CASC16

Summary

CASC16 (cancer susceptibility 16, HGNC:48608) is a long non-coding RNA gene on chromosome 16q12.1-q12.2.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48608
Approved symbol	CASC16
Name	cancer susceptibility 16
Location	16q12.1-q12.2
Locus type	RNA, long non-coding
Status	Approved
Aliases	LOC643714
Ensembl gene	ENSG00000249231
Ensembl biotype	lncRNA
Entrez	643714
RNAcentral	URS000075AB2F — lncRNA, 1001 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 29 lncRNA

ENST00000510238, ENST00000563844, ENST00000565755, ENST00000652959, ENST00000671536, ENST00000826535, ENST00000826536, ENST00000826537, ENST00000826538, ENST00000826539, ENST00000826540, ENST00000826541, ENST00000826542, ENST00000826543, ENST00000826544, ENST00000826545, ENST00000826546, ENST00000826547, ENST00000826548, ENST00000826549, ENST00000826550, ENST00000826551, ENST00000826552, ENST00000826553, ENST00000826554, ENST00000826555, ENST00000826556, ENST00000826557, ENST00000826558

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000510238 — 4 exons

Exon	Start	End
ENSE00004237524	52552055	52552434
ENSE00004237530	52562814	52562862
ENSE00004237536	52606504	52606992
ENSE00004237555	52590936	52591067

Expression profiles

Bgee: expression breadth ubiquitous, 115 present calls, max score 95.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0668 / max 63.1519, expressed in 5 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157386	0.0336	4
157387	0.0212	4
157385	0.0120	3

Top tissues by expression

217 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.90	gold quality
sperm	CL:0000019	88.38	gold quality
left testis	UBERON:0004533	87.73	gold quality
right testis	UBERON:0004534	86.42	gold quality
testis	UBERON:0000473	84.59	gold quality
pancreatic ductal cell	CL:0002079	72.64	silver quality
mucosa of transverse colon	UBERON:0004991	68.94	gold quality
ileal mucosa	UBERON:0000331	68.42	gold quality
left ventricle myocardium	UBERON:0006566	65.13	gold quality
rectum	UBERON:0001052	65.03	gold quality
cardiac muscle of right atrium	UBERON:0003379	64.40	gold quality
ganglionic eminence	UBERON:0004023	63.57	gold quality
tibialis anterior	UBERON:0001385	62.88	silver quality
hindlimb stylopod muscle	UBERON:0004252	61.64	gold quality
transverse colon	UBERON:0001157	60.59	gold quality
deltoid	UBERON:0001476	59.83	silver quality
vermiform appendix	UBERON:0001154	59.50	gold quality
adult organism	UBERON:0007023	58.09	gold quality
epithelial cell of pancreas	CL:0000083	58.05	gold quality
adult mammalian kidney	UBERON:0000082	56.76	gold quality
small intestine Peyer’s patch	UBERON:0003454	56.74	gold quality
myocardium	UBERON:0002349	55.70	gold quality
kidney epithelium	UBERON:0004819	55.50	gold quality
small intestine	UBERON:0002108	55.20	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	55.13	gold quality
colon	UBERON:0001155	54.96	gold quality
intestine	UBERON:0000160	54.62	gold quality
large intestine	UBERON:0000059	54.34	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
nasal cavity epithelium	UBERON:0005384	53.38	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.56

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 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. (PMID:19398914)
• LOC643714 Polymorphism was associated with Elevated Susceptibility to Breast Cancer (meta analysis). (PMID:31324582)
• Association of polymorphisms in LOC105377871 and CASC16 with breast cancer in the northwest Chinese Han population. (PMID:31655495)
• The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population. (PMID:31996122)
• Association between the rs4784227-CASC16 polymorphism and the risk of breast cancer: A meta-analysis. (PMID:36042591)
• Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population. (PMID:36540803)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.