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SHMT1 (serine hydroxymethyltransferase 1)

Identity

Alias_namesserine hydroxymethyltransferase 1 (soluble)
Alias_symbol (synonym)CSHMT
SHMT
MGC15229
MGC24556
Other alias
HGNC (Hugo) SHMT1
LocusID (NCBI) 6470
Atlas_Id 45764
Location 17p11.2  [Link to chromosome band 17p11]
Location_base_pair Starts at 18327860 and ends at 18363563 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
GIT1 (17q11.2) / SHMT1 (17p11.2)SHMT1 (17p11.2) / MLLT11 (1q21.3)TFCP2L1 (2q14.2) / SHMT1 (17p11.2)

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)SHMT1   10850
Cards
Entrez_Gene (NCBI)SHMT1  6470  serine hydroxymethyltransferase 1
AliasesCSHMT; SHMT
GeneCards (Weizmann)SHMT1
Ensembl hg19 (Hinxton)ENSG00000176974 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000176974 [Gene_View]  chr17:18327860-18363563 [Contig_View]  SHMT1 [Vega]
ICGC DataPortalENSG00000176974
TCGA cBioPortalSHMT1
AceView (NCBI)SHMT1
Genatlas (Paris)SHMT1
WikiGenes6470
SOURCE (Princeton)SHMT1
Genetics Home Reference (NIH)SHMT1
Genomic and cartography
GoldenPath hg38 (UCSC)SHMT1  -     chr17:18327860-18363563 -  17p11.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SHMT1  -     17p11.2   [Description]    (hg19-Feb_2009)
EnsemblSHMT1 - 17p11.2 [CytoView hg19]  SHMT1 - 17p11.2 [CytoView hg38]
Mapping of homologs : NCBISHMT1 [Mapview hg19]  SHMT1 [Mapview hg38]
OMIM182144   
Gene and transcription
Genbank (Entrez)AF017065 AK223552 AK298415 AK302834 AU185281
RefSeq transcript (Entrez)NM_001281786 NM_004169 NM_148918
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SHMT1
Cluster EST : UnigeneHs.636044 [ NCBI ]
CGAP (NCI)Hs.636044
Alternative Splicing GalleryENSG00000176974
Gene ExpressionSHMT1 [ NCBI-GEO ]   SHMT1 [ EBI - ARRAY_EXPRESS ]   SHMT1 [ SEEK ]   SHMT1 [ MEM ]
Gene Expression Viewer (FireBrowse)SHMT1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6470
GTEX Portal (Tissue expression)SHMT1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP34896   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP34896  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP34896
Splice isoforms : SwissVarP34896
PhosPhoSitePlusP34896
Domaine pattern : Prosite (Expaxy)SHMT (PS00096)   
Domains : Interpro (EBI)PyrdxlP-dep_Trfase    PyrdxlP-dep_Trfase_major_sub1    PyrdxlP-dep_Trfase_major_sub2    Ser_HO-MeTrfase    Ser_HO-MeTrfase_PLP_BS   
Domain families : Pfam (Sanger)SHMT (PF00464)   
Domain families : Pfam (NCBI)pfam00464   
Conserved Domain (NCBI)SHMT1
DMDM Disease mutations6470
Blocks (Seattle)SHMT1
PDB (SRS)1BJ4   
PDB (PDBSum)1BJ4   
PDB (IMB)1BJ4   
PDB (RSDB)1BJ4   
Structural Biology KnowledgeBase1BJ4   
SCOP (Structural Classification of Proteins)1BJ4   
CATH (Classification of proteins structures)1BJ4   
SuperfamilyP34896
Human Protein AtlasENSG00000176974
Peptide AtlasP34896
HPRD01643
IPIIPI00002519   IPI00220668   IPI00220669   IPI01015924   IPI00984053   IPI00008665   IPI00793862   
Protein Interaction databases
DIP (DOE-UCLA)P34896
IntAct (EBI)P34896
FunCoupENSG00000176974
BioGRIDSHMT1
STRING (EMBL)SHMT1
ZODIACSHMT1
Ontologies - Pathways
QuickGOP34896
