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    LINS1 lines homolog 1 [ Homo sapiens (human) ]

    Gene ID: 55180, updated on 5-Mar-2024

    Summary

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    Official Symbol
    LINS1provided by HGNC
    Official Full Name
    lines homolog 1provided by HGNC
    Primary source
    HGNC:HGNC:30922
    See related
    Ensembl:ENSG00000140471 MIM:610350; AllianceGenome:HGNC:30922
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LINS; MRT27; WINS1
    Summary
    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]
    Expression
    Ubiquitous expression in lymph node (RPKM 3.7), spleen (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q26.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (100566924..100602184, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (98321577..98357861, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (101107129..101142389, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723335 Neighboring gene PRKX pseudogene 1 Neighboring gene RNA, U6 small nuclear 181, pseudogene Neighboring gene MPRA-validated peak2454 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101172275-101172774 Neighboring gene ankyrin repeat and SOCS box containing 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:101175533-101176034 Neighboring gene WD repeat domain 12 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101209681-101210180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10173 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:101253262-101254461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101254609-101255442 Neighboring gene uncharacterized LOC105371024 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:101262004-101263203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101305027-101305654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101305655-101306282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:101308892-101309392 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:101322275-101322904 Neighboring gene protein enabled homolog

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of a novel nonsense homozygous mutation of LINS1 gene in two sisters with intellectual disability, schizophrenia, and anxiety. Chen CH, et al. Biomed J, 2021 Dec. PMID 34450347, Free PMC Article
    2. [Identification of LINS1 gene variant in a patient with severe mental retardation]. Zhang X, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2020 Jan 10. PMID 31922598
    3. Novel LINS1 missense mutation in a family with non-syndromic intellectual disability. Sheth J, et al. Am J Med Genet A, 2017 Apr. PMID 28181389
    4. LINS, a modulator of the WNT signaling pathway, is involved in human cognition. Akawi NA, et al. Orphanet J Rare Dis, 2013 Jun 17. PMID 23773660, Free PMC Article
    5. Molecular cloning and characterization of human WINS1 and mouse Wins2, homologous to Drosophila segment polarity gene Lines (Lin). Katoh M. Int J Mol Med, 2002 Aug. PMID 12119551

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of a novel nonsense homozygous mutation of LINS1 gene in two sisters with intellectual disability, schizophrenia, and anxiety.
      Title: Identification of a novel nonsense homozygous mutation of LINS1 gene in two sisters with intellectual disability, schizophrenia, and anxiety.
    2. A novel pathogenic variant of the LINS1 gene has been identified in a child with idiopathic mental retardation
      Title: [Identification of LINS1 gene variant in a patient with severe mental retardation].
    3. Study confirms that LINS, a modulator of the WNT pathway, is an indispensable gene to human cognition and this finding sheds further light on the importance of WNT signaling in human brain development and/or function.
      Title: LINS, a modulator of the WNT signaling pathway, is involved in human cognition.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Human WINS1 encoded 757 AA protein. Human WINS1 mRNA was expressed in adult testis, prostate, spleen, thymus, skeletal muscle, fetal kidney & brain. This is the first report on molecular cloning & initial characterization of human WINS1.
      Title: Molecular cloning and characterization of human WINS1 and mouse Wins2, homologous to Drosophila segment polarity gene Lines (Lin).
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, autosomal recessive 27
    MedGen: C3280538 OMIM: 614340 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat upregulates the expression of lines homolog (LINS) in human primary T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10583

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cognition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein Lines homolog 1
    Names
    WINS1 protein with Drosophila Lines (Lin) homologous domain
    wnt-signaling molecule Lines homolog 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_034076.2 RefSeqGene

      Range
      5849..41109
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001040616.3 → NP_001035706.2  protein Lines homolog 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC027020, AC090695
      Consensus CDS
      CCDS10385.1
      UniProtKB/Swiss-Prot
      Q8NG48, Q96FW2, Q9NVQ3
      Related
      ENSP00000318423.8, ENST00000314742.13
      Conserved Domains (2) summary
      pfam14694
      Location:194 → 542
      LINES_N; Lines N-terminus
      pfam14695
      Location:712 → 747
      LINES_C; Lines C-terminus

