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Aliases for HELLS Gene

Aliases for HELLS Gene

  • Helicase, Lymphoid Specific 2 3 5
  • Proliferation-Associated SNF2-Like Protein 2 3 4
  • SWI/SNF2-Related, Matrix-Associated, Actin-Dependent Regulator Of Chromatin, Subfamily A, Member 6 2 3
  • SMARCA6 3 4
  • PASG 3 4
  • SWI/SNF2-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily A Member 6 4
  • Lymphoid-Specific Helicase 3
  • EC 3.6.4.- 4
  • Nbla10143 3
  • EC 3.6.1 56
  • ICF4 3
  • LSH 3

External Ids for HELLS Gene

Previous GeneCards Identifiers for HELLS Gene

  • GC10P095198
  • GC10P095539
  • GC10P096436
  • GC10P095970
  • GC10P096295
  • GC10P096261
  • GC10P089932
  • GC10P096305

Summaries for HELLS Gene

Entrez Gene Summary for HELLS 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 may play a role in leukemogenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2014]

GeneCards Summary for HELLS Gene

HELLS (Helicase, Lymphoid Specific) is a Protein Coding gene. Diseases associated with HELLS include Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome 4 and Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome. Among its related pathways are PEDF Induced Signaling and AMPK Enzyme Complex Pathway. Gene Ontology (GO) annotations related to this gene include chromatin binding and helicase activity.

UniProtKB/Swiss-Prot for HELLS Gene

  • 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 DNA methylation. May play a role in formation and organization of heterochromatin, implying a functional role in the regulation of transcription and mitosis (By similarity).

Gene Wiki entry for HELLS Gene

Additional gene information for HELLS Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HELLS Gene

Genomics for HELLS Gene

GeneHancer (GH) Regulatory Elements for HELLS Gene

Promoters and enhancers for HELLS Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I094543 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 564.7 +44.1 44132 3.7 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 BRCA1 YY1 HELLS ENSG00000273450 PDE6C ACSM6 NOC3L GC10P094552
GH10I094531 Promoter 0.5 EPDnew 550.3 +29.8 29832 0.1 HELLS GC10P094552 TBC1D12
GH10I094401 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 20.2 -98.2 -98196 3.5 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B TBC1D12 NOC3L HELLS PDE6C PIR44069
GH10I093701 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.7 -799.0 -798952 2.3 ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 FRA10AC1 RPL17P34 NOC3L PDE6C ENSG00000273450 MYOF HELLS
GH10I095182 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE 10 +682.2 682175 1.6 ATF1 SIN3A ZNF2 YY1 ETS1 ZNF121 GLIS2 ZNF213 ZNF207 ZNF143 PAWRP1 ZNF518A TCTN3 CCNJ PDLIM1 HELLS ENTPD1-AS1 CYP2C8 ACSM6 SORBS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HELLS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HELLS gene promoter:

Genomic Locations for HELLS Gene

Genomic Locations for HELLS Gene
chr10:94,501,434-94,613,905
(GRCh38/hg38)
Size:
112,472 bases
Orientation:
Plus strand
chr10:96,305,547-96,373,662
(GRCh37/hg19)

Genomic View for HELLS Gene

Genes around HELLS on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HELLS Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HELLS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HELLS Gene

Proteins for HELLS Gene

  • Protein details for HELLS Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NRZ9-HELLS_HUMAN
    Recommended name:
    Lymphoid-specific helicase
    Protein Accession:
    Q9NRZ9
    Secondary Accessions:
    • B2RB41
    • Q3LID1
    • Q6I7N7
    • Q76H76
    • Q76H77
    • Q76H78
    • Q76H79
    • Q76H80
    • Q76H81
    • Q7Z397
    • Q7Z5X2
    • Q8N6P4
    • Q9H4P5

    Protein attributes for HELLS Gene

    Size:
    838 amino acids
    Molecular mass:
    97074 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAG01987.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH29381.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH30963.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH31004.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for HELLS Gene

neXtProt entry for HELLS Gene

Selected DME Specific Peptides for HELLS Gene

Q9NRZ9:
  • DEMGLGKT
  • LRRLKSDV
  • TGTPLQN
  • DSDWNPQ
  • AGGLGINL
  • RCHRIGQ
  • NGILADE
  • LLNFLLPD
  • GLGKTVQ

Post-translational modifications for HELLS Gene

  • Ubiquitination at isoforms=2, 3, 4, 5, 6, 7, 8, 974, isoforms=2, 3, 4, 5, 6, 7, 8, 980, isoforms=2, 3, 4, 5, 6, 7, 8204, isoforms=2, 3, 4, 5, 6731, and isoforms=2, 3, 4, 5, 6753

