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Aliases for HYLS1 Gene

Aliases for HYLS1 Gene

  • HYLS1, Centriolar And Ciliogenesis Associated 2 3 5
  • Hydrolethalus Syndrome 1 2 3
  • HLS 3 4
  • Hydrolethalus Syndrome Protein 1 3

External Ids for HYLS1 Gene

Previous GeneCards Identifiers for HYLS1 Gene

  • GC11P125259
  • GC11P125753
  • GC11P121695

Summaries for HYLS1 Gene

Entrez Gene Summary for HYLS1 Gene

  • This gene encodes a protein localized to the cytoplasm. Mutations in this gene are associated with hydrolethalus syndrome. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Oct 2008]

GeneCards Summary for HYLS1 Gene

HYLS1 (HYLS1, Centriolar And Ciliogenesis Associated) is a Protein Coding gene. Diseases associated with HYLS1 include Hydrolethalus Syndrome 1 and Joubert Syndrome 1.

UniProtKB/Swiss-Prot for HYLS1 Gene

  • Plays a role in ciliogenesis.

Gene Wiki entry for HYLS1 Gene

Additional gene information for HYLS1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HYLS1 Gene

Genomics for HYLS1 Gene

GeneHancer (GH) Regulatory Elements for HYLS1 Gene

Promoters and enhancers for HYLS1 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
GH11J125800 Enhancer 0.4 FANTOM5 5.8 -83.2 -83235 0.4 REST ZNF507 DDX25 CHEK1 PATE4 HYLS1 PATE1 PATE2 GC11P125812 PATE3
GH11J126317 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 1.2 +435.2 435173 3.2 PKNOX1 KLF1 ATF1 MAX GLIS2 POLR2A EED ATF7 IKZF2 RUNX3 FOXRED1 ST3GAL4 TIRAP SRPRA DCPS FAM118B HYLS1 HP11014 PIR55528
GH11J126305 Enhancer 0.9 FANTOM5 ENCODE 1.4 +422.2 422242 0.5 HDGF SCRT1 PKNOX1 ZNF687 TRIM22 EBF1 MEF2B DPF2 SCRT2 IKZF1 HP11014 FOXRED1 FAM118B DCPS HYLS1 PIR55528
GH11J125886 Promoter/Enhancer 1.5 Ensembl ENCODE 0.7 +4.1 4144 2.1 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF207 PIR58536 GC11P125889 HP11014 TMEM218 STT3A CHEK1 DDX25 PUS3 HYLS1 PIR36090
GH11J125890 Enhancer 0.7 ENCODE 0.4 +7.1 7106 1.1 MEIS2 LEF1 PKNOX1 ZNF316 FOXK2 NFE2 MAFK SMARCE1 GATAD2A CBFA2T3 RPUSD4 PUS3 CHEK1 GC11P125889 PIR58536 HYLS1 PIR36090
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HYLS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HYLS1 gene promoter:
  • TBP
  • Pbx1a
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • NF-Y
  • NF-YA

Genomic Locations for HYLS1 Gene

Genomic Locations for HYLS1 Gene
17,035 bases
Plus strand
17,035 bases
Plus strand

Genomic View for HYLS1 Gene

Genes around HYLS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HYLS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HYLS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HYLS1 Gene

Proteins for HYLS1 Gene

  • Protein details for HYLS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hydrolethalus syndrome protein 1
    Protein Accession:
    Secondary Accessions:
    • B3KXI8
    • Q96BX9

    Protein attributes for HYLS1 Gene

    299 amino acids
    Molecular mass:
    34359 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH15047.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for HYLS1 Gene

Post-translational modifications for HYLS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HYLS1 Gene

Domains & Families for HYLS1 Gene

Gene Families for HYLS1 Gene

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

Protein Domains for HYLS1 Gene


Suggested Antigen Peptide Sequences for HYLS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HYLS1 family.
  • Belongs to the HYLS1 family.
genes like me logo Genes that share domains with HYLS1: view

Function for HYLS1 Gene

Molecular function for HYLS1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in ciliogenesis.

Gene Ontology (GO) - Molecular Function for HYLS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with HYLS1: view
genes like me logo Genes that share phenotypes with HYLS1: view

Human Phenotype Ontology for HYLS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for HYLS1 Gene

miRTarBase miRNAs that target HYLS1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HYLS1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for HYLS1 Gene

Localization for HYLS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HYLS1 Gene

Cytoplasm. Cell projection, cilium. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole.

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 HYLS1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
nucleus 5
cytosol 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HYLS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 15843405
GO:0005737 cytoplasm IDA 15843405
GO:0005813 centrosome IDA 21399614
GO:0005814 centriole IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with HYLS1: view

Pathways & Interactions for HYLS1 Gene

SuperPathways for HYLS1 Gene

No Data Available

Interacting Proteins for HYLS1 Gene

Gene Ontology (GO) - Biological Process for HYLS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030030 cell projection organization IEA --
GO:0060271 cilium assembly ISS --
genes like me logo Genes that share ontologies with HYLS1: view

No data available for Pathways by source and SIGNOR curated interactions for HYLS1 Gene

Drugs & Compounds for HYLS1 Gene

No Compound Related Data Available

Transcripts for HYLS1 Gene

mRNA/cDNA for HYLS1 Gene

Unigene Clusters for HYLS1 Gene

Hydrolethalus syndrome 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HYLS1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HYLS1 Gene

No ASD Table

Relevant External Links for HYLS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HYLS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HYLS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HYLS1 Gene

This gene is overexpressed in Testis (x5.3).

