This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017] See more...

Aliases for CASC15 Gene

Data sources for CASC15 Gene:

RNA type for CASC15 Gene

lncRNA

Aliases for CASC15 Gene

External Ids for CASC15 Gene

Previous HGNC Symbols for CASC15 Gene

  • LINC00340

Summaries for CASC15 Gene

Entrez Gene Summary for CASC15 Gene

  • This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017]

GeneCards Summary for CASC15 Gene

CASC15 (Cancer Susceptibility 15) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with CASC15 include Basal Cell Carcinoma and Neuroblastoma.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CASC15 Gene

Genomics for CASC15 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CASC15 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J021664 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +3.0 3016 6.8 ZNF600 POLR2A ZIC2 ZNF341 PRDM6 ZSCAN5A ZNF189 ZFP37 TAF1 ZNF664 CASC15 SOX4 HSALNG0048532 RF00017-4868 RF00017-4865 PRL
GH06J022145 Promoter/Enhancer 2.1 VISTA EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250 +484.0 484035 6.3 ZIC2 REST CTCF FOXA2 RXRA SMAD4 TEAD3 RAD21 FOXP1 BHLHE40 NBAT1 CASC15 HSALNG0048533-001 piR-31534-583 PRL SOX4
GH06J022044 Enhancer 0.7 ENCODE dbSUPER 18 +381.3 381266 1 TRIM22 IRF5 BMI1 NR2F1 ARID3A ZSCAN4 IKZF2 MTA2 NBN RUNX3 CASC15 piR-43105-568 lnc-PRL-4 PRL SOX4
GH06J022042 Enhancer 0.6 ENCODE dbSUPER 20.8 +379.0 379038 1.5 IKZF1 GATAD2A NR2F2 CASC15 piR-43105-568 lnc-PRL-4 PRL SOX4
GH06J022041 Enhancer 0.7 Ensembl ENCODE dbSUPER 7.8 +377.9 377854 0.7 MAFK EMSY CASC15 piR-43105-568 lnc-PRL-4 PRL SOX4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CASC15 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for CASC15 Gene

Latest Assembly
chr6:21,664,185-22,654,455
(GRCh38/hg38)
Size:
990,271 bases
Orientation:
Plus strand

Previous Assembly
chr6:21,666,644-22,196,049
(GRCh37/hg19 by Entrez Gene)
Size:
529,406 bases
Orientation:
Plus strand

chr6:21,665,003-22,214,734
(GRCh37/hg19 by Ensembl)
Size:
549,732 bases
Orientation:
Plus strand

Genomic View for CASC15 Gene

Genes around CASC15 on UCSC Golden Path with GeneCards custom track
CASC15 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
CASC15 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CASC15 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CASC15 Gene

Proteins for CASC15 Gene

Post-translational modifications for CASC15 Gene

No Post-translational modifications

No data available for DME Specific Peptides for CASC15 Gene

Domains & Families for CASC15 Gene

Gene Families for CASC15 Gene

genes like me logo Genes that share domains with CASC15: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CASC15 Gene

Function for CASC15 Gene

Phenotypes From GWAS Catalog for CASC15 Gene

Phenotypes for CASC15 Gene

genes like me logo Genes that share phenotypes with CASC15: view

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CASC15 Gene

Localization for CASC15 Gene

Subcellular locations from

COMPARTMENTS
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 CASC15 gene
Compartment Confidence
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
golgi apparatus 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for CASC15 Gene

Pathways & Interactions for CASC15 Gene

PathCards logo

SuperPathways for CASC15 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CASC15 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for CASC15 Gene

Drugs & Compounds for CASC15 Gene

No Compound Related Data Available

Transcripts for CASC15 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for CASC15 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS0000A99515_9606 lncRNA 1177 3

Ensembl: ENST00000636388 (view in UCSC) ,

LncBook: HSALNT0102451,

LNCipedia: CASC15:57,

URS00007818DB_9606 lncRNA 4461 2

Ensembl: ENST00000605917 (view in UCSC) ,

LNCipedia: CASC15:19,

URS00002F09F7_9606 lncRNA 1901 2

Ensembl: ENST00000606851 (view in UCSC) ,

LNCipedia: CASC15:44, CASC15:5,

URS000029A240_9606 lncRNA 1646 2

Ensembl: ENST00000607048 (view in UCSC) ,

LNCipedia: CASC15:7,

URS000027A919_9606 lncRNA 1508 2

Ensembl: ENST00000444265 (view in UCSC) ,

LNCipedia: CASC15:13,

CASC15 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for CASC15 Gene

10 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for CASC15 Gene

No ASD Table

Relevant External Links for CASC15 Gene

GeneLoc Exon Structure for
CASC15

Expression for CASC15 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CASC15 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CASC15

genes like me logo Genes that share expression patterns with CASC15: view

No data available for 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 , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CASC15 Gene

Orthologs for CASC15 Gene

Evolution for CASC15 Gene

ENSEMBL:
Gene Tree for CASC15 (if available)
TreeFam:
Gene Tree for CASC15 (if available)
Alliance of Genome Resources:
Additional Orthologs for CASC15

No data available for Orthologs for CASC15 Gene

Paralogs for CASC15 Gene

No data available for Paralogs for CASC15 Gene

Variants for CASC15 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CASC15 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
974732 Uncertain Significance: Aganglionic megacolon 22,008,000(+) TATTATTGAGCAATGA
NC_000006.12:g.22008001_22092880del

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CASC15 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CASC15 Gene