Domains & Families for HELLS Gene

Gene Families for HELLS Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for HELLS Gene

Graphical View of Domain Structure for InterPro Entry

Q9NRZ9

UniProtKB/Swiss-Prot:

HELLS_HUMAN :
  • Belongs to the SNF2/RAD54 helicase family.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with HELLS: view

Function for HELLS Gene

Molecular function for HELLS Gene

GENATLAS Biochemistry:
helicase lymphoid specific,expressed in early thymocytes and testis,SNF2/RAD54 family potentially involved in DNA repair,homologous to S cerivisiae YFK8
UniProtKB/Swiss-Prot 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 DNA methylation. May play a role in formation and organization of heterochromatin, implying a functional role in the regulation of transcription and mitosis (By similarity).
UniProtKB/Swiss-Prot Induction:
By concanavalin-A in peripheral blood leukocytes.

Enzyme Numbers (IUBMB) for HELLS Gene

Phenotypes From GWAS Catalog for HELLS Gene

Gene Ontology (GO) - Molecular Function for HELLS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 22157815
GO:0005524 ATP binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HELLS: view
genes like me logo Genes that share phenotypes with HELLS: view

Human Phenotype Ontology for HELLS Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HELLS Gene

MGI Knock Outs for HELLS:

Animal Model Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for HELLS Gene

Localization for HELLS Gene

Subcellular locations from UniProtKB/Swiss-Prot for HELLS Gene

Nucleus. Note=Closely associated with pericentric heterochromatin. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HELLS gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HELLS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region ISS --
GO:0005634 nucleus IEA --
GO:0005721 pericentric heterochromatin ISS --
genes like me logo Genes that share ontologies with HELLS: view

Pathways & Interactions for HELLS Gene

genes like me logo Genes that share pathways with HELLS: view

Pathways by source for HELLS Gene

Gene Ontology (GO) - Biological Process for HELLS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001655 urogenital system development IEA --
GO:0006306 DNA methylation IEA --
GO:0006342 chromatin silencing IEA --
GO:0006346 methylation-dependent chromatin silencing ISS --
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with HELLS: view

No data available for SIGNOR curated interactions for HELLS Gene

Drugs & Compounds for HELLS Gene

(27) Drugs for HELLS Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(29) Additional Compounds for HELLS Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HELLS: view

Transcripts for HELLS Gene

Unigene Clusters for HELLS Gene

Helicase, lymphoid-specific:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HELLS Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a ·
SP1: -
SP2:
SP3: - - - - -
SP4: -
SP5:
SP6: - - - - - - -
SP7: -
SP8:
SP9:

ExUns: 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for HELLS Gene

GeneLoc Exon Structure for
HELLS
ECgene alternative splicing isoforms for
HELLS

Expression for HELLS Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HELLS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HELLS Gene

This gene is overexpressed in Breast (41.0) and Tlymphocyte (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HELLS Gene



NURSA nuclear receptor signaling pathways regulating expression of HELLS Gene:

HELLS

SOURCE GeneReport for Unigene cluster for HELLS Gene:

Hs.655830

mRNA Expression by UniProt/SwissProt for HELLS Gene:

Q9NRZ9-HELLS_HUMAN
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 derived from myeloid and lymphoid leukemias.

