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SHMT2 (serine hydroxymethyltransferase 2)

Identity

Alias_namesSHMT
serine hydroxymethyltransferase 2 (mitochondrial)
Other aliasGLYA
HEL-S-51e
HGNC (Hugo) SHMT2
LocusID (NCBI) 6472
Atlas_Id 55419
Location 12q13.3  [Link to chromosome band 12q13]
Location_base_pair Starts at 57229573 and ends at 57234935 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
COX8A (11q13.1) / SHMT2 (12q13.3)

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

 


External links

Nomenclature
HGNC (Hugo)SHMT2   10852
Cards
Entrez_Gene (NCBI)SHMT2  6472  serine hydroxymethyltransferase 2
AliasesGLYA; HEL-S-51e; SHMT
GeneCards (Weizmann)SHMT2
Ensembl hg19 (Hinxton)ENSG00000182199 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000182199 [Gene_View]  chr12:57229573-57234935 [Contig_View]  SHMT2 [Vega]
ICGC DataPortalENSG00000182199
TCGA cBioPortalSHMT2
AceView (NCBI)SHMT2
Genatlas (Paris)SHMT2
WikiGenes6472
SOURCE (Princeton)SHMT2
Genetics Home Reference (NIH)SHMT2
Genomic and cartography
GoldenPath hg38 (UCSC)SHMT2  -     chr12:57229573-57234935 +  12q13.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SHMT2  -     12q13.3   [Description]    (hg19-Feb_2009)
EnsemblSHMT2 - 12q13.3 [CytoView hg19]  SHMT2 - 12q13.3 [CytoView hg38]
Mapping of homologs : NCBISHMT2 [Mapview hg19]  SHMT2 [Mapview hg38]
OMIM138450   
Gene and transcription
Genbank (Entrez)###############################################################################################################################################################################################################################################################
RefSeq transcript (Entrez)NM_001166356 NM_001166357 NM_001166358 NM_001166359 NM_005412
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SHMT2
Cluster EST : UnigeneHs.741179 [ NCBI ]
CGAP (NCI)Hs.741179
Alternative Splicing GalleryENSG00000182199
Gene ExpressionSHMT2 [ NCBI-GEO ]   SHMT2 [ EBI - ARRAY_EXPRESS ]   SHMT2 [ SEEK ]   SHMT2 [ MEM ]
Gene Expression Viewer (FireBrowse)SHMT2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6472
GTEX Portal (Tissue expression)SHMT2
Protein : pattern, domain, 3D structure
UniProt/SwissProtP34897   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP34897  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP34897
Splice isoforms : SwissVarP34897
PhosPhoSitePlusP34897
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)SHMT2
DMDM Disease mutations6472
Blocks (Seattle)SHMT2
PDB (SRS)3OU5    4PVF   
PDB (PDBSum)3OU5    4PVF   
PDB (IMB)3OU5    4PVF   
PDB (RSDB)3OU5    4PVF   
Structural Biology KnowledgeBase3OU5    4PVF   
SCOP (Structural Classification of Proteins)3OU5    4PVF   
CATH (Classification of proteins structures)3OU5    4PVF   
SuperfamilyP34897
Human Protein AtlasENSG00000182199
Peptide AtlasP34897
HPRD00717
IPIIPI00002520   IPI00794549   IPI00748411   IPI00794572   IPI01025911   IPI01026021   IPI01025897   IPI01025630   IPI01025494   IPI01026371   IPI01024788   IPI01025008   IPI01024876   IPI01026271   IPI01026131   IPI01025090   IPI00795816   IPI01025505   IPI00789370   
Protein Interaction databases
DIP (DOE-UCLA)P34897
IntAct (EBI)P34897
FunCoupENSG00000182199
BioGRIDSHMT2
STRING (EMBL)SHMT2
ZODIACSHMT2
Ontologies - Pathways
QuickGOP34897
