This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The g... See more...

Aliases for SHMT2 Gene

Aliases for SHMT2 Gene

  • Serine Hydroxymethyltransferase 2 2 3 5
  • Serine Hydroxymethyltransferase 2 (Mitochondrial) 2 3
  • Serine Hydroxymethyltransferase, Mitochondrial 3 4
  • Glycine Hydroxymethyltransferase 3 4
  • Serine Methylase 3 4
  • EC 2.1.2.1 4 51
  • SHMT 3 4
  • Epididymis Secretory Sperm Binding Protein Li 51e 3
  • Glycine Auxotroph A, Human Complement For Hamster 3
  • Serine Hydroxymethylase 3
  • Threonine Aldolase 3
  • Serine Aldolase 3
  • HEL-S-51e 3
  • GLY A+ 3
  • SHMT2 5
  • GLYA 3

External Ids for SHMT2 Gene

Previous HGNC Symbols for SHMT2 Gene

  • SHMT

Previous GeneCards Identifiers for SHMT2 Gene

  • GC12U990093
  • GC12P057340
  • GC12P055909
  • GC12P055886
  • GC12P057623
  • GC12P054662

Summaries for SHMT2 Gene

Entrez Gene Summary for SHMT2 Gene

  • This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

GeneCards Summary for SHMT2 Gene

SHMT2 (Serine Hydroxymethyltransferase 2) is a Protein Coding gene. Diseases associated with SHMT2 include Pyridoxine Deficiency and Campylobacteriosis. Among its related pathways are One carbon pool by folate and Folate Metabolism. Gene Ontology (GO) annotations related to this gene include identical protein binding and pyridoxal phosphate binding. An important paralog of this gene is SHMT1.

UniProtKB/Swiss-Prot Summary for SHMT2 Gene

  • Catalyzes the cleavage of serine to glycine accompanied with the production of 5,10-methylenetetrahydrofolate, an essential intermediate for purine biosynthesis (PubMed:24075985, PubMed:29364879, PubMed:25619277). Serine provides the major source of folate one-carbon in cells by catalyzing the transfer of one carbon from serine to tetrahydrofolate (PubMed:25619277). Contributes to the de novo mitochondrial thymidylate biosynthesis pathway via its role in glycine and tetrahydrofolate metabolism: thymidylate biosynthesis is required to prevent uracil accumulation in mtDNA (PubMed:21876188). Also required for mitochondrial translation by producing 5,10-methylenetetrahydrofolate; 5,10-methylenetetrahydrofolate providing methyl donors to produce the taurinomethyluridine base at the wobble position of some mitochondrial tRNAs (PubMed:29452640, PubMed:29364879). Associates with mitochondrial DNA (PubMed:18063578). In addition to its role in mitochondria, also plays a role in the deubiquitination of target proteins as component of the BRISC complex: required for IFNAR1 deubiquitination by the BRISC complex (PubMed:24075985).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHMT2 Gene

Genomics for SHMT2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHMT2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J057229 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.1 65 5.3 CEBPG HNRNPL CREB1 ATF7 PRDM10 ZNF629 REST TFE3 SIX5 POLR2A ENSG00000276727 RF00019-020 SHMT2 MIR1228 STAT6 ENSG00000224713 NDUFA4L2
GH12J057279 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 11.4 +50.8 50828 3.6 SP1 CREB1 GATAD2A ZNF629 TFE3 LEF1 ZHX2 JUND MTA2 ZNF143 piR-61945-104 R3HDM2 EEF1AKMT3 NEMP1 PAN2 CDK4 ENSG00000224713 TSPAN31 CTDSP2 LOC283387
GH12J057248 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 12.2 +20.4 20370 3.9 CTCF ZNF24 RELB EGR1 ZBTB40 ELF1 NBN HDGF SPI1 ZNF513 STAC3 ARHGAP9 SHMT2 NXPH4 INHBE MYO1A LRP1 STAT6 ENSG00000224713 NDUFA4L2
GH12J057255 Promoter 0.4 EPDnew 11.6 +24.9 24947 0.1 REST R3HDM2 SHMT2 NXPH4 GLI1 INHBE STAC3 piR-50852-038 lnc-R3HDM2-1 ENSG00000258830
GH12J057283 Enhancer 0.3 Ensembl 11.4 +53.9 53928 0.2 STAT1 KLF1 piR-61945-104 SHMT2 NXPH4 INHBE GLI1 ENSG00000258830 lnc-R3HDM2-1 piR-40838 STAC3 R3HDM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHMT2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHMT2

