CASC17 (cancer susceptibility 17) - Rat Genome Database

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Gene: CASC17 (cancer susceptibility 17) Homo sapiens
Analyze
Symbol: CASC17
Name: cancer susceptibility 17
RGD ID: 7267115
HGNC Page HGNC:43911
Description: ASSOCIATED WITH campomelic dysplasia
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: cancer susceptibility 17 (non-protein coding); cancer susceptibility candidate 17 (non-protein coding); LINC00600; RP11-879D6.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381771,097,774 - 71,202,179 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1771,097,774 - 71,202,203 (-)EnsemblGRCh38hg38GRCh38
GRCh371769,093,915 - 69,198,320 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17q24.3NCBI
HuRef1764,392,905 - 64,590,633 (-)NCBIHuRef
CHM1_11769,064,501 - 69,262,434 (-)NCBICHM1_1
T2T-CHM13v2.01771,970,472 - 72,074,817 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:12477932   PMID:17603485   PMID:18264097   PMID:19767753   PMID:21743057   PMID:23284291   PMID:24753544  


Genomics

Variants

.
Variants in CASC17
12 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_104152.1(CASC17):n.137-660A>G single nucleotide variant Lung cancer [RCV000100630] Chr17:71133130 [GRCh38]
Chr17:69129271 [GRCh37]
Chr17:17q24.3
uncertain significance
NR_104152.1(CASC17):n.137-8352G>T single nucleotide variant Lung cancer [RCV000100631] Chr17:71140822 [GRCh38]
Chr17:69136963 [GRCh37]
Chr17:17q24.3
uncertain significance
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1
pathogenic
GRCh38/hg38 17q24.3(chr17:70089117-71111424)x3 copy number gain See cases [RCV000141126] Chr17:70089117..71111424 [GRCh38]
Chr17:68085258..69107565 [GRCh37]
Chr17:65596853..66619160 [NCBI36]
Chr17:17q24.3
likely benign|uncertain significance
GRCh38/hg38 17q24.2-24.3(chr17:68420514-71351235)x1 copy number loss See cases [RCV000143113] Chr17:68420514..71351235 [GRCh38]
Chr17:66416655..69347376 [GRCh37]
Chr17:63928250..66858971 [NCBI36]
Chr17:17q24.2-24.3
pathogenic
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3
pathogenic
NC_000017.11:g.(?_70643580)_(71603774_?)del deletion Acampomelic campomelic dysplasia with autosomal sex reversal [RCV000032999] Chr17:70643580..71603774 [GRCh38]
Chr17:68639721..69599915 [GRCh37]
Chr17:66151316..67111510 [NCBI36]
Chr17:17q24.3
pathogenic
GRCh38/hg38 17q24.3(chr17:69766783-71154921)x1 copy number loss See cases [RCV000051104] Chr17:69766783..71154921 [GRCh38]
Chr17:67762924..69151062 [GRCh37]
Chr17:65274519..66662657 [NCBI36]
Chr17:17q24.3
uncertain significance
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3
pathogenic
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:158
Interacting mature miRNAs:159
Transcripts:ENST00000569074
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage
High
Medium 24
Low 2 3 2 3 2 2 1 4 335 14
Below cutoff 105 69 189 59 48 23 225 64 1652 29 73 111 44 48 117

Sequence


RefSeq Acc Id: ENST00000569074
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,097,775 - 71,202,177 (-)Ensembl
RefSeq Acc Id: ENST00000659322
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,893 - 71,202,185 (-)Ensembl
RefSeq Acc Id: ENST00000659670
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,097,774 - 71,202,185 (-)Ensembl
RefSeq Acc Id: ENST00000662323
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,834 - 71,202,203 (-)Ensembl
RefSeq Acc Id: ENST00000662349
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,873 - 71,202,179 (-)Ensembl
RefSeq Acc Id: ENST00000664372
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,897 - 71,202,185 (-)Ensembl
RefSeq Acc Id: ENST00000664398
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,896 - 71,202,170 (-)Ensembl
RefSeq Acc Id: ENST00000665992
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,097,786 - 71,131,324 (-)Ensembl
RefSeq Acc Id: ENST00000667642
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,894 - 71,202,181 (-)Ensembl
RefSeq Acc Id: ENST00000668160
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,891 - 71,202,185 (-)Ensembl
RefSeq Acc Id: ENST00000668920
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,895 - 71,202,185 (-)Ensembl
RefSeq Acc Id: ENST00000669182
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,893 - 71,185,650 (-)Ensembl
RefSeq Acc Id: ENST00000669562
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,899 - 71,202,179 (-)Ensembl
RefSeq Acc Id: ENST00000671130
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1771,098,896 - 71,202,180 (-)Ensembl
RefSeq Acc Id: NR_104152
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381771,097,774 - 71,202,179 (-)NCBI
HuRef1764,486,259 - 64,590,633 (-)NCBI
CHM1_11769,158,042 - 69,262,434 (-)NCBI
T2T-CHM13v2.01771,970,472 - 72,074,817 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC CASC17 COSMIC
Ensembl Genes ENSG00000260785 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000569074 ENTREZGENE
GTEx ENSG00000260785 GTEx
HGNC ID HGNC:43911 ENTREZGENE
Human Proteome Map CASC17 Human Proteome Map
NCBI Gene CASC17 ENTREZGENE
RNAcentral URS000075E2D4 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 CASC17  cancer susceptibility 17    cancer susceptibility 17 (non-protein coding)  Symbol and/or name change 5135510 APPROVED
2017-01-31 CASC17  cancer susceptibility 17 (non-protein coding)    cancer susceptibility candidate 17 (non-protein coding)  Symbol and/or name change 5135510 APPROVED