Browse SMN1 in pancancer

Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Domain, Function and Classification
> Gene Ontology
> KEGG and Reactome Pathway
> Domain, Function and Classification
 
Domain PF06003 Survival motor neuron protein (SMN)
Function

The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. Ensures the correct splicing of U12 intron-containing genes that may be important for normal motor and proprioceptive neurons development. Also required for resolving RNA-DNA hybrids created by RNA polymerase II, that form R-loop in transcription terminal regions, an important step in proper transcription termination. May also play a role in the metabolism of small nucleolar ribonucleoprotein (snoRNPs).

Classification
Class Modification Substrate Product PubMed
# # # # #
> Gene Ontology
 
Biological Process GO:0000245 spliceosomal complex assembly
GO:0000375 RNA splicing, via transesterification reactions
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
GO:0000387 spliceosomal snRNP assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006353 DNA-templated transcription, termination
GO:0006397 mRNA processing
GO:0006913 nucleocytoplasmic transport
GO:0008380 RNA splicing
GO:0022613 ribonucleoprotein complex biogenesis
GO:0022618 ribonucleoprotein complex assembly
GO:0051169 nuclear transport
GO:0051170 nuclear import
GO:0071826 ribonucleoprotein complex subunit organization
Molecular Function -
Cellular Component GO:0015030 Cajal body
GO:0016604 nuclear body
GO:0030016 myofibril
GO:0030017 sarcomere
GO:0030018 Z disc
GO:0031674 I band
GO:0032797 SMN complex
GO:0034719 SMN-Sm protein complex
GO:0035770 ribonucleoprotein granule
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0043025 neuronal cell body
GO:0043204 perikaryon
GO:0043292 contractile fiber
GO:0044297 cell body
GO:0044449 contractile fiber part
GO:0097504 Gemini of coiled bodies
> KEGG and Reactome Pathway
 
KEGG hsa03013 RNA transport
Reactome R-HSA-74160: Gene Expression
R-HSA-194441: Metabolism of non-coding RNA
R-HSA-191859: snRNP Assembly
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Mutation landscape in primary tumor tissue from TCGA
> Mutation landscape in cancer cell line from CCLE
> All mutations from COSMIC database V81
> Variations from text mining
> The Cancer Genome Atlas (TCGA)
 
There is no record for SMN1.
> Cancer Cell Line Encyclopedia (CCLE)
 
There is no record.
> Catalogue of Somatic Mutations in Cancer (COSMIC)
 
COSMIC ID CDS change AA change Mutation Type Anatomical Site
COSM3683877c.738A>Cp.P246PSubstitution - coding silentHaematopoietic_and_lymphoid_tissue
COSM4405580c.876C>Tp.S292SSubstitution - coding silentSkin
> Text Mining based Variations
 
There is no record for SMN1.
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Post-translational modification (PTM)
> Post-translational modification (PTM)
 
 Filter By:
Uniprot ID Position Amino Acid Description Upstream Enzyme Affected By Mutation Amino Acid Sequence Variant
Q166374SPhosphoserinePKANoNone detected
Q166375SPhosphoserinePKANoNone detected
Q166378SPhosphoserinePKANoNone detected
Q1663725TPhosphothreonine-NoNone detected
Q1663728SPhosphoserine-NoNone detected
Q1663731SPhosphoserine-NoNone detected
Q1663769TPhosphothreonine-NoNone detected
Q1663785TPhosphothreoninePKANoNone detected
Q16637187SPhosphoserinePKANoNone detected
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Expression analysis in primary tumor tissue from TCGA
> Expression level in cancer cell line from CCLE
> Expression level in human normal tissue from HPA
> Text mining based expression change
> The Cancer Genome Atlas (TCGA)
 


  Differential expression analysis for cancers with more than 10 normal samples
Cancer Full Name # N # T Median (N) Median (T) LogFC Adj. P Status
COADColon adenocarcinoma41459-2.542-1.4081.3291.58e-05Over
ESCAEsophageal carcinoma11185-2.082-0.7511.2030.0525NS
GBMGlioblastoma multiforme5166-1.883-0.391NANANA
LAMLAcute Myeloid Leukemia0173NA-1.013NANANA
OVOvarian serous cystadenocarcinoma0307NA0.935NANANA
PCPGPheochromocytoma and Paraganglioma3184-3.05-1.935NANANA
READRectum adenocarcinoma10167-2.708-1.5641.1260.0634NS
STADStomach adenocarcinoma354150.636-0.643-0.6170.12NS
TGCTTesticular Germ Cell Tumors0156NA-1.574NANANA
UCECUterine Corpus Endometrial Carcinoma35546-2.191-0.8470.930.00425Over
> Cancer Cell Line Encyclopedia (CCLE)
 

There is no record.
> The Human Protein Atlas (HPA)
 


