Gene Gene information from NCBI Gene database.
Entrez ID 3070
Gene name Helicase, lymphoid specific
Gene symbol HELLS
Synonyms (NCBI Gene)
ICF4LSHNbla10143PASGSALNRSMARCA6
Chromosome 10
Chromosome location 10q23.33
Summary 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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
43
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0000724 Process Double-strand break repair via homologous recombination IDA 31802118
GO:0000775 Component Chromosome, centromeric region IEA
GO:0000775 Component Chromosome, centromeric region ISS
GO:0001655 Process Urogenital system development IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603946 4861 ENSG00000119969
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
RERAVVEVNIPVESEVNLKLQNIMMLLRKCCNHPYLI
EYPIDPVTQEFKIDEELVTNSGK
FLILDRMLPELKKRGHKVLLFSQMTSMLDILMDYCHLRDFNFSRLDGSMSYSEREKNMHS
FNTDPEVFIFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIG
QTKPVVVY
RLVTANTIDQKIVERAAAKRKLEKLIIHKNHFKGGQSGLNLSKNFLDPKELMELLKSRDY
EREIKGSREKVISDKDLELLLDRSDLIDQMNASGPIKEKMGIFKILENSEDSSPECLF
Sequence length 838
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
7
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Immunodeficiency-centromeric instability-facial anomalies syndrome 4 Pathogenic; Likely pathogenic rs879253733, rs140316223, rs879253734, rs879253735, rs879253736, rs879253737 RCV000210912
RCV000210918
RCV000210919
RCV000210911
RCV000210917
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Colon adenocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
HELLS-related disorder Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
HYPERTENSION GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ICF SYNDROME Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 26658322
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma CTD_human_DG 27602772
★☆☆☆☆
Found in Text Mining only
Adrenocortical Carcinoma Adrenocortical carcinoma Pubtator 36039643 Associate
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 31541170
★☆☆☆☆
Found in Text Mining only
Agammaglobulinemia Agammaglobulinemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Anemia Anemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma BEFREE 28042322
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma Pubtator 28042322 Associate
★☆☆☆☆
Found in Text Mining only
Autoimmune Diseases Autoimmune Diseases BEFREE 29074164
★☆☆☆☆
Found in Text Mining only
B-Cell Lymphomas B-Cell Lymphoma BEFREE 30964110
★☆☆☆☆
Found in Text Mining only