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CASC16 cancer susceptibility 16 [ Homo sapiens (human) ]

Gene ID: 643714, updated on 10-Oct-2023

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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Location:
16q12.1-q12.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (52552087..52606975, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (58349967..58404850, complement)
105.20220307 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
  • 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 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
  2. 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
  3. 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
  4. 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
  5. 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

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
    ENST00000510238.8

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_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

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Chemical Information
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