Variant ID Type Subtype PubMed ID
dgv1002n67 CNV loss 20364138
dgv10319n54 CNV loss 21841781
dgv10320n54 CNV loss 21841781
dgv10321n54 CNV loss 21841781
dgv10322n54 CNV loss 21841781
dgv10323n54 CNV loss 21841781
dgv10324n54 CNV loss 21841781
dgv1078e199 CNV deletion 23128226
dgv1170e214 CNV loss 21293372
dgv1717e212 CNV loss 25503493
dgv1718e212 CNV loss 25503493
dgv3285n106 CNV deletion 24896259
dgv374n21 CNV loss 19592680
esv24725 CNV loss 19812545
esv25369 CNV loss 19812545
esv2621401 CNV deletion 19546169
esv2659390 CNV deletion 23128226
esv2660578 CNV deletion 23128226
esv2667198 CNV deletion 23128226
esv2670770 CNV deletion 23128226
esv2675345 CNV deletion 23128226
esv2678070 CNV deletion 23128226
esv2678811 CNV deletion 23128226
esv27155 CNV loss 19812545
esv2731677 CNV deletion 23290073
esv2731678 CNV deletion 23290073
esv2731679 CNV deletion 23290073
esv2731680 CNV deletion 23290073
esv2763540 CNV loss 21179565
esv3303671 CNV mobile element insertion 20981092
esv3308781 CNV mobile element insertion 20981092
esv3322146 CNV insertion 20981092
esv3336232 CNV insertion 20981092
esv3339910 CNV insertion 20981092
esv3376599 CNV insertion 20981092
esv3419255 CNV insertion 20981092
esv3431161 CNV insertion 20981092
esv3451137 CNV insertion 20981092
esv3567393 CNV deletion 23714750
esv3567396 CNV deletion 23714750
esv3570795 CNV loss 25503493
esv3570797 CNV loss 25503493
esv3570799 CNV loss 25503493
esv3570800 CNV loss 25503493
esv3570802 CNV loss 25503493
esv3570804 CNV loss 25503493
esv3576104 CNV gain 25503493
esv3608312 CNV loss 21293372
esv3608313 CNV loss 21293372
esv3608314 CNV loss 21293372
esv3608315 CNV loss 21293372
esv3608317 CNV gain 21293372
esv3608320 CNV loss 21293372
esv3608323 CNV loss 21293372
esv3608324 CNV loss 21293372
esv3608325 CNV loss 21293372
esv3608328 CNV loss 21293372
esv3608330 CNV loss 21293372
esv3608331 CNV gain 21293372
esv3890797 CNV loss 25118596
esv3890798 CNV loss 25118596
nsv1025837 CNV loss 25217958
nsv1073194 CNV deletion 25765185
nsv1124044 CNV deletion 24896259
nsv1129268 CNV deletion 24896259
nsv1161343 CNV deletion 26073780
nsv348606 CNV deletion 16902084
nsv348739 CNV deletion 16902084
nsv349514 CNV deletion 16902084
nsv349883 CNV deletion 16902084
nsv437478 CNV loss 16327808
nsv475311 CNV novel sequence insertion 20440878
nsv499608 CNV loss 21111241
nsv510019 OTHER sequence alteration 20534489
nsv511855 CNV loss 21212237
nsv516009 CNV loss 19592680
nsv516909 CNV loss 19592680
nsv5223 CNV deletion 18451855
nsv5224 CNV insertion 18451855
nsv525875 CNV loss 19592680
nsv601097 CNV loss 21841781
nsv601104 CNV loss 21841781
nsv818402 CNV loss 17921354
nsv819249 CNV loss 19587683
nsv823444 CNV loss 20364138
nsv823445 CNV loss 20364138
nsv823450 CNV loss 20364138
nsv830602 CNV gain 17160897

Additional Variant Information for CASC15 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CASC15
Leiden Open Variation Database (LOVD)
CASC15

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for CASC15 Gene

Disorders for CASC15 Gene

MalaCards: The human disease database

(10) MalaCards diseases for CASC15 Gene - From: LNC, COP, and GCD

Disorder Aliases PubMed IDs
basal cell carcinoma
  • basal cell cancer
neuroblastoma
  • nb
melanoma
  • malignant melanoma
glioma susceptibility 1
  • glm1
hepatocellular carcinoma
  • hcc
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CASC15

genes like me logo Genes that share disorders with CASC15: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CASC15 Gene

Publications for CASC15 Gene

  1. The CASC15 Long Intergenic Noncoding RNA Locus Is Involved in Melanoma Progression and Phenotype Switching. (PMID: 26016895) Lessard L … Hoon DSB (The Journal of investigative dermatology 2015) 2 3 72
  2. CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. (PMID: 26100672) Russell MR … Cole KA (Cancer research 2015) 2 3 72
  3. Long non-coding RNA CASC15 regulates gastric cancer cell proliferation, migration and epithelial mesenchymal transition by targeting CDKN1A and ZEB1. (PMID: 29489064) Wu Q … Wang Y (Molecular oncology 2018) 3 72
  4. The lncRNA CASC15 regulates SOX4 expression in RUNX1-rearranged acute leukemia. (PMID: 28724437) Fernando TR … Rao DS (Molecular cancer 2017) 2 3
  5. Long non-coding RNA CASC15 is upregulated in hepatocellular carcinoma and facilitates hepatocarcinogenesis. (PMID: 29075788) He T … Wang W (International journal of oncology 2017) 3 72

Products for CASC15 Gene

Sources for CASC15 Gene