Top Transcription factor binding sites by QIAGEN in the SHMT2 gene promoter:
  • E2F-1
  • E2F-2
  • E2F-3a
  • GATA-1
  • Sp1

Genomic Locations for SHMT2 Gene

Genomic Locations for SHMT2 Gene
chr12:57,229,573-57,234,935
(GRCh38/hg38)
Size:
5,363 bases
Orientation:
Plus strand
chr12:57,623,110-57,628,718
(GRCh37/hg19)
Size:
5,609 bases
Orientation:
Plus strand

Genomic View for SHMT2 Gene

Genes around SHMT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHMT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHMT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHMT2 Gene

Proteins for SHMT2 Gene

  • Protein details for SHMT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P34897-GLYM_HUMAN
    Recommended name:
    Serine hydroxymethyltransferase, mitochondrial
    Protein Accession:
    P34897
    Secondary Accessions:
    • B7Z9F1
    • E7EQ19
    • E7EU43
    • O00740
    • Q8N1A5

    Protein attributes for SHMT2 Gene

    Size:
    504 amino acids
    Molecular mass:
    55993 Da
    Cofactor:
    Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homotetramer; in the presence of bound pyridoxal 5'-phosphate (PubMed:29180469, PubMed:25619277). Homodimer; in the absence of bound pyridoxal 5'-phosphate (PubMed:29180469, PubMed:25619277). Pyridoxal 5'-phosphate binding mediates an important conformation change that is required for tetramerization (PubMed:25619277). Interacts with ABRAXAS2; the interaction is direct. Identified in a complex with ABRAXAS2 and the other subunits of the BRISC complex, at least composed of the ABRAXAS2, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1. Identified in a complex with ABRAXAS2 and IFNAR1 (PubMed:24075985). Interacts with KIRREL3 (PubMed:25902260).
    Miscellaneous:
    • In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.

    Three dimensional structures from OCA and Proteopedia for SHMT2 Gene

    Alternative splice isoforms for SHMT2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHMT2 Gene

Selected DME Specific Peptides for SHMT2 Gene

P34897:
  • LIASENF
  • LQGGPHNH
  • GGTDNHL
  • GGHLTHG
  • NKNTCPGD
  • TTHKTLRG
  • TTTTHKTL
  • EGYPGKRYY
  • AVALKQA
  • SGGTDNH
  • DGARAERVLEL
  • FPSLQGGP
  • VTTTTHK
  • LVSGGTD
  • NKYSEGYPG
  • HLVLVDLR
  • NVQPYSGS
  • DMAHISGLV
  • ELLCQRRALEAF
  • ITANKNT
  • LVDLRPK
  • IFYRKGV

Post-translational modifications for SHMT2 Gene

  • Succinylation at Lys-280 inhibits the hydroxymethyltransferase activity. Desuccinylation by SIRT5 restores the activity, leading to promote cell proliferation.
  • Ubiquitination at Lys95, Lys200, Lys409, Lys469, and Lys474
  • Modification sites at PhosphoSitePlus

Domains & Families for SHMT2 Gene

Gene Families for SHMT2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SHMT2 Gene

Suggested Antigen Peptide Sequences for SHMT2 Gene

GenScript: Design optimal peptide antigens:
  • Serine hydroxymethyltransferase (B4DLV4_HUMAN)
  • Serine hydroxymethyltransferase (B7Z9F1_HUMAN)
  • Serine methylase (GLYM_HUMAN)
  • Serine hydroxymethyltransferase (Q5BJF5_HUMAN)
  • Serine hydroxymethyltransferase (Q8N1A5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P34897

UniProtKB/Swiss-Prot:

GLYM_HUMAN :
  • Belongs to the SHMT family.
Family:
  • Belongs to the SHMT family.
genes like me logo Genes that share domains with SHMT2: view

