Aliases for HCLS1 Gene

Aliases for HCLS1 Gene

  • Hematopoietic Cell-Specific Lyn Substrate 1 2 3 5
  • HS1 2 3 4
  • Hematopoietic Lineage Cell-Specific Protein 3 4
  • LckBP1 3 4
  • CTTNL 2 3
  • P75 3 4
  • Hematopoietic Cell-Specific LYN Substrate 1 4
  • Cortactin-Like 2
  • HCLS1 5

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. Among its related pathways are Proteoglycans in cancer and Development Slit-Robo signaling. Gene Ontology (GO) annotations related to this gene include protein kinase binding. An important paralog of this gene is CTTN.

UniProtKB/Swiss-Prot Summary 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

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HCLS1 Gene

Genomics for HCLS1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HCLS1 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HCLS1

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

Genomic Locations for HCLS1 Gene

Latest Assembly
29,529 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
29,505 bases
Minus strand

(GRCh37/hg19 by Ensembl)
29,529 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

  • SH3 domain signature
  • Hs1/Cortactin

Suggested Antigen Peptide Sequences for HCLS1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54279, highly similar to Hematopoietic lineage cell-specific protein (B4DQ69_HUMAN)
  • p75 (HCLS1_HUMAN)
genes like me logo Genes that share domains with HCLS1: view

No data available for Graphical View of Domain Structure and 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 16189514
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:

miRNA for HCLS1 Gene

miRTarBase miRNAs that target HCLS1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCLS1

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
cytosol 5
plasma membrane 4
cytoskeleton 4
nucleus 4
mitochondrion 3
extracellular 1
endoplasmic reticulum 1
lysosome 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 --
GO:0005667 transcription factor complex IDA 23001182
GO:0005737 cytoplasm ISS --
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:
Other effect:

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

17 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HCLS1

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

Expression for HCLS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HCLS1

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(4.7)
  • Liver(4.4)
  • Blood(4)
  • Nervous system(2.8)
  • Lymph node(2.7)
  • Bone marrow(2.5)
  • Heart(2.4)
  • Lung(2.2)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with HCLS1: view

Primer products for research

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 29 30
  • 99.17 (n)
(Bos Taurus)
Mammalia HCLS1 29 30
  • 89.12 (n)
(Canis familiaris)
Mammalia HCLS1 29 30
  • 86.85 (n)
(Mus musculus)
Mammalia Hcls1 29 16 30
  • 86.2 (n)
(Rattus norvegicus)
Mammalia Hcls1 29
  • 86.09 (n)
(Monodelphis domestica)
Mammalia HCLS1 30
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia HCLS1 30
  • 43 (a)
(Gallus gallus)
Aves HCLS1 29 30
  • 65.87 (n)
(Anolis carolinensis)
Reptilia HCLS1 30
  • 41 (a)
(Danio rerio)
Actinopterygii hcls1 30
  • 46 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta Cortactin 30 31
  • 37 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.7160 30
  • 39 (a)
Species where no ortholog for HCLS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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
Alliance of Genome Resources:
Additional Orthologs for HCLS1

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HCLS1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs2070179 -- p.Thr235Ala
rs2070180 -- p.Glu361Lys
rs9869984 -- p.Val436Leu

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HCLS1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

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

Disorders for HCLS1 Gene

Additional Disease Information for HCLS1

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for HCLS1 Gene.

No data available for MalaCards , 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
  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 40
  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
  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
  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

Products for HCLS1 Gene

Sources for HCLS1 Gene