Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SMNDC1 (survival motor neuron domain containing 1)

Identity

Alias (NCBI)SMNR
SPF30
TDRD16C
HGNC (Hugo) SMNDC1
HGNC Alias symbSPF30
SMNR
TDRD16C
HGNC Alias namesplicing factor 30, survival of motor neuron-related
 tudor domain containing 16C
LocusID (NCBI) 10285
Atlas_Id 73588
Location 10q25.2  [Link to chromosome band 10q25]
Location_base_pair Starts at 110290731 and ends at 110304920 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CLCN3 (4q33) / SMNDC1 (10q25.2)LOC100507217 () / SMNDC1 (10q25.2)SMNDC1 (10q25.2) / DAZAP2 (12q13.13)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 



External links

 

Nomenclature
HGNC (Hugo)SMNDC1   16900
Cards
Entrez_Gene (NCBI)SMNDC1    survival motor neuron domain containing 1
AliasesSMNR; SPF30; TDRD16C
GeneCards (Weizmann)SMNDC1
Ensembl hg19 (Hinxton)ENSG00000119953 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000119953 [Gene_View]  ENSG00000119953 [Sequence]  chr10:110290731-110304920 [Contig_View]  SMNDC1 [Vega]
ICGC DataPortalENSG00000119953
TCGA cBioPortalSMNDC1
AceView (NCBI)SMNDC1
Genatlas (Paris)SMNDC1
SOURCE (Princeton)SMNDC1
Genetics Home Reference (NIH)SMNDC1
Genomic and cartography
GoldenPath hg38 (UCSC)SMNDC1  -     chr10:110290731-110304920 -  10q25.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMNDC1  -     10q25.2   [Description]    (hg19-Feb_2009)
GoldenPathSMNDC1 - 10q25.2 [CytoView hg19]  SMNDC1 - 10q25.2 [CytoView hg38]
ImmunoBaseENSG00000119953
Genome Data Viewer NCBISMNDC1 [Mapview hg19]  
OMIM603519   
Gene and transcription
Genbank (Entrez)AF083385 AF107463 AK314013 BC011234 BC039110
RefSeq transcript (Entrez)NM_005871
Consensus coding sequences : CCDS (NCBI)SMNDC1
Gene ExpressionSMNDC1 [ NCBI-GEO ]   SMNDC1 [ EBI - ARRAY_EXPRESS ]   SMNDC1 [ SEEK ]   SMNDC1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMNDC1 [ Firebrowse - Broad ]
GenevisibleExpression of SMNDC1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10285
GTEX Portal (Tissue expression)SMNDC1
Human Protein AtlasENSG00000119953-SMNDC1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75940   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75940  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75940
PhosPhoSitePlusO75940
Domaine pattern : Prosite (Expaxy)TUDOR (PS50304)   
Domains : Interpro (EBI)Survival_motor_neuron    Tudor   
Domain families : Pfam (Sanger)SMN (PF06003)   
Domain families : Pfam (NCBI)pfam06003   
Domain families : Smart (EMBL)TUDOR (SM00333)  
Conserved Domain (NCBI)SMNDC1
PDB (RSDB)4A4F    4A4H   
PDB Europe4A4F    4A4H   
PDB (PDBSum)4A4F    4A4H   
PDB (IMB)4A4F    4A4H   
Structural Biology KnowledgeBase4A4F    4A4H   
SCOP (Structural Classification of Proteins)4A4F    4A4H   
CATH (Classification of proteins structures)4A4F    4A4H   
SuperfamilyO75940
AlphaFold pdb e-kbO75940   
Human Protein Atlas [tissue]ENSG00000119953-SMNDC1 [tissue]
HPRD04627
Protein Interaction databases
DIP (DOE-UCLA)O75940
IntAct (EBI)O75940
BioGRIDSMNDC1
STRING (EMBL)SMNDC1
ZODIACSMNDC1
Ontologies - Pathways
QuickGOO75940
Ontology : AmiGORNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  RNA binding  protein binding  nucleus  nucleoplasm  spliceosomal complex  cytoplasm  apoptotic process  Cajal body  nuclear speck  
Ontology : EGO-EBIRNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  RNA binding  protein binding  nucleus  nucleoplasm  spliceosomal complex  cytoplasm  apoptotic process  Cajal body  nuclear speck  
NDEx NetworkSMNDC1
Atlas of Cancer Signalling NetworkSMNDC1
Wikipedia pathwaysSMNDC1
Orthology - Evolution
OrthoDB10285
GeneTree (enSembl)ENSG00000119953
Phylogenetic Trees/Animal Genes : TreeFamSMNDC1
Homologs : HomoloGeneSMNDC1
Homology/Alignments : Family Browser (UCSC)SMNDC1
Gene fusions - Rearrangements
Fusion : QuiverSMNDC1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMNDC1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMNDC1
dbVarSMNDC1
ClinVarSMNDC1
MonarchSMNDC1
1000_GenomesSMNDC1 
Exome Variant ServerSMNDC1
GNOMAD BrowserENSG00000119953
Varsome BrowserSMNDC1
ACMGSMNDC1 variants
VarityO75940
Genomic Variants (DGV)SMNDC1 [DGVbeta]
DECIPHERSMNDC1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMNDC1 
Mutations
ICGC Data PortalSMNDC1 
TCGA Data PortalSMNDC1 
Broad Tumor PortalSMNDC1
OASIS PortalSMNDC1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMNDC1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSMNDC1
Mutations and Diseases : HGMDSMNDC1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaSMNDC1
DgiDB (Drug Gene Interaction Database)SMNDC1
DoCM (Curated mutations)SMNDC1
CIViC (Clinical Interpretations of Variants in Cancer)SMNDC1
Cancer3DSMNDC1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603519   
Orphanet
DisGeNETSMNDC1
MedgenSMNDC1
Genetic Testing Registry SMNDC1
NextProtO75940 [Medical]
GENETestsSMNDC1
Target ValidationSMNDC1
Huge Navigator SMNDC1 [HugePedia]
ClinGenSMNDC1
Clinical trials, drugs, therapy
MyCancerGenomeSMNDC1
Protein Interactions : CTDSMNDC1
Pharm GKB GenePA134990780
PharosO75940
Clinical trialSMNDC1
Miscellaneous
canSAR (ICR)SMNDC1
HarmonizomeSMNDC1
DataMed IndexSMNDC1
Probes
Litterature
PubMed49 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSMNDC1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 16:21:34 CEST 2021

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