Tissue Expression Level (TPM)
Adipose tissue 2.7
Adrenal gland 2.1
Appendix 5.4
Bone marrow 14.3
Breast 3.3
Cerebral cortex 6.8
Cervix, uterine 5.4
Colon 1.8
Duodenum 2.2
Endometrium 6.6
Epididymis 6.8
Esophagus 5.6
Fallopian tube 4
Gallbladder 16.7
Heart muscle 0.3
Kidney 5.6
Liver 1.7
Lung 5.3
Lymph node 17.9
Ovary 4.3
Pancreas 0.3
Parathyroid gland 7.7
Placenta 5.4
Prostate 5.7
Rectum 5.1
Salivary gland 0.6
Seminal vesicle 3.9
Skeletal muscle 0.6
Skin 5.7
Small intestine 1.9
Smooth muscle 10.7
Spleen 6.1
Stomach 4.6
Testis 11.1
Thyroid gland 6.3
Tonsil 1.9
Urinary bladder 12.1
> Text Mining based Expression
 
PMID Expression Cancer Evidence
25699170loss of expressionSynovial SarcomaSMA, Desmin, CD34, CD117 and S100 were negative in all cases, whereas EMA and/or CK AE1/AE3 were positive in all cases.
25471503loss of expressionNasopharyngeal Papillary AdenocarcinomaThese five cases were all negative for TG, CK5/6, CK20, S-100 protein, p63, Calponin and SMA.
24777337overexpressionEsophageal CarcinomaEsophageal cancer tissues showed positive expression of FGF-2, CD31, and SMA; in contrast, FGF-2 expression was not detected and only little staining for CD31 and SMA was noted in normal epithelium.
24341853aberrant expressionRhabdomyosarcomaBy immunohistochemistry, the tumor cells were positive for vimentin, desmin, smooth muscle actin (SMA), muscle-specific actin (MSA), CD10, CD56, CD99, β-catenin and D2-40.
24040461loss of expressionEpithelioid Malignant Peripheral Nerve Sheath TumorUnlike other epithelial tumors, smooth muscle actin (SMA), cytokeratin, EMA and S-100 were all negative in the epithelioid tumor cells.
23650991aberrant expressionGiant Cell Tumor of BoneAll immunostained cases were found positive for smooth muscle actin (SMA) and/or muscle specific actin (MSA), most in 1-33% of the MSCs.
23468260loss of expressionGastrointestinal Stromal TumorNearly 49% (38 cases) of the GISTs were negative for SMA by immunohistochemistry.
22775584aberrant expressionCellular Benign Fibrous HistiocytomaSMA positivity was found in tumor cells in 93 of 100 cases (93%).
22543453aberrant expressionBone NeoplasmAlpha isoform of smooth muscle actin (SMA) expression has been reported in giant cell tumour of bone (GCTB) and other benign and malignant bone tumours, but the pattern of SMA expression and the precise nature of SMA-expressing cells in these lesions is uncertain.
22486319aberrant expressionMyofibromaSolitary and multifocal myofibromas stained positively for smooth muscle actin (SMA) in 95% and 92% of cases, muscle-specific actin (MSA) in 75% and 50% of cases, and desmin in 10% and 14% of cases, respectively.
20032423loss of expressionEpithelial-Myoepithelial CarcinomaThe tumor cells were negative for vimentin, alpha-smooth muscle actin (SMA) (except one case), glial fibrillar acid protein (GFAP) and MIB1.
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Somatic copy number alteration in primary tomur tissue
> The Cancer Genome Atlas (TCGA)
 


  Correlation between expression and SCNA as well as percentage of patients in different status.
Cancer Full Name # Sample R P % Loss % Neutral % Gain Status
COADColon adenocarcinoma4490.1680.00034424.368.86.9Neutral
ESCAEsophageal carcinoma1830.1120.13161.734.43.8Loss
GBMGlioblastoma multiforme1470.130.11612.980.36.8Neutral
LAMLAcute Myeloid Leukemia1660.0390.6224.895.20Neutral
OVOvarian serous cystadenocarcinoma3000.3421.12e-0973.324.32.3Loss
PCPGPheochromocytoma and Paraganglioma1620.0830.2926.290.13.7Neutral
READRectum adenocarcinoma1640.1680.031432.958.58.5Neutral
STADStomach adenocarcinoma4130.1420.0037238.557.14.4Loss
TGCTTesticular Germ Cell Tumors1500.0680.4067027.32.7Loss
UCECUterine Corpus Endometrial Carcinoma5370.1520.00040620.3763.7Neutral
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Methylation level in the promoter region of CR
> Methylation level in the promoter region of CR
 
There is no record.
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Primary tumor tissue from TCGA
> Normal tumor tissue from HPA
>The Cancer Genome Atlas (TCGA)
 