Function for SHMT2 Gene

Molecular function for SHMT2 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the cleavage of serine to glycine accompanied with the production of 5,10-methylenetetrahydrofolate, an essential intermediate for purine biosynthesis (PubMed:24075985, PubMed:29364879, PubMed:25619277). Serine provides the major source of folate one-carbon in cells by catalyzing the transfer of one carbon from serine to tetrahydrofolate (PubMed:25619277). Contributes to the de novo mitochondrial thymidylate biosynthesis pathway via its role in glycine and tetrahydrofolate metabolism: thymidylate biosynthesis is required to prevent uracil accumulation in mtDNA (PubMed:21876188). Also required for mitochondrial translation by producing 5,10-methylenetetrahydrofolate; 5,10-methylenetetrahydrofolate providing methyl donors to produce the taurinomethyluridine base at the wobble position of some mitochondrial tRNAs (PubMed:29452640, PubMed:29364879). Associates with mitochondrial DNA (PubMed:18063578). In addition to its role in mitochondria, also plays a role in the deubiquitination of target proteins as component of the BRISC complex: required for IFNAR1 deubiquitination by the BRISC complex (PubMed:24075985).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481, ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384, ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1; Evidence={ECO:0000269|PubMed:24075985, ECO:0000269|PubMed:25619277, ECO:0000269|PubMed:29364879};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=278 uM for L-serine {ECO:0000269|PubMed:25619277}; KM=23 uM for tetrahydrofolate {ECO:0000269|PubMed:25619277};
UniProtKB/Swiss-Prot EnzymeRegulation:
Hydroxymethyltransferase is inhibited by succinylation at Lys-280.
GENATLAS Biochemistry:
serine hydroxy-methyltransferase,pyridoxal dependent,mitochondrial,catalyzing 5-10 methylene THF synthesis,"one-carbone" metabolism,putative regulator of cell growth and proliferation

Enzyme Numbers (IUBMB) for SHMT2 Gene

Phenotypes From GWAS Catalog for SHMT2 Gene

Gene Ontology (GO) - Molecular Function for SHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000900 translation repressor activity, mRNA regulatory element binding IBA 21873635
GO:0003682 chromatin binding IDA 18063578
GO:0003824 catalytic activity IEA --
GO:0004372 glycine hydroxymethyltransferase activity IEA,IDA 8505317
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SHMT2: view
genes like me logo Genes that share phenotypes with SHMT2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SHMT2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHMT2

Clone Products

  • Addgene plasmids for SHMT2

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SHMT2 Gene

Localization for SHMT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHMT2 Gene

Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid. Mitochondrion inner membrane. Cytoplasm. Nucleus. Note=Mainly localizes in the mitochondrion. Also found in the cytoplasm and nucleus as part of the BRISC complex (PubMed:24075985). {ECO:0000269 PubMed:24075985}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SHMT2 gene
Compartment Confidence
cytoskeleton 5
mitochondrion 5
nucleus 5
extracellular 4
peroxisome 3
plasma membrane 2
cytosol 2
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubules (4)
  • Mitochondria (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 24075985
GO:0005737 cytoplasm IEA,IDA 24075985
GO:0005739 mitochondrion IDA 17482557
GO:0005743 mitochondrial inner membrane TAS --
GO:0005758 mitochondrial intermembrane space IEA --
genes like me logo Genes that share ontologies with SHMT2: view

Pathways & Interactions for SHMT2 Gene

genes like me logo Genes that share pathways with SHMT2: view

UniProtKB/Swiss-Prot P34897-GLYM_HUMAN

  • Pathway: One-carbon metabolism; tetrahydrofolate interconversion.

Gene Ontology (GO) - Biological Process for SHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002082 regulation of oxidative phosphorylation IMP 29364879
GO:0006544 glycine metabolic process IDA 25619277
GO:0006545 glycine biosynthetic process IEA --
GO:0006563 L-serine metabolic process IDA 25619277
GO:0006564 L-serine biosynthetic process IEA --
genes like me logo Genes that share ontologies with SHMT2: view

No data available for SIGNOR curated interactions for SHMT2 Gene

Drugs & Compounds for SHMT2 Gene

(15) Drugs for SHMT2 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved, Vet_approved Nutra Agonist, Full agonist, Target, product of 196
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 16
Levoleucovorin Approved, Investigational Pharma Target 948
Water Approved Pharma 0
(6R)-Folinic acid Experimental Pharma Target 0

(8) Additional Compounds for SHMT2 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5,10-Methylenetetrahydromethanopterin
  • N5,N10-Methylenetetrahydromethanopterin
5,10-Methylene-THF
  • (6R)-5,10-Methylenetetrahydrofolate
  • (6R)-5,10-Methylenetetrahydrofolic acid
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-hydrofolate
  • 5,10-Methylene-6-hydrofolic acid
31690-11-6
5,6,7,8-Tetrahydromethanopterin
  • 1-(4-{(1R)-1-[(6S,7S)-2-amino-7-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]ethylamino}phenyl)-1-deoxy-5-O-{5-O-[(1S)-1,3-dicarboxypropylphosphonato]-alpha-D-ribofuranosyl}-D-ribitol
  • H4MPT
  • Tetrahydromethanopterin
  • 1-(4-{(1R)-1-[(6S,7S)-2-amino-7-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]ethylamino}phenyl)-1-deoxy-5-O-{5-O-[(1S)-1,3-dicarboxypropylphosphonato]-a-D-ribofuranosyl}-D-ribitol
  • 1-(4-{(1R)-1-[(6S,7S)-2-amino-7-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]ethylamino}phenyl)-1-deoxy-5-O-{5-O-[(1S)-1,3-dicarboxypropylphosphonato]-α-D-ribofuranosyl}-D-ribitol
genes like me logo Genes that share compounds with SHMT2: view

