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Aliases for LINS1 Gene

Aliases for LINS1 Gene

  • Lines Homolog 1 2 3 5
  • Wnt-Signaling Molecule Lines Homolog 1 3 4
  • WINS1 3 4
  • LINS 3 4
  • WINS1 Protein With Drosophila Lines (Lin) Homologous Domain 3
  • Lines Homolog 1 (Drosophila) 2
  • Lines Homolog (Drosophila) 2
  • Protein Lines Homolog 1 3
  • MRT27 3

External Ids for LINS1 Gene

Previous HGNC Symbols for LINS1 Gene

  • LINS

Previous GeneCards Identifiers for LINS1 Gene

  • GC15M098927
  • GC15M101107
  • GC15M100593
  • GC15M100599
  • GC15M100605
  • GC15M100611
  • GC15M100670
  • GC15M100678

Summaries for LINS1 Gene

Entrez Gene Summary for LINS1 Gene

  • The Drosophila segment polarity gene lin encodes a protein, lines, which plays important roles in development of the epidermis and hindgut. This gene encodes a protein containing a lines-like domain. This gene is located on chromosome 15 and clustered with the gene encoding ankyrin repeat and SOCS box-containing protein 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2017]

GeneCards Summary for LINS1 Gene

LINS1 (Lines Homolog 1) is a Protein Coding gene. Diseases associated with LINS1 include Mental Retardation, Autosomal Recessive 27 and Autosomal Recessive Non-Syndromic Intellectual Disability.

Additional gene information for LINS1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LINS1 Gene

Genomics for LINS1 Gene

GeneHancer (GH) Regulatory Elements for LINS1 Gene

Promoters and enhancers for LINS1 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
GH15I100600 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 561.9 +1.1 1082 3.8 HDGF PKNOX1 ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF213 ZNF143 ZNF207 LINS1 ASB7 ENSG00000270127 PRKXP1 PIR58933
GH15I101293 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 45.3 -692.1 -692124 4.7 PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B POLR2B SNRPA1 ENSG00000259172 LINS1 LOC100419174 CERS3-AS1 PRKXP1 RNU6-807P WASH3P LRRK1 ENSG00000270127
GH15I101197 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 14.7 -601.0 -601013 14.3 HDGF PKNOX1 FOXA2 SMAD1 SIN3A FEZF1 IRF4 TCF12 GATA2 ZNF143 GC15M101194 CHSY1 SNRPA1 LOC100419174 LINS1 PRKXP1 TM2D3 WASH3P ASB7 LRRK1
GH15I101182 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 16.3 -585.7 -585684 13.8 BATF RAD21 ARID2 SCRT2 ATF7 FOS BCLAF1 IKZF2 RUNX3 EGR2 CHSY1 LINS1 LOC100419174 SNRPA1 WASH3P TM2D3 ASB7 PIR58100 GC15M101194
GH15I101254 Enhancer 1.2 Ensembl ENCODE 20.2 -652.4 -652430 2 PKNOX1 ATF1 FOXA2 ARNT ARID4B FEZF1 TCF12 CBX5 GATA2 ARID2 LINS1 CERS3-AS1 SNRPA1 LRRK1 LOC100419174 LOC100128108 ASB7 CHSY1 PIR39927 GC15M101273
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LINS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LINS1 gene promoter:

Genomic Locations for LINS1 Gene

Genomic Locations for LINS1 Gene
43,862 bases
Minus strand

Genomic View for LINS1 Gene

Genes around LINS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LINS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINS1 Gene

Proteins for LINS1 Gene

  • Protein details for LINS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Lines homolog 1
    Protein Accession:
    Secondary Accessions:
    • Q96FW2
    • Q9NVQ3

    Protein attributes for LINS1 Gene

    757 amino acids
    Molecular mass:
    85857 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LINS1 Gene


neXtProt entry for LINS1 Gene

Post-translational modifications for LINS1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINS1 Gene

Domains & Families for LINS1 Gene

Gene Families for LINS1 Gene

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

Protein Domains for LINS1 Gene

Suggested Antigen Peptide Sequences for LINS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the protein lines family.
  • Belongs to the protein lines family.
genes like me logo Genes that share domains with LINS1: view

Function for LINS1 Gene

Phenotypes From GWAS Catalog for LINS1 Gene

Phenotypes for LINS1 Gene

genes like me logo Genes that share phenotypes with LINS1: view

Human Phenotype Ontology for LINS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for LINS1 Gene

Localization for LINS1 Gene

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 LINS1 gene
Compartment Confidence
nucleus 3
cytosol 2
plasma membrane 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LINS1 Gene

Pathways & Interactions for LINS1 Gene

SuperPathways for LINS1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LINS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050890 cognition IMP 23773660
genes like me logo Genes that share ontologies with LINS1: view

No data available for Pathways by source and SIGNOR curated interactions for LINS1 Gene

Drugs & Compounds for LINS1 Gene

No Compound Related Data Available

Transcripts for LINS1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LINS1 Gene

No ASD Table

Relevant External Links for LINS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LINS1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LINS1 Gene:


mRNA Expression by UniProt/SwissProt for LINS1 Gene:

Tissue specificity: Expressed in adult testis, prostate, prostate, spleen, thymus, skeletal muscle, fetal kidney and brain.