There is no record.
> The Human Protein Atlas (HPA)
 


Tissue Level Level Name
Adrenal gland 2 Medium
Appendix 2 Medium
Bone marrow 3 High
Breast 2 Medium
Bronchus 3 High
Caudate 3 High
Cerebellum 3 High
Cerebral cortex 3 High
Cervix, uterine 2 Medium
Colon 2 Medium
Duodenum 2 Medium
Endometrium 2 Medium
Epididymis 2 Medium
Esophagus 2 Medium
Fallopian tube 2 Medium
Gallbladder 3 High
Heart muscle 2 Medium
Hippocampus 2 Medium
Kidney 2 Medium
Liver 0 Not detected
Lung 1 Low
Lymph node 3 High
Nasopharynx 3 High
Oral mucosa 2 Medium
Ovary 0 Not detected
Pancreas 3 High
Parathyroid gland 2 Medium
Placenta 2 Medium
Prostate 2 Medium
Rectum 2 Medium
Salivary gland 2 Medium
Seminal vesicle 1 Low
Skeletal muscle 2 Medium
Skin 2 Medium
Small intestine 2 Medium
Smooth muscle 2 Medium
Soft tissue 0 Not detected
Spleen 1 Low
Stomach 2 Medium
Testis 3 High
Thyroid gland 2 Medium
Tonsil 2 Medium
Urinary bladder 3 High
Vagina 2 Medium
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Association between expresson and subtype
> Overall survival analysis based on expression
> Association between expresson and stage
> Association between expresson and grade
> Subtype
 


  Association between expresson and subtype.
Cancer Full Name # Patients P Value (Kruskal-Wallis) Association Source
COADColon adenocarcinoma1490.287NS22810696
GBMGlioblastoma multiforme1570.77NS26824661
OVOvarian serous cystadenocarcinoma2870.897NS21720365
READRectum adenocarcinoma670.598NS22810696
STADStomach adenocarcinoma2770.118NS25079317
UCECUterine Corpus Endometrial Carcinoma2320.185NS23636398
> Overall survival
 

  Overall survival analysis based on expression.
Cancer Full Name # Patients Hazard Ratio P Value (Log Rank Test) Association
COADColon adenocarcinoma439 1.0430.886NS
ESCAEsophageal carcinoma184 0.7880.476NS
GBMGlioblastoma multiforme158 1.1320.639NS
LAMLAcute Myeloid Leukemia149 0.5850.0586NS
OVOvarian serous cystadenocarcinoma303 0.8730.501NS
PCPGPheochromocytoma and Paraganglioma179 2.1450.524NS
READRectum adenocarcinoma159 0.5960.45NS
STADStomach adenocarcinoma388 0.8560.49NS
TGCTTesticular Germ Cell Tumors134 594299981.2920.317NS
UCECUterine Corpus Endometrial Carcinoma543 1.2780.407NS
> Stage
 

  Association between expresson and stage.
Cancer Full Name # Patients R Value (Spearman) P Value (Spearman) Association
COADColon adenocarcinoma445 -0.0470.324NS
ESCAEsophageal carcinoma162 -0.260.000827Lower
OVOvarian serous cystadenocarcinoma302 -0.1270.0279Lower
READRectum adenocarcinoma156 -0.1450.0705NS
STADStomach adenocarcinoma392 -0.0650.2NS
TGCTTesticular Germ Cell Tumors81 -0.0240.828NS
UCECUterine Corpus Endometrial Carcinoma501 0.0030.942NS
> Grade
 

  Association between expresson and grade.
Cancer Full Name # Patients R Value (Spearman) P Value (Spearman) Association
OVOvarian serous cystadenocarcinoma296 0.0060.917NS
STADStomach adenocarcinoma406 -0.0070.884NS
UCECUterine Corpus Endometrial Carcinoma534 -0.0990.0224Lower
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Targets inferred by reverse engineering method
> Targets identified by ChIP-seq data
> Targets inferred by reverse engineering method
 
> Targets identified by ChIP-seq data
 
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Drugs from DrugBank database
> Drugs from DrugBank database
 
There is no record for SMN1.
Summary
SymbolSMN1
Namesurvival of motor neuron 1, telomeric
Aliases SMNT; SMA1; SMA2; SMA3; TDRD16A; tudor domain containing 16A; SMA@; SMA; spinal muscular atrophy (Werdnig-Ho ......
Location5q13.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Cancer Gene Databases ONGene (Oncogene) , TSGene (Tumor suppressor gene) , NCG (Network of Cancer Genes)
Content > Protein-Protein Interaction Network
> miRNA Regulatory Relationship
> Interactions from Text Mining
> Protein-Protein Interaction Network
 
> miRNA Regulatory Relationship
 
> Interactions from Text Mining
 
There is no record for SMN1.