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Aliases for HCLS1 Gene

Aliases for HCLS1 Gene

  • Hematopoietic Cell-Specific Lyn Substrate 1 2 3 5
  • LckBP1 3 4
  • HS1 3 4
  • P75 3 4
  • Hematopoietic Lineage Cell-Specific Protein 3
  • Hematopoietic Cell-Specific LYN Substrate 1 4
  • Cortactin-Like 2
  • CTTNL 3

External Ids for HCLS1 Gene

Previous GeneCards Identifiers for HCLS1 Gene

  • GC03U990043
  • GC03M120991
  • GC03M122631
  • GC03M122671
  • GC03M122832
  • GC03M121350
  • GC03M118724

Summaries for HCLS1 Gene

GeneCards Summary for HCLS1 Gene

HCLS1 (Hematopoietic Cell-Specific Lyn Substrate 1) is a Protein Coding gene. Diseases associated with HCLS1 include Spherocytosis, Type 1 and Congenital Hemolytic Anemia. Among its related pathways are Immune response Fc epsilon RI pathway and Proteoglycans in cancer. Gene Ontology (GO) annotations related to this gene include protein kinase binding. An important paralog of this gene is CTTN.

UniProtKB/Swiss-Prot for HCLS1 Gene

  • Substrate of the antigen receptor-coupled tyrosine kinase. Plays a role in antigen receptor signaling for both clonal expansion and deletion in lymphoid cells. May also be involved in the regulation of gene expression.

Gene Wiki entry for HCLS1 Gene

Additional gene information for HCLS1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HCLS1 Gene

Genomics for HCLS1 Gene

GeneHancer (GH) Regulatory Elements for HCLS1 Gene

Promoters and enhancers for HCLS1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J121658 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 663.9 +0.9 878 3.9 HDGF PKNOX1 ATF1 SMAD1 RB1 ZBTB40 KLF5 E2F8 ZNF207 ZNF143 HCLS1 IQCB1 SLC15A2 GOLGB1 CD86 RNU4-62P GC03M121324
GH03J121747 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.5 -88.3 -88325 3.3 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ZFP64 ARID4B NEUROD1 SIN3A DMAP1 GOLGB1 GC03P121749 PIR33653 IQCB1 LOC102723582 HCLS1 PIR54680 GC03M121324
GH03J121833 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.5 -174.5 -174519 3.2 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF213 ZNF143 IQCB1 EAF2 GOLGB1 HCLS1 SLC15A2 GC03M121324
GH03J121655 Enhancer 0.7 FANTOM5 dbSUPER 10.3 +5.3 5332 0.2 ZFP64 ZNF140 ZNF623 RNU4-62P RN7SL172P GOLGB1 IQCB1 LOC102723582 HCLS1 SLC15A2 EAF2 GC03M121324
GH03J121757 Enhancer 0.4 ENCODE 16.6 -96.5 -96548 1.7 SP1 NR2F2 HCLS1 IQCB1 RNU4-62P RN7SL172P SLC15A2 GOLGB1 GC03M121324
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HCLS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HCLS1 gene promoter:
  • AML1a
  • YY1
  • FOXO4
  • MZF-1
  • Sox5
  • POU2F1a
  • POU2F1
  • Pax-3
  • FOXJ2
  • FOXJ2 (long isoform)

Genomic Locations for HCLS1 Gene

Genomic Locations for HCLS1 Gene
29,551 bases
Minus strand
29,546 bases
Minus strand

Genomic View for HCLS1 Gene

Genes around HCLS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HCLS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HCLS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HCLS1 Gene

Proteins for HCLS1 Gene

  • Protein details for HCLS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hematopoietic lineage cell-specific protein
    Protein Accession:
    Secondary Accessions:
    • B4DQ69
    • Q53Y93
    • Q6IBK9
    • Q9UDK0

    Protein attributes for HCLS1 Gene

    486 amino acids
    Molecular mass:
    54014 Da
    Quaternary structure:
    • Associates with the SH2 and SH3 domains of LCK. Binding to he LCK SH3 domain occurs constitutively, while binding to the LCK SH2 domain occurs only upon TCR stimulation. A similar binding pattern was observed with LYN, but not with FYN in which the FYN SH2 region associates upon TCR stimulation but the FYN SH3 region does not associate regardless of TCR stimulation. Directly associates with HAX1, through binding to its C-terminal region. Interacts with HS1BP3. Interacts with FES/FPS (By similarity). Interacts (via SH2 domain) with FGR. Forms a multiprotein complex with LYN and ANKRD54 (By similarity).