Evidence on tissue expression from TISSUES for LINS1 Gene

  • Nervous system(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LINS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
  • chest wall
  • heart
  • abdominal wall
  • foot
  • lower limb
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for LINS1 Gene

Orthologs for LINS1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LINS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LINS 33 34
  • 99.25 (n)
(Bos Taurus)
Mammalia LINS 33 34
  • 82.51 (n)
(Canis familiaris)
Mammalia LINS 33 34
  • 81.89 (n)
(Rattus norvegicus)
Mammalia Lins 33
  • 73.24 (n)
(Mus musculus)
Mammalia Lins 33 34
  • 71.92 (n)
Lins1 16
(Monodelphis domestica)
Mammalia -- 34
  • 53 (a)
-- 34
  • 53 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 53 (a)
-- 34
  • 51 (a)
(Gallus gallus)
Aves LINS 33 34
  • 55.45 (n)
(Anolis carolinensis)
Reptilia LINS 34
  • 38 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lins 33
  • 53.01 (n)
(Danio rerio)
Actinopterygii LOC798262 33
  • 45.77 (n)
  • 31 (a)
Species where no ortholog for LINS1 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LINS1 Gene

Gene Tree for LINS1 (if available)
Gene Tree for LINS1 (if available)

Paralogs for LINS1 Gene

No data available for Paralogs for LINS1 Gene

Variants for LINS1 Gene

Sequence variations from dbSNP and Humsavar for LINS1 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1057519019 likely-pathogenic, Mental retardation, autosomal recessive 27, retardation, autosomal recessive 27 (MRT27) [MIM:614340] 100,573,936(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs149644940 pathogenic, not provided, Mental retardation, autosomal recessive 27 100,573,695(-) A/C coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs587777225 pathogenic, Mental retardation, autosomal recessive 27 100,573,885(-) CATG/ coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs587777226 pathogenic, Mental retardation, autosomal recessive 27 100,573,650(-) CCTTTC/C coding_sequence_variant, non_coding_transcript_variant, splice_donor_variant
rs869312932 pathogenic, Inborn genetic diseases 100,571,893(-) C/A splice_donor_variant

Structural Variations from Database of Genomic Variants (DGV) for LINS1 Gene

Variant ID Type Subtype PubMed ID
nsv833107 CNV gain 17160897
nsv570779 CNV gain 21841781
nsv523884 CNV loss 19592680
nsv471265 CNV gain 18288195
nsv457284 CNV gain 19166990
nsv1148455 CNV duplication 26484159
nsv1041172 CNV gain 25217958
esv3637481 CNV gain 21293372
esv3637480 CNV gain 21293372
esv2750137 CNV deletion 23290073
esv2750136 CNV deletion 23290073
esv2670823 CNV deletion 23128226
esv2562323 CNV deletion 19546169
esv1000983 CNV deletion 20482838
dgv313e201 CNV deletion 23290073

Variation tolerance for LINS1 Gene

Residual Variation Intolerance Score: 83.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.15; 90.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LINS1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LINS1 Gene

Disorders for LINS1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LINS1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LINS1 in MalaCards View complete list of genes associated with diseases


  • Mental retardation, autosomal recessive 27 (MRT27) [MIM:614340]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:21937992, ECO:0000269 PubMed:23773660, ECO:0000269 PubMed:28181389}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LINS1

genes like me logo Genes that share disorders with LINS1: view

No data available for Genatlas for LINS1 Gene

Publications for LINS1 Gene

  1. Molecular cloning and characterization of human WINS1 and mouse Wins2, homologous to Drosophila segment polarity gene Lines (Lin). (PMID: 12119551) Katoh M (International journal of molecular medicine 2002) 2 3 4 58
  2. LINS, a modulator of the WNT signaling pathway, is involved in human cognition. (PMID: 23773660) Akawi NA … Al-Gazali L (Orphanet journal of rare diseases 2013) 3 4 58
  3. 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
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Normalization and subtraction: two approaches to facilitate gene discovery. (PMID: 8889548) Bonaldo MF … Soares MB (Genome research 1996) 2 3 58

Products for LINS1 Gene

Sources for LINS1 Gene

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