domain	Family
PF00271	Helicase_C	599 → 712	Helicase conserved C-terminal domain	Family

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in proliferative tissues such as adult thymus and testis, and expressed at lower levels in uterus, small intestine, colon, and peripheral blood mononuclear cells. Also expressed in neoplastic cell lines including those

Sequence

MPAERPAGSGGSEAPAMVEQLDTAVITPAMLEEEEQLEAAGLERERKMLEKARMSWDRES
TEIRYRRLQHLLEKSNIYSKFLLTKMEQQQLEEQKKKEKLERKKESLKVKKGKNSIDASE
EKPVMRKKRGREDESYNISEVMSKEEILSVAKKNKKENEDENSSSTNLCVEDLQKNKDSN
SIIKDRLSETVRQNTKFFFDPVRKCNGQPVPFQQPKHFTGGVMRWYQVEGMEWLRMLWEN
GINGILADEMGLGKTVQCIATIALMIQRGVPGPFLVCGPLSTLPNWMAEFKRFTPDIPTM
LYHGTQEERQKLVRNIYKRKGTLQIHPVVITSFEIAMRDRNALQHCYWKYLIVDEGHRIK
NMKCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSL
SETAEDIIAKEREQNVLHMLHQILTPFLLRRLKSDVALEVPPKREVVVYAPLSKKQEIFY
TAIVNRTIANMFGSSEKETIELSPTGRPKRRTRKSINYSKIDDFPNELEKLISQIQPEVD
RERAVVEVNIPVESEVNLKLQNIMMLLRKCCNHPYLIEYPIDPVTQEFKIDEELVTNSGK
FLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCHLRDFNFSRLDGSMSYSEREKNMHS
FNTDPEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVY
RLVTANTIDQKIVERAAAKRKLEKLIIHKNHFKGGQSGLNLSKNFLDPKELMELLKSRDY
EREIKGSREKVISDKDLELLLDRSDLIDQMNASGPIKEKMGIFKILENSEDSSPECLF

Sequence length

838

Interactions

View interactions

Show/Hide Causal Diseases (8)

Disease term	Disease name	dbSNP ID	References
Causal
Agammaglobulinemia	Agammaglobulinemia	rs2134166251, rs128620183, rs128620185, rs128621193, rs128621201, rs128621204, rs121912424, rs267606711, rs376256147, rs281865422, rs1600631593, rs1555843601, rs267606871, rs879255271, rs2142904392 View all (17 more)
Anemia	Anemia	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966 View all (89 more)
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Immunodeficiency-centromeric instability-facial anomalies syndrome	ICF syndrome, IMMUNODEFICIENCY-CENTROMERIC INSTABILITY-FACIAL ANOMALIES SYNDROME 4	rs121908939, rs121908940, rs121908941, rs121908942, rs121908943, rs547940069, rs121908944, rs121908945, rs121908946, rs121908947, rs387907104, rs1582683374, rs387907105, rs387907106, rs1562305058 View all (13 more)	26216346, 16395332
Immunodeficiency	Immunodeficiency syndrome, variable	rs1565678077, rs121908002, rs1421444086, rs1565688667, rs944235493, rs121918314, rs587776713, rs137852678, rs587776714, rs128620188, rs2147483647, rs1569556522, rs137853331, rs137853332, rs179363866 View all (256 more)	16395332
Lung adenocarcinoma	Adenocarcinoma of lung (disorder)	rs28934576, rs121913530, rs397516975, rs587776805, rs121913469, rs121913364, rs121913351, rs121913366, rs397516896, rs397516977, rs397516981, rs397517127, rs121913344, rs727504233, rs121913370 View all (5 more)	27602772
Macrocephaly	Macrocephaly	rs786204854, rs764333096, rs1557739557
Mental retardation	Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)

Show/Hide Unknown Diseases (2)

Disease term	Disease name	Source
Unknown
Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome	immunodeficiency-centromeric instability-facial anomalies syndrome	GenCC
Hypertension	Hypertension	GWAS

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text Mining
Adenocarcinoma of Lung	Associate	26658322, 30587197
Adrenocortical Carcinoma	Associate	36039643
Aging Premature	Associate	19561196
Astrocytoma	Associate	28042322
Breast Neoplasms	Associate	21880597
Burkitt Lymphoma	Associate	30964110
Carcinoma Non Small Cell Lung	Associate	15305370, 37569873
Colorectal Neoplasms	Associate	37414755
Epstein Barr Virus Infections	Stimulate	27473869, 30964110
Glioblastoma	Associate	28042322
Glioma	Associate	28042322
Growth Disorders	Associate	19561196
Immunodeficiency syndrome variable	Associate	30307408, 31802118, 33082427
Immunologic Deficiency Syndromes	Associate	30307408, 39178260
Inflammation	Associate	37569873
Leukemia Lymphocytic Chronic B Cell	Associate	35845961
Lung Diseases	Associate	15305370
Lung Neoplasms	Associate	26658322, 28900510
Lupus Erythematosus Systemic	Associate	29074164
Lymphoma B Cell	Associate	30964110
Lymphoma Large B Cell Diffuse	Associate	30964110
Lymphoma Large Cell Anaplastic	Associate	33504766
Melanoma	Associate	17611626
Nasopharyngeal Carcinoma	Stimulate	27473869
Neoplasms	Associate	15305370, 22157815, 26658322, 27473869, 28042322, 28900510, 31802118, 35774795
Optic Nerve Glioma	Associate	28042322
Orofaciodigital syndrome 11	Associate	39178260
Pancreatic Neoplasms	Associate	34315468
Prostatic Neoplasms	Stimulate	22157815
Prostatic Neoplasms	Associate	27191985
Sarcoma	Associate	34982796
Squamous Cell Carcinoma of Head and Neck	Associate	19287496, 22461910
Uterine Cervical Neoplasms	Associate	32181600, 33302814, 38453655
Uterine Cervical Neoplasms	Stimulate	38047020

HELLS (helicase, lymphoid specific)