    Alternative splice isoforms for HCLS1 Gene


neXtProt entry for HCLS1 Gene

Post-translational modifications for HCLS1 Gene

  • Phosphorylated by FES (By similarity). Phosphorylated by LYN, FYN and FGR after cross-linking of surface IgM on B-cells. Phosphorylation by LYN, FYN and FGR requires prior phosphorylation by SYK or FES.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HCLS1 Gene

No data available for DME Specific Peptides for HCLS1 Gene

Domains & Families for HCLS1 Gene

Gene Families for HCLS1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for HCLS1 Gene

Suggested Antigen Peptide Sequences for HCLS1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HCLS1: view

No data available for UniProtKB/Swiss-Prot for HCLS1 Gene

Function for HCLS1 Gene

Molecular function for HCLS1 Gene

UniProtKB/Swiss-Prot Function:
Substrate of the antigen receptor-coupled tyrosine kinase. Plays a role in antigen receptor signaling for both clonal expansion and deletion in lymphoid cells. May also be involved in the regulation of gene expression.
GENATLAS Biochemistry:
hematopoietic cell-specific Lyn substrate 1,75kDa,involved in signal transduction

Phenotypes From GWAS Catalog for HCLS1 Gene

Gene Ontology (GO) - Molecular Function for HCLS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001085 RNA polymerase II transcription factor binding IPI 23001182
GO:0003779 actin binding IEA --
GO:0005515 protein binding IPI 15795233
GO:0017124 SH3 domain binding IEA --
GO:0019901 protein kinase binding IPI 23001182
genes like me logo Genes that share ontologies with HCLS1: view
genes like me logo Genes that share phenotypes with HCLS1: view

Animal Models for HCLS1 Gene

MGI Knock Outs for HCLS1:

Animal Model Products

miRNA for HCLS1 Gene

miRTarBase miRNAs that target HCLS1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HCLS1 Gene

Localization for HCLS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HCLS1 Gene

Membrane; Peripheral membrane protein. Cytoplasm. Mitochondrion.

Subcellular locations from

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 HCLS1 gene
Compartment Confidence
plasma membrane 5
cytosol 5
nucleus 4
mitochondrion 3
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HCLS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS,IDA --
GO:0005667 transcription factor complex IDA 23001182
GO:0005737 cytoplasm ISS,IDA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with HCLS1: view

Pathways & Interactions for HCLS1 Gene

genes like me logo Genes that share pathways with HCLS1: view

SIGNOR curated interactions for HCLS1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HCLS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006355 regulation of transcription, DNA-templated TAS 2587259
GO:0008284 positive regulation of cell proliferation ISS --
GO:0009725 response to hormone ISS --
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling IMP 23001182
genes like me logo Genes that share ontologies with HCLS1: view

Drugs & Compounds for HCLS1 Gene

(3) Drugs for HCLS1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HCLS1: view

Transcripts for HCLS1 Gene

mRNA/cDNA for HCLS1 Gene

Unigene Clusters for HCLS1 Gene

Hematopoietic cell-specific Lyn substrate 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HCLS1 Gene

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

ExUns: 14b ^ 15

Relevant External Links for HCLS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HCLS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HCLS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HCLS1 Gene

This gene is overexpressed in Whole Blood (x25.1) and Spleen (x5.6).

Protein differential expression in normal tissues from HIPED for HCLS1 Gene

This gene is overexpressed in Lymph node (28.4) and Peripheral blood mononuclear cells (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HCLS1 Gene

Protein tissue co-expression partners for HCLS1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HCLS1 Gene:


SOURCE GeneReport for Unigene cluster for HCLS1 Gene:


mRNA Expression by UniProt/SwissProt for HCLS1 Gene:

Tissue specificity: Expressed only in tissues and cells of hematopoietic origin.

