Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SFTPD (surfactant protein D)

Identity

Alias_namesSFTP4
surfactant
Alias_symbol (synonym)SP-D
COLEC7
Other aliasPSP-D
HGNC (Hugo) SFTPD
LocusID (NCBI) 6441
Atlas_Id 45631
Location 10q22.3  [Link to chromosome band 10q22]
Location_base_pair Starts at 79937740 and ends at 79949105 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)
DNAJC1 (10p12.31) / SFTPD (10q22.3)TSPAN14 (10q23.1) / SFTPD (10q22.3)VCL (10q22.2) / SFTPD (10q22.3)
TSPAN14 10q23.1 / SFTPD 10q22.3VCL 10q22.2 / SFTPD 10q22.3

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(10;10)(p12;q22) DNAJC1/SFTPD
VCL/SFTPD (10q22)
t(10;10)(q22;q23) TSPAN14/SFTPD

External links

Nomenclature
HGNC (Hugo)SFTPD   10803
Cards
Entrez_Gene (NCBI)SFTPD  6441  surfactant protein D
AliasesCOLEC7; PSP-D; SFTP4; SP-D
GeneCards (Weizmann)SFTPD
Ensembl hg19 (Hinxton)ENSG00000133661 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000133661 [Gene_View]  ENSG00000133661 [Sequence]  chr10:79937740-79949105 [Contig_View]  SFTPD [Vega]
ICGC DataPortalENSG00000133661
TCGA cBioPortalSFTPD
AceView (NCBI)SFTPD
Genatlas (Paris)SFTPD
WikiGenes6441
SOURCE (Princeton)SFTPD
Genetics Home Reference (NIH)SFTPD
Genomic and cartography
GoldenPath hg38 (UCSC)SFTPD  -     chr10:79937740-79949105 -  10q22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SFTPD  -     10q22.3   [Description]    (hg19-Feb_2009)
EnsemblSFTPD - 10q22.3 [CytoView hg19]  SFTPD - 10q22.3 [CytoView hg38]
Mapping of homologs : NCBISFTPD [Mapview hg19]  SFTPD [Mapview hg38]
OMIM178635   
Gene and transcription
Genbank (Entrez)BC022318 BI820265 BM985387 CR541948 X65018
RefSeq transcript (Entrez)NM_003019
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SFTPD
Cluster EST : UnigeneHs.253495 [ NCBI ]
CGAP (NCI)Hs.253495
Alternative Splicing GalleryENSG00000133661
Gene ExpressionSFTPD [ NCBI-GEO ]   SFTPD [ EBI - ARRAY_EXPRESS ]   SFTPD [ SEEK ]   SFTPD [ MEM ]
Gene Expression Viewer (FireBrowse)SFTPD [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6441
GTEX Portal (Tissue expression)SFTPD
Human Protein AtlasENSG00000133661-SFTPD [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP35247   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP35247  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP35247
Splice isoforms : SwissVarP35247
PhosPhoSitePlusP35247
Domaine pattern : Prosite (Expaxy)C_TYPE_LECTIN_1 (PS00615)    C_TYPE_LECTIN_2 (PS50041)   
Domains : Interpro (EBI)C-type_lectin-like    C-type_lectin-like/link_sf    C-type_lectin_CS    Collagen    Collectin_CTLD    CTDL_fold    Surfac_D-trimer   
Domain families : Pfam (Sanger)Collagen (PF01391)    Lectin_C (PF00059)    Surfac_D-trimer (PF09006)   
Domain families : Pfam (NCBI)pfam01391    pfam00059    pfam09006   
Domain families : Smart (EMBL)CLECT (SM00034)  
Conserved Domain (NCBI)SFTPD
DMDM Disease mutations6441
Blocks (Seattle)SFTPD
PDB (SRS)1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
PDB (PDBSum)1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
PDB (IMB)1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
PDB (RSDB)1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
Structural Biology KnowledgeBase1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
SCOP (Structural Classification of Proteins)1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
CATH (Classification of proteins structures)1B08    1M7L    1PW9    1PWB    2GGU    2GGX    2ORJ    2ORK    2OS9    2RIA    2RIB    2RIC    2RID    2RIE    3DBZ    3G81    3G83    3G84    3IKN    3IKP    3IKQ    3IKR    4E52    4M17    4M18   
SuperfamilyP35247
Human Protein Atlas [tissue]ENSG00000133661-SFTPD [tissue]
Peptide AtlasP35247
HPRD01522
IPIIPI00291878   IPI00514934   
Protein Interaction databases
DIP (DOE-UCLA)P35247
IntAct (EBI)P35247
FunCoupENSG00000133661
BioGRIDSFTPD
STRING (EMBL)SFTPD
ZODIACSFTPD
Ontologies - Pathways
QuickGOP35247