Ontology : AmiGOchromatin binding  glycine hydroxymethyltransferase activity  glycine hydroxymethyltransferase activity  protein binding  nucleus  cytoplasm  mitochondrion  mitochondrial inner membrane  mitochondrial inner membrane  mitochondrial intermembrane space  mitochondrial matrix  glycine metabolic process  L-serine metabolic process  L-serine biosynthetic process  one-carbon metabolic process  positive regulation of cell proliferation  L-allo-threonine aldolase activity  microtubule cytoskeleton  amino acid binding  glycine biosynthetic process from serine  pyridoxal phosphate binding  response to type I interferon  tetrahydrofolate interconversion  mitochondrial nucleoid  identical protein binding  tetrahydrofolate metabolic process  folic acid metabolic process  protein tetramerization  protein homotetramerization  extracellular exosome  protein K63-linked deubiquitination  BRISC complex  
Ontology : EGO-EBIchromatin binding  glycine hydroxymethyltransferase activity  glycine hydroxymethyltransferase activity  protein binding  nucleus  cytoplasm  mitochondrion  mitochondrial inner membrane  mitochondrial inner membrane  mitochondrial intermembrane space  mitochondrial matrix  glycine metabolic process  L-serine metabolic process  L-serine biosynthetic process  one-carbon metabolic process  positive regulation of cell proliferation  L-allo-threonine aldolase activity  microtubule cytoskeleton  amino acid binding  glycine biosynthetic process from serine  pyridoxal phosphate binding  response to type I interferon  tetrahydrofolate interconversion  mitochondrial nucleoid  identical protein binding  tetrahydrofolate metabolic process  folic acid metabolic process  protein tetramerization  protein homotetramerization  extracellular exosome  protein K63-linked deubiquitination  BRISC complex  
Pathways : KEGGGlycine, serine and threonine metabolism    Cyanoamino acid metabolism    Glyoxylate and dicarboxylate metabolism    One carbon pool by folate   
NDEx NetworkSHMT2
Atlas of Cancer Signalling NetworkSHMT2
Wikipedia pathwaysSHMT2
Orthology - Evolution
OrthoDB6472
GeneTree (enSembl)ENSG00000182199
Phylogenetic Trees/Animal Genes : TreeFamSHMT2
HOVERGENP34897
HOGENOMP34897
Homologs : HomoloGeneSHMT2
Homology/Alignments : Family Browser (UCSC)SHMT2
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSHMT2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SHMT2
dbVarSHMT2
ClinVarSHMT2
1000_GenomesSHMT2 
Exome Variant ServerSHMT2
ExAC (Exome Aggregation Consortium)SHMT2 (select the gene name)
Genetic variants : HAPMAP6472
Genomic Variants (DGV)SHMT2 [DGVbeta]
DECIPHERSHMT2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSHMT2 
Mutations
ICGC Data PortalSHMT2 
TCGA Data PortalSHMT2 
Broad Tumor PortalSHMT2
OASIS PortalSHMT2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSHMT2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSHMT2
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 SHMT2
DgiDB (Drug Gene Interaction Database)SHMT2
DoCM (Curated mutations)SHMT2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SHMT2 (select a term)
intoGenSHMT2
Cancer3DSHMT2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM138450   
Orphanet
MedgenSHMT2
Genetic Testing Registry SHMT2
NextProtP34897 [Medical]
TSGene6472
GENETestsSHMT2
Target ValidationSHMT2
Huge Navigator SHMT2 [HugePedia]
snp3D : Map Gene to Disease6472
BioCentury BCIQSHMT2
ClinGenSHMT2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6472
Chemical/Pharm GKB GenePA35755
Clinical trialSHMT2
Miscellaneous
canSAR (ICR)SHMT2 (select the gene name)
Probes
Litterature
PubMed68 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSHMT2
EVEXSHMT2
GoPubMedSHMT2
iHOPSHMT2
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 12:55:27 CEST 2017

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