Evidence on tissue expression from TISSUES for HCLS1 Gene

  • Spleen(4.6)
  • Liver(4.4)
  • Blood(4)
  • Nervous system(2.4)
  • Lung(2.2)
  • Heart(2.1)
  • Intestine(2.1)
  • Lymph node(2.1)
genes like me logo Genes that share expression patterns with HCLS1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for HCLS1 Gene

Orthologs for HCLS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HCLS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HCLS1 34 33
  • 99.17 (n)
(Bos Taurus)
Mammalia HCLS1 34 33
  • 89.12 (n)
(Canis familiaris)
Mammalia HCLS1 34 33
  • 86.85 (n)
(Mus musculus)
Mammalia Hcls1 16 34 33
  • 86.2 (n)
(Rattus norvegicus)
Mammalia Hcls1 33
  • 86.09 (n)
(Monodelphis domestica)
Mammalia HCLS1 34
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia HCLS1 34
  • 43 (a)
(Gallus gallus)
Aves HCLS1 34 33
  • 65.87 (n)
(Anolis carolinensis)
Reptilia HCLS1 34
  • 41 (a)
(Danio rerio)
Actinopterygii hcls1 34
  • 46 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cortactin 34 35
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7160 34
  • 39 (a)
Species where no ortholog for HCLS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HCLS1 Gene

Gene Tree for HCLS1 (if available)
Gene Tree for HCLS1 (if available)
Evolutionary constrained regions (ECRs) for HCLS1: view image

Paralogs for HCLS1 Gene

Paralogs for HCLS1 Gene

(6) SIMAP similar genes for HCLS1 Gene using alignment to 5 proteins:

  • B4DQ69_HUMAN
genes like me logo Genes that share paralogs with HCLS1: view

Variants for HCLS1 Gene

Sequence variations from dbSNP and Humsavar for HCLS1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000048902 -- 121,639,000(-) G/A intron_variant
rs1000067413 -- 121,645,235(-) C/G intron_variant
rs1000113737 -- 121,662,459(-) G/A upstream_transcript_variant
rs1000276262 -- 121,662,016(-) A/G upstream_transcript_variant
rs1000352366 -- 121,630,909(-) T/C downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HCLS1 Gene

Variant ID Type Subtype PubMed ID
dgv8524n54 CNV gain 21841781
esv3451038 OTHER inversion 20981092
esv3575598 CNV gain 25503493
esv3575599 CNV gain 25503493
esv3597587 CNV gain 21293372
esv3597593 CNV gain 21293372
esv3597597 CNV loss 21293372
esv3893771 CNV loss 25118596
nsv1007522 CNV gain 25217958
nsv1073241 CNV deletion 25765185
nsv1141890 OTHER inversion 24896259
nsv998740 CNV gain 25217958
nsv999335 CNV gain 25217958
nsv999349 CNV gain 25217958

Variation tolerance for HCLS1 Gene

Residual Variation Intolerance Score: 98.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.68; 93.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HCLS1 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HCLS1 Gene

Disorders for HCLS1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for HCLS1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
spherocytosis, type 1
  • sph1
congenital hemolytic anemia
  • hereditary hemolytic anemia
hereditary spherocytosis
  • spherocytosis, type 1
- elite association - COSMIC cancer census association via MalaCards
Search HCLS1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HCLS1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HCLS1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HCLS1 Gene

Publications for HCLS1 Gene

  1. Comparative genome analysis of cortactin and HS1: the significance of the F-actin binding repeat domain. (PMID: 15710041) van Rossum AG … Schuuring E (BMC genomics 2005) 2 3 22 58
  2. Association of a four-amino acid residue insertion polymorphism of the HS1 gene with systemic lupus erythematosus: molecular and functional analysis. (PMID: 15022330) Otsuka J … Harada M (Arthritis and rheumatism 2004) 3 22 44 58
  3. Molecular features underlying the sequential phosphorylation of HS1 protein and its association with c-Fgr protein-tyrosine kinase. (PMID: 10066823) Brunati AM … Pinna LA (The Journal of biological chemistry 1999) 3 4 22 58
  4. The human HCLS1 gene maps to chromosome 3q13 by fluorescence in situ hybridization. (PMID: 8978766) Egashira M … Niikawa N (Cytogenetics and cell genetics 1996) 2 3 22 58
  5. Identification of HS1 protein as a major substrate of protein-tyrosine kinase(s) upon B-cell antigen receptor-mediated signaling. (PMID: 7682714) Yamanashi Y … Yamamoto T (Proceedings of the National Academy of Sciences of the United States of America 1993) 3 4 22 58

Products for HCLS1 Gene

Sources for HCLS1 Gene

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