    2. NM_001352507.2 → NP_001339436.1  protein Lines homolog 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC027020, AC090695
      Conserved Domains (2) summary
      pfam14694
      Location:1 → 293
      LINES_N; Lines N-terminus
      pfam14695
      Location:463 → 498
      LINES_C; Lines C-terminus

    3. NM_001352508.2 → NP_001339437.1  protein Lines homolog 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC027020, AC090695
      Conserved Domains (2) summary
      pfam14694
      Location:179 → 491
      LINES_N; Lines N-terminus
      pfam14695
      Location:661 → 696
      LINES_C; Lines C-terminus

    RNA

    1. NR_148017.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC027020, AC090695

    2. NR_148018.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC027020, AC090695

    3. NR_148019.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC027020, AC090695

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      100566924..100602184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005254943.3 → XP_005255000.1  protein Lines homolog 1 isoform X2

      Conserved Domains (2) summary
      pfam14694
      Location:194 → 506
      LINES_N; Lines N-terminus
      pfam14695
      Location:676 → 711
      LINES_C; Lines C-terminus

    2. XM_047432784.1 → XP_047288740.1  protein Lines homolog 1 isoform X2

    3. XM_005254941.3 → XP_005254998.1  protein Lines homolog 1 isoform X1

      See identical proteins and their annotated locations for XP_005254998.1

      UniProtKB/Swiss-Prot
      Q8NG48, Q96FW2, Q9NVQ3
      Conserved Domains (2) summary
      pfam14694
      Location:194 → 542
      LINES_N; Lines N-terminus
      pfam14695
      Location:712 → 747
      LINES_C; Lines C-terminus

    4. XM_047432785.1 → XP_047288741.1  protein Lines homolog 1 isoform X2

    5. XM_024449980.2 → XP_024305748.1  protein Lines homolog 1 isoform X1

      UniProtKB/Swiss-Prot
      Q8NG48, Q96FW2, Q9NVQ3
      Conserved Domains (2) summary
      pfam14694
      Location:194 → 542
      LINES_N; Lines N-terminus
      pfam14695
      Location:712 → 747
      LINES_C; Lines C-terminus

    6. XM_017022399.3 → XP_016877888.1  protein Lines homolog 1 isoform X4

      Conserved Domains (2) summary
      pfam14694
      Location:1 → 293
      LINES_N; Lines N-terminus
      pfam14695
      Location:463 → 498
      LINES_C; Lines C-terminus

    7. XM_047432786.1 → XP_047288742.1  protein Lines homolog 1 isoform X3

      Related
      ENST00000559149.5

    8. XM_047432787.1 → XP_047288743.1  protein Lines homolog 1 isoform X3

    RNA

    1. XR_007064471.1 RNA Sequence

    2. XR_007064472.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      98321577..98357861 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378364.1 → XP_054234339.1  protein Lines homolog 1 isoform X2

    2. XM_054378361.1 → XP_054234336.1  protein Lines homolog 1 isoform X1

    3. XM_054378362.1 → XP_054234337.1  protein Lines homolog 1 isoform X2

    4. XM_054378359.1 → XP_054234334.1  protein Lines homolog 1 isoform X1

    5. XM_054378363.1 → XP_054234338.1  protein Lines homolog 1 isoform X2

    6. XM_054378360.1 → XP_054234335.1  protein Lines homolog 1 isoform X1

    7. XM_054378367.1 → XP_054234342.1  protein Lines homolog 1 isoform X4

    8. XM_054378365.1 → XP_054234340.1  protein Lines homolog 1 isoform X3

    9. XM_054378366.1 → XP_054234341.1  protein Lines homolog 1 isoform X3

    RNA

    1. XR_008488984.1 RNA Sequence

    2. XR_008488985.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001040614.1: Suppressed sequence

      Description
      NM_001040614.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.

    2. NM_001040615.1: Suppressed sequence

      Description
      NM_001040615.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.

    3. NM_018148.4: Suppressed sequence

      Description
      NM_018148.4: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.

    4. NM_181739.1: Suppressed sequence

      Description
      NM_181739.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    5. NM_181740.1: Suppressed sequence

      Description
      NM_181740.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NG48.2 GenPept UniProtKB/Swiss-Prot:Q8NG48

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