Ontology : AmiGOtranslation repressor activity, nucleic acid binding  glycine hydroxymethyltransferase activity  glycine hydroxymethyltransferase activity  protein binding  nucleus  mitochondrion  cytosol  cytosol  dTMP biosynthetic process  glycine metabolic process  L-serine metabolic process  L-serine catabolic process  L-allo-threonine aldolase activity  purine nucleobase biosynthetic process  negative regulation of translation  glycine biosynthetic process from serine  pyridoxal phosphate binding  tetrahydrofolate interconversion  tetrahydrofolate interconversion  identical protein binding  protein homodimerization activity  carnitine biosynthetic process  tetrahydrofolate metabolic process  folic acid metabolic process  folic acid metabolic process  mRNA 5'-UTR binding  protein tetramerization  protein homotetramerization  extracellular exosome  serine binding  cellular response to tetrahydrofolate  
Ontology : EGO-EBItranslation repressor activity, nucleic acid binding  glycine hydroxymethyltransferase activity  glycine hydroxymethyltransferase activity  protein binding  nucleus  mitochondrion  cytosol  cytosol  dTMP biosynthetic process  glycine metabolic process  L-serine metabolic process  L-serine catabolic process  L-allo-threonine aldolase activity  purine nucleobase biosynthetic process  negative regulation of translation  glycine biosynthetic process from serine  pyridoxal phosphate binding  tetrahydrofolate interconversion  tetrahydrofolate interconversion  identical protein binding  protein homodimerization activity  carnitine biosynthetic process  tetrahydrofolate metabolic process  folic acid metabolic process  folic acid metabolic process  mRNA 5'-UTR binding  protein tetramerization  protein homotetramerization  extracellular exosome  serine binding  cellular response to tetrahydrofolate  
Pathways : KEGGGlycine, serine and threonine metabolism    Cyanoamino acid metabolism    Glyoxylate and dicarboxylate metabolism    One carbon pool by folate   
NDEx NetworkSHMT1
Atlas of Cancer Signalling NetworkSHMT1
Wikipedia pathwaysSHMT1
Orthology - Evolution
OrthoDB6470
GeneTree (enSembl)ENSG00000176974
Phylogenetic Trees/Animal Genes : TreeFamSHMT1
HOVERGENP34896
HOGENOMP34896
Homologs : HomoloGeneSHMT1
Homology/Alignments : Family Browser (UCSC)SHMT1
Gene fusions - Rearrangements
Fusion : MitelmanGIT1/SHMT1 [17q11.2/17p11.2]  [dup(17)(p11q11)]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSHMT1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SHMT1
dbVarSHMT1
ClinVarSHMT1
1000_GenomesSHMT1 
Exome Variant ServerSHMT1
ExAC (Exome Aggregation Consortium)SHMT1 (select the gene name)
Genetic variants : HAPMAP6470
Genomic Variants (DGV)SHMT1 [DGVbeta]
DECIPHERSHMT1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSHMT1 
Mutations
ICGC Data PortalSHMT1 
TCGA Data PortalSHMT1 
Broad Tumor PortalSHMT1
OASIS PortalSHMT1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSHMT1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSHMT1
intOGen PortalSHMT1
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
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch SHMT1
DgiDB (Drug Gene Interaction Database)SHMT1
DoCM (Curated mutations)SHMT1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SHMT1 (select a term)
intoGenSHMT1
Cancer3DSHMT1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM182144   
Orphanet
MedgenSHMT1
Genetic Testing Registry SHMT1
NextProtP34896 [Medical]
TSGene6470
GENETestsSHMT1
Target ValidationSHMT1
Huge Navigator SHMT1 [HugePedia]
snp3D : Map Gene to Disease6470
BioCentury BCIQSHMT1
ClinGenSHMT1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6470
Chemical/Pharm GKB GenePA35753
Clinical trialSHMT1
Miscellaneous
canSAR (ICR)SHMT1 (select the gene name)
Probes
Litterature
PubMed129 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSHMT1
EVEXSHMT1
GoPubMedSHMT1
iHOPSHMT1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:55:26 CEST 2017

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