Transcripts for SHMT2 Gene

mRNA/cDNA for SHMT2 Gene

5 REFSEQ mRNAs :
29 NCBI additional mRNA sequence :
35 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHMT2

Clone Products

  • Addgene plasmids for SHMT2

Alternative Splicing Database (ASD) splice patterns (SP) for SHMT2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5a · 5b · 5c ·
SP1: - - - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - - - - -
SP5: - - - - - - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - - - - - -
SP8: - - - - - - - - - - - - - - - - -
SP9: - - - - - - - - - - - - - - - - -
SP10: - - - - - - - - - - - - - - - - -
SP11: - - - - - - - - - - - - - - - - - - -
SP12: - - - - - - - - - - - - - - - - -
SP13: - - - - - - - - - - - - - - - - -
SP14: - - - - - - - - - -
SP15: - - - - -
SP16: -
SP17: - - -
SP18: - - - -
SP19: - - - - - - - - - - - - - - - - -
SP20:
SP21: - - - - - - - - - - -
SP22: - - - - - - - - - - - - - - - - -
SP23:
SP24:
SP25: - - - - - - - - - - - - - - - - -
SP26: - - - - - - - - - - - - - - - - - - -
SP27: - - - - - - - - - - - -
SP28: - - - - - - - - -
SP29: - - - - - - -
SP30: - - - - -
SP31:
SP32: - - - - - - - - - - - - - - - - -
SP33: -
SP34: -
SP35:
SP36:
SP37:
SP38: - -

ExUns: 5d · 5e ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c · 9d · 9e · 9f · 9g ^ 10a · 10b · 10c · 10d ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^
SP1: - - -
SP2: - - - -
SP3: - - - - - - - - - - - - - - - - -
SP4: - - -
SP5: - - - - - - -
SP6: - - - - - - - - - -
SP7: - - - -
SP8: - -
SP9: - -
SP10: -
SP11: - - - - - - - - - -
SP12: - - - - - - - -
SP13: - - - - - -
SP14: - - - - -
SP15: - - -
SP16: - -
SP17: - -
SP18: - -
SP19: - - - - - - - - - - - - - - - -
SP20:
SP21: - -
SP22: - - - -
SP23:
SP24:
SP25: - - -
SP26: - - - - - - - - -
SP27: -
SP28: -
SP29: -
SP30: - - - - -
SP31: - -
SP32: - - - -
SP33: -
SP34: - - - -
SP35: - - - - -
SP36: -
SP37:
SP38:

ExUns: 14a · 14b · 14c · 14d · 14e ^ 15 ^ 16a · 16b · 16c ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b · 20c
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19: - - - - - - - - - - - - - - -
SP20: - - -
SP21:
SP22:
SP23: - - -
SP24: - - - - -
SP25:
SP26:
SP27:
SP28:
SP29:
SP30:
SP31:
SP32:
SP33:
SP34:
SP35:
SP36:
SP37: -
SP38:

Relevant External Links for SHMT2 Gene

GeneLoc Exon Structure for
SHMT2

Expression for SHMT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHMT2 Gene

mRNA differential expression in normal tissues according to GTEx for SHMT2 Gene

This gene is overexpressed in Liver (x6.4).

Protein differential expression in normal tissues from HIPED for SHMT2 Gene

This gene is overexpressed in Liver (12.6), Lymph node (8.4), and Peripheral blood mononuclear cells (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHMT2 Gene



Protein tissue co-expression partners for SHMT2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHMT2

SOURCE GeneReport for Unigene cluster for SHMT2 Gene:

Hs.741179

Evidence on tissue expression from TISSUES for SHMT2 Gene

  • Muscle(5)
  • Nervous system(4.9)
  • Liver(4.8)
  • Lung(4.6)
  • Intestine(4.1)
  • Skin(4)
  • Eye(3.8)
  • Kidney(3.7)
  • Blood(3.6)
  • Bone marrow(2.8)
  • Lymph node(2.6)
  • Spleen(2.5)
  • Stomach(2.4)
  • Heart(2.3)
  • Pancreas(2.3)
  • Thyroid gland(2.1)
genes like me logo Genes that share expression patterns with SHMT2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHMT2 Gene