Protein differential expression in normal tissues from HIPED for HYLS1 Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HYLS1 Gene

Protein tissue co-expression partners for HYLS1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HYLS1 Gene:


SOURCE GeneReport for Unigene cluster for HYLS1 Gene:


Evidence on tissue expression from TISSUES for HYLS1 Gene

  • Nervous system(4.3)
  • Blood(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HYLS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • chin
  • cranial nerve
  • ear
  • epiglottis
  • eye
  • face
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • skull
  • tooth
  • vocal cord
  • bronchus
  • diaphragm
  • heart
  • lung
  • trachea
  • abdominal wall
  • adrenal gland
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • placenta
  • uterus
  • vagina
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • shin
  • tibia
  • toe
  • upper limb
  • blood vessel
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with HYLS1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for HYLS1 Gene

Orthologs for HYLS1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HYLS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HYLS1 34 33
  • 99.55 (n)
(Canis familiaris)
Mammalia HYLS1 34 33
  • 90.64 (n)
(Bos Taurus)
Mammalia HYLS1 34 33
  • 88.52 (n)
(Mus musculus)
Mammalia Hyls1 16 34 33
  • 84.5 (n)
(Rattus norvegicus)
Mammalia Hyls1 33
  • 84.17 (n)
(Monodelphis domestica)
Mammalia HYLS1 34
  • 69 (a)
(Gallus gallus)
Aves HYLS1 33
  • 56.87 (n)
(Anolis carolinensis)
Reptilia HYLS1 34
  • 51 (a)
(Danio rerio)
Actinopterygii LOC100147862 33
  • 47.9 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8204 34
  • 27 (a)
Species where no ortholog for HYLS1 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 HYLS1 Gene

Gene Tree for HYLS1 (if available)
Gene Tree for HYLS1 (if available)
Evolutionary constrained regions (ECRs) for HYLS1: view image

Paralogs for HYLS1 Gene

No data available for Paralogs for HYLS1 Gene

Variants for HYLS1 Gene

Sequence variations from dbSNP and Humsavar for HYLS1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs104894232 pathogenic, Hydrolethalus syndrome, Hydrolethalus syndrome 1, Hydrolethalus syndrome 1 (HLS1) [MIM:236680] 125,900,000(+) A/G coding_sequence_variant, missense_variant
rs11382127 uncertain-significance, benign, Hydrolethalus syndrome 125,891,484(+) AAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAAA intron_variant
rs117414825 uncertain-significance, Hydrolethalus syndrome 125,900,597(+) T/G 3_prime_UTR_variant
rs138284572 uncertain-significance, Hydrolethalus syndrome 125,899,836(+) A/G coding_sequence_variant, synonymous_variant
rs143124884 uncertain-significance, Hydrolethalus syndrome 125,883,989(+) A/G 5_prime_UTR_variant, genic_upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HYLS1 Gene

Variant ID Type Subtype PubMed ID
dgv248n67 CNV gain 20364138
esv32964 CNV gain+loss 17666407
nsv1127238 CNV deletion 24896259
nsv468888 CNV loss 19166990
nsv556525 CNV gain 21841781
nsv556526 CNV loss 21841781

Variation tolerance for HYLS1 Gene

Residual Variation Intolerance Score: 56.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.74; 89.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HYLS1 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 HYLS1 Gene

Disorders for HYLS1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for HYLS1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hydrolethalus syndrome 1
  • hls1
joubert syndrome 1
  • jbts1
mental retardation, autosomal recessive 55
  • mrt55
orbital cyst
granulomatous angiitis
  • vasculitis, central nervous system
- elite association - COSMIC cancer census association via MalaCards
Search HYLS1 in MalaCards View complete list of genes associated with diseases


  • Hydrolethalus syndrome 1 (HLS1) [MIM:236680]: A lethal syndrome characterized by polydactyly, central nervous system malformation, and hydrocephalus. The polydactyly is postaxial in the hands and preaxial in the feet. A highly characteristic hallux duplex is seen in almost no other situation. In half of the cases, a large atrioventricular communis defect of the heart is found. The pregnancy is characterized by hydramnios, which is often massive, and by preterm delivery. {ECO:0000269 PubMed:15843405}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Defects in HYLS1 may be involved in ciliopathies other than hydrolethalus syndrome 1. A homozygous mutation resulting in a C-terminal extension of 11 residues has been found in patients diagnosed as Joubert syndrome, a ciliopathy presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. {ECO:0000269 PubMed:26830932}.

Additional Disease Information for HYLS1

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 HYLS1: view

No data available for Genatlas for HYLS1 Gene

Publications for HYLS1 Gene

  1. Hydrolethalus syndrome is caused by a missense mutation in a novel gene HYLS1. (PMID: 15843405) Mee L … Peltonen L (Human molecular genetics 2005) 2 3 4 22 58
  2. The hydrolethalus syndrome protein HYLS-1 links core centriole structure to cilia formation. (PMID: 19656802) Dammermann A … Oegema K (Genes & development 2009) 2 3 22 58
  3. A novel HYLS1 homozygous mutation in living siblings with Joubert syndrome. (PMID: 26830932) Oka M … Kobayashi K (Clinical genetics 2016) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for HYLS1 Gene

Sources for HYLS1 Gene

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