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    CASC16 cancer susceptibility 16 [ Homo sapiens (human) ]

    Gene ID: 643714, updated on 22-Oct-2024

    Summary

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    Official Symbol
    CASC16provided by HGNC
    Official Full Name
    cancer susceptibility 16provided by HGNC
    Primary source
    HGNC:HGNC:48608
    See related
    Ensembl:ENSG00000249231 AllianceGenome:HGNC:48608
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LINC00918
    Expression
    Restricted expression toward testis (RPKM 9.4) See more
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    Genomic context

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    See CASC16 in Genome Data Viewer
    Location:
    16q12.1-q12.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (52552087..52606975, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (58349967..58404850, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (52585999..52640887, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371262 Neighboring gene VISTA enhancer hs1300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:52472926-52473426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:52473427-52473927 Neighboring gene TOX high mobility group box family member 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:52504393-52505003 Neighboring gene NANOG hESC enhancer GRCh37_chr16:52567073-52567576 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:52611160-52612359 Neighboring gene uncharacterized LOC105371265 Neighboring gene long intergenic non-protein coding RNA 3064 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:52662737-52663936 Neighboring gene tropomyosin 3 pseudogene

    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 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. Association between the rs4784227-CASC16 polymorphism and the risk of breast cancer: A meta-analysis. Xu W, et al. Medicine (Baltimore), 2022 Aug 26. PMID 36042591, Free PMC Article
    2. The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population. Zuo X, et al. Mol Med, 2020 Jan 29. PMID 31996122, Free PMC Article
    3. LOC643714 Polymorphisms Contribute to an Elevated Susceptibility to Breast Cancer: A Meta-analysis of 231,191 Subjects. Gao F, et al. Clin Breast Cancer, 2019 Oct. PMID 31324582
    4. TNRC9/LOC643714 polymorphisms are not associated with breast cancer risk in Chinese women. Li L, et al. Eur J Cancer Prev, 2009 Aug. PMID 19398914
    5. Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population. Zhang Y, et al. PeerJ, 2022. PMID 36540803, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population.
      Title: Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population.
    2. Association between the rs4784227-CASC16 polymorphism and the risk of breast cancer: A meta-analysis.
      Title: Association between the rs4784227-CASC16 polymorphism and the risk of breast cancer: A meta-analysis.
    3. The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population.
      Title: The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population.
    4. Association of polymorphisms in LOC105377871 and CASC16 with breast cancer in the northwest Chinese Han population.
      Title: Association of polymorphisms in LOC105377871 and CASC16 with breast cancer in the northwest Chinese Han population.
    5. LOC643714 Polymorphism was associated with Elevated Susceptibility to Breast Cancer (meta analysis).
      Title: LOC643714 Polymorphisms Contribute to an Elevated Susceptibility to Breast Cancer: A Meta-analysis of 231,191 Subjects.
    6. There is no significant association between the risk of breast cancer and three single nucleotide polymorphisms (SNPs) of TNRC9/LOC643714 genes and their haplotypes.
      Title: TNRC9/LOC643714 polymorphisms are not associated with breast cancer risk in Chinese women.
    7. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Genetic variants in trinucleotide repeat-containing 9 (TNRC9) are associated with risk of estrogen receptor positive breast cancer in a Chinese population.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphisms in the TOX3/LOC643714 locus and risk of breast cancer in African-American women.
    9. Meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Association between invasive ovarian cancer susceptibility and 11 best candidate SNPs from breast cancer genome-wide association study.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A combined analysis of genome-wide association studies in breast cancer.
    EBI GWAS Catalog
    A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1).
    EBI GWAS Catalog
    Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer.
    EBI GWAS Catalog
    Genome-wide association studies identify four ER negative-specific breast cancer risk loci.
    EBI GWAS Catalog
    Genome-wide association study identifies a common variant in RAD51B associated with male breast cancer risk.
    EBI GWAS Catalog
    Genome-wide association study identifies five new breast cancer susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study identifies novel breast cancer susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study identifies novel restless legs syndrome susceptibility loci on 2p14 and 16q12.1.
    EBI GWAS Catalog
    Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25.
    EBI GWAS Catalog
    Genome-wide association study of breast cancer in the Japanese population.
    EBI GWAS Catalog
    Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium.
    EBI GWAS Catalog
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog
    Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study.
    EBI GWAS Catalog

    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

    General gene information

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    Markers

    Other Names

    • cancer susceptibility 16 (non-protein coding)
    • cancer susceptibility candidate 16 (non-protein coding)
    • long intergenic non-protein coding RNA 918

    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.

    RNA

    1. NR_033920.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC034767, DB462404, DB523777
      Related
      ENST00000510238.9

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      52552087..52606975 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      58349967..58404850 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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    Research Materials