Orthologs for SHMT2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SHMT2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHMT2 30 31
  • 99.28 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SHMT2 30 31
  • 91.52 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SHMT2 30 31
  • 90.34 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shmt2 30
  • 88.4 (n)
Mouse
(Mus musculus)
Mammalia Shmt2 30 17 31
  • 87.87 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 79 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia SHMT2 31
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia shmt2 30
  • 72.59 (n)
Str.6934 30
Zebrafish
(Danio rerio)
Actinopterygii shmt2 30 31
  • 71.75 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.849 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG3011 31 32
  • 53 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea mel-32 31 32
  • 54 (a)
OneToMany
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AEL188W 30
  • 55.2 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01210g 30
  • 54.32 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SHM2 31 33
  • 54 (a)
ManyToMany
SHM1 30 31
  • 53.84 (n)
ManyToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons SHM1 30
  • 59.99 (n)
Rice
(Oryza sativa)
Liliopsida Os03g0738400 30
  • 59.81 (n)
Os.12148 30
Barley
(Hordeum vulgare)
Liliopsida Hv.3767 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.8216 31
  • 65 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU05805 30
  • 59.45 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes shm2 30
  • 55.63 (n)
Species where no ortholog for SHMT2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SHMT2 Gene

ENSEMBL:
Gene Tree for SHMT2 (if available)
TreeFam:
Gene Tree for SHMT2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHMT2: view image

Paralogs for SHMT2 Gene

Paralogs for SHMT2 Gene

(3) SIMAP similar genes for SHMT2 Gene using alignment to 17 proteins:

  • GLYM_HUMAN
  • B4DLV4_HUMAN
  • G3V241_HUMAN
  • G3V2D2_HUMAN
  • G3V2E4_HUMAN
  • G3V2W0_HUMAN
  • G3V2Y1_HUMAN
  • G3V2Y4_HUMAN
  • G3V3C6_HUMAN
  • G3V3Y8_HUMAN
  • G3V4T0_HUMAN
  • G3V4W5_HUMAN
  • G3V4X0_HUMAN
  • G3V540_HUMAN
  • G3V5L0_HUMAN
  • H0YIZ0_HUMAN
  • Q5BJF5_HUMAN
genes like me logo Genes that share paralogs with SHMT2: view

Variants for SHMT2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHMT2 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
708408 Benign: not provided 57,231,707(+) C/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for SHMT2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SHMT2 Gene

Variant ID Type Subtype PubMed ID
dgv96n21 CNV loss 19592680
nsv482992 CNV gain+loss 15286789
nsv519293 CNV loss 19592680
nsv952189 CNV deletion 24416366

Variation tolerance for SHMT2 Gene

Residual Variation Intolerance Score: 34.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.45; 54.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHMT2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHMT2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHMT2 Gene

Disorders for SHMT2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SHMT2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pyridoxine deficiency
  • vitamin b6 deficiency
campylobacteriosis
  • campylobacter infections
neural tube defects
  • neural tube defects, susceptibility to
glycogen storage disease iii
  • gsd3
glycine encephalopathy
  • gce
- elite association - COSMIC cancer census association via MalaCards
Search SHMT2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SHMT2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SHMT2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHMT2 Gene

Publications for SHMT2 Gene

  1. Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. (PMID: 8999870) Stover PJ … Shane B (The Journal of biological chemistry 1997) 2 3 4
  2. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PMID: 8505317) Garrow TA … Shane B (The Journal of biological chemistry 1993) 3 4 23
  3. Mitochondrial translation requires folate-dependent tRNA methylation. (PMID: 29364879) Morscher RJ … Rabinowitz JD (Nature 2018) 3 4
  4. SHMT2 Desuccinylation by SIRT5 Drives Cancer Cell Proliferation. (PMID: 29180469) Yang X … Luo J (Cancer research 2018) 3 4
  5. Serine Catabolism by SHMT2 Is Required for Proper Mitochondrial Translation Initiation and Maintenance of Formylmethionyl-tRNAs. (PMID: 29452640) Minton DR … Possemato R (Molecular cell 2018) 3 4

Products for SHMT2 Gene

  • Signalway Proteins for SHMT2

Sources for SHMT2 Gene