Evidence on tissue expression from TISSUES for HELLS Gene

  • Nervous system(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HELLS Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • sinus
  • skull
  • tongue
Thorax:
  • bronchus
  • lung
Abdomen:
  • intestine
  • large intestine
  • small intestine
General:
  • blood
  • bone marrow
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with HELLS: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for HELLS Gene

Orthologs for HELLS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HELLS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HELLS 33 34
  • 99.74 (n)
dog
(Canis familiaris)
Mammalia HELLS 33 34
  • 92.35 (n)
cow
(Bos Taurus)
Mammalia HELLS 33 34
  • 91.75 (n)
mouse
(Mus musculus)
Mammalia Hells 33 16 34
  • 89.36 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HELLS 34
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HELLS 34
  • 44 (a)
OneToOne
chicken
(Gallus gallus)
Aves HELLS 34
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HELLS 34
  • 72 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii hells 34
  • 64 (a)
OneToOne
sbcb65 33
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E04159g 33
  • 54.42 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IRC5 33 34 36
  • 53.68 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL098C 33
  • 52.36 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.2667 33
wheat
(Triticum aestivum)
Liliopsida Ta.23819 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 57 (a)
OneToMany
CSA.5063 34
  • 48 (a)
OneToMany
-- 34
  • 45 (a)
OneToMany
-- 34
  • 35 (a)
OneToMany
Species where no ortholog for HELLS was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • worm (Caenorhabditis elegans)

Evolution for HELLS Gene

ENSEMBL:
Gene Tree for HELLS (if available)
TreeFam:
Gene Tree for HELLS (if available)

Paralogs for HELLS Gene

No data available for Paralogs for HELLS Gene

Variants for HELLS Gene

Sequence variations from dbSNP and Humsavar for HELLS Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs140316223 pathogenic, Immunodeficiency-centromeric instability-facial anomalies syndrome 4 94,562,729(+) T/A genic_upstream_transcript_variant, splice_donor_variant
rs879253733 pathogenic, Immunodeficiency-centromeric instability-facial anomalies syndrome 4, Immunodeficiency-centromeric instability-facial anomalies syndrome 4 (ICF4) [MIM:616911] 94,594,702(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs879253734 pathogenic, Immunodeficiency-centromeric instability-facial anomalies syndrome 4 94,596,891(+) TCTGTCT/TCT coding_sequence_variant, frameshift, non_coding_transcript_variant
rs879253735 pathogenic, Immunodeficiency-centromeric instability-facial anomalies syndrome 4 94,574,092(+) A/T 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs879253736 pathogenic, Immunodeficiency-centromeric instability-facial anomalies syndrome 4 94,562,814(+) ATGAGGAAA/ATGAGGAAATGAGGAAA 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, initiator_codon_variant, intron_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for HELLS Gene

Variant ID Type Subtype PubMed ID
nsv517681 CNV gain 19592680
esv3546703 CNV deletion 23714750

Variation tolerance for HELLS Gene

Residual Variation Intolerance Score: 7.73% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.65; 31.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HELLS Gene

Human Gene Mutation Database (HGMD)
HELLS
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HELLS

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HELLS Gene

Disorders for HELLS Gene

MalaCards: The human disease database

(16) MalaCards diseases for HELLS Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search HELLS in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HELLS_HUMAN
  • Immunodeficiency-centromeric instability-facial anomalies syndrome 4 (ICF4) [MIM:616911]: A rare disorder characterized by a variable immunodeficiency resulting in recurrent infections, facial anomalies, and branching of chromosomes 1, 9, and 16. Other variable symptoms include growth retardation, failure to thrive, and psychomotor retardation. Laboratory studies show limited hypomethylation of DNA in a small fraction of the genome in some, but not all, patients. {ECO:0000269 PubMed:26216346}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HELLS

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HELLS: view

No data available for Genatlas for HELLS Gene

Publications for HELLS Gene

  1. Proliferation-associated SNF2-like gene (PASG): a SNF2 family member altered in leukemia. (PMID: 10910076) Lee DW … Arceci RJ (Cancer research 2000) 2 3 4 22 58
  2. Characterization of gene expression, genomic structure, and chromosomal localization of Hells (Lsh). (PMID: 9878251) Geiman TM … Muegge K (Genomics 1998) 2 3 22 58
  3. Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome. (PMID: 26216346) Thijssen PE … Sasaki H (Nature communications 2015) 3 4 58
  4. Senescence delay and repression of p16INK4a by Lsh via recruitment of histone deacetylases in human diploid fibroblasts. (PMID: 19561196) Zhou R … Tong T (Nucleic acids research 2009) 3 22 58
  5. Polymorphism in the IL18 gene and epithelial ovarian cancer in non-Hispanic white women. (PMID: 19064572) Palmieri RT … Australian Ovarian Cancer Study Group (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2008) 3 44 58

Products for HELLS Gene

Sources for HELLS Gene

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