Ontology : AmiGOlipopolysaccharide binding  regulation of cytokine production  toll-like receptor signaling pathway  protein binding  extracellular region  collagen trimer  extracellular space  lysosome  multivesicular body  endoplasmic reticulum membrane  rough endoplasmic reticulum  receptor-mediated endocytosis  respiratory gaseous exchange  endocytic vesicle  carbohydrate binding  negative regulation of T cell proliferation  defense response to bacterium  identical protein binding  surfactant homeostasis  surfactant homeostasis  induction of bacterial agglutination  cellular protein metabolic process  negative regulation of interleukin-2 biosynthetic process  innate immune response  clathrin-coated endocytic vesicle  monosaccharide binding  macrophage chemotaxis  lung alveolus development  positive regulation of phagocytosis  positive regulation of phagocytosis  regulation of immune response  negative regulation by host of symbiont molecular function  reactive oxygen species metabolic process  regulation of adhesion of symbiont to host epithelial cell  
Ontology : EGO-EBIlipopolysaccharide binding  regulation of cytokine production  toll-like receptor signaling pathway  protein binding  extracellular region  collagen trimer  extracellular space  lysosome  multivesicular body  endoplasmic reticulum membrane  rough endoplasmic reticulum  receptor-mediated endocytosis  respiratory gaseous exchange  endocytic vesicle  carbohydrate binding  negative regulation of T cell proliferation  defense response to bacterium  identical protein binding  surfactant homeostasis  surfactant homeostasis  induction of bacterial agglutination  cellular protein metabolic process  negative regulation of interleukin-2 biosynthetic process  innate immune response  clathrin-coated endocytic vesicle  monosaccharide binding  macrophage chemotaxis  lung alveolus development  positive regulation of phagocytosis  positive regulation of phagocytosis  regulation of immune response  negative regulation by host of symbiont molecular function  reactive oxygen species metabolic process  regulation of adhesion of symbiont to host epithelial cell  
Pathways : KEGGPhagosome   
NDEx NetworkSFTPD
Atlas of Cancer Signalling NetworkSFTPD
Wikipedia pathwaysSFTPD
Orthology - Evolution
OrthoDB6441
GeneTree (enSembl)ENSG00000133661
Phylogenetic Trees/Animal Genes : TreeFamSFTPD
HOVERGENP35247
HOGENOMP35247
Homologs : HomoloGeneSFTPD
Homology/Alignments : Family Browser (UCSC)SFTPD
Gene fusions - Rearrangements
Fusion : MitelmanDNAJC1/SFTPD [10p12.31/10q22.3]  [t(10;10)(p12;q22)]  
Fusion : MitelmanTSPAN14/SFTPD [10q23.1/10q22.3]  [t(10;10)(q22;q23)]  
Fusion : MitelmanVCL/SFTPD [10q22.2/10q22.3]  [t(10;10)(q22;q22)]  
Fusion PortalTSPAN14 10q23.1 SFTPD 10q22.3 BRCA
Fusion PortalVCL 10q22.2 SFTPD 10q22.3 LUSC
Fusion : QuiverSFTPD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSFTPD [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SFTPD
dbVarSFTPD
ClinVarSFTPD
1000_GenomesSFTPD 
Exome Variant ServerSFTPD
ExAC (Exome Aggregation Consortium)ENSG00000133661
GNOMAD BrowserENSG00000133661
Varsome BrowserSFTPD
Genetic variants : HAPMAP6441
Genomic Variants (DGV)SFTPD [DGVbeta]
DECIPHERSFTPD [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSFTPD 
Mutations
ICGC Data PortalSFTPD 
TCGA Data PortalSFTPD 
Broad Tumor PortalSFTPD
OASIS PortalSFTPD [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSFTPD  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSFTPD
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SFTPD
DgiDB (Drug Gene Interaction Database)SFTPD
DoCM (Curated mutations)SFTPD (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SFTPD (select a term)
intoGenSFTPD
Cancer3DSFTPD(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM178635   
Orphanet
DisGeNETSFTPD
MedgenSFTPD
Genetic Testing Registry SFTPD
NextProtP35247 [Medical]
TSGene6441
GENETestsSFTPD
Target ValidationSFTPD
Huge Navigator SFTPD [HugePedia]
snp3D : Map Gene to Disease6441
BioCentury BCIQSFTPD
ClinGenSFTPD
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6441
Chemical/Pharm GKB GenePA35715
Clinical trialSFTPD
Miscellaneous
canSAR (ICR)SFTPD (select the gene name)
Probes
Litterature
PubMed230 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSFTPD
EVEXSFTPD
GoPubMedSFTPD
iHOPSFTPD
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 6 11:38:43 CET 2018
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