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This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smi... See more...
Aliases for SHMT1 Gene
Aliases for SHMT1 Gene
External Ids for SHMT1 Gene
- HGNC: 10850
- NCBI Entrez Gene: 6470
- Ensembl: ENSG00000176974
- OMIM®: 182144
- UniProtKB/Swiss-Prot: P34896
Previous GeneCards Identifiers for SHMT1 Gene
- GC17M018476
- GC17M019823
- GC17M018174
- GC17M018431
- GC17M018171
- GC17M017984
- GC17M018231
- GC17M018330
- GC17M018332
- GC17M018333
- GC17M018334
- GC17M018365
- GC17M018331
- GC17M019857
Summaries for SHMT1 Gene
-
This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
GeneCards Summary for SHMT1 Gene
SHMT1 (Serine Hydroxymethyltransferase 1) is a Protein Coding gene. Diseases associated with SHMT1 include Adult Acute Lymphocytic Leukemia and Smith-Magenis Syndrome. Among its related pathways are Glycine, serine and threonine metabolism and One carbon pool by folate. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and pyridoxal phosphate binding. An important paralog of this gene is SHMT2.
UniProtKB/Swiss-Prot Summary for SHMT1 Gene
-
Interconversion of serine and glycine (PubMed:8505317, PubMed:24698160).
Additional gene information for SHMT1 Gene
- HGNC (10850)
- NCBI Entrez Gene (6470)
- Ensembl (ENSG00000176974)
- OMIM® (182144)
- UniProtKB/Swiss-Prot (P34896)
- Open Targets Platform(ENSG00000176974)
- Monarch Initiative
- Search for SHMT1 at DataMed
- Search for SHMT1 at HumanCyc
No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHMT1 Gene
Genomics for SHMT1 Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for SHMT1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication |
Request up-to-date GeneHancer data (full dataset)
GeneHancers around SHMT1 on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHMT1
- Top Transcription factor binding sites by QIAGEN in the SHMT1 gene promoter:
-
- AhR
- c-Myb
- C/EBPalpha
- CBF(2)
- CBF-A
- CBF-B
- CHOP-10
- CP1A
- NF-Y
- NF-YA
Genomic Locations for SHMT1 Gene
Latest Assembly
- chr17:18,327,860-18,363,563
- (GRCh38/hg38)
- Size:
- 35,704 bases
- Orientation:
- Minus strand
Previous Assembly
- chr17:18,231,187-18,266,864
- (GRCh37/hg19 by Entrez Gene)
- Size:
- 35,678 bases
- Orientation:
- Minus strand
- chr17:18,231,187-18,266,856
- (GRCh37/hg19 by Ensembl)
- Size:
- 35,670 bases
- Orientation:
- Minus strand
Genomic View for SHMT1 Gene
Genes around SHMT1 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 17p11.2 by HGNC
- 17p11.2 by Entrez Gene
- 17p11.2 by Ensembl
SHMT1 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for SHMT1 Gene
Proteins for SHMT1 Gene
-
Protein details for SHMT1 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- P34896-GLYC_HUMAN
- Recommended name:
- Serine hydroxymethyltransferase, cytosolic
- Protein Accession:
- P34896
- B4DPM9
- D3DXD0
- Q96HY0
- Q9UMD1
- Q9UMD2
Protein attributes for SHMT1 Gene
- Size:
- 483 amino acids
- Molecular mass:
- 53083 Da
- Cofactor:
- Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
- Quaternary structure:
-
- Homotetramer (PubMed:24698160, PubMed:25619277, PubMed:9753690). Identified in complex with ABRAXAS2 and the other subunits of the BRISC complex, at least composed of ABRAXAS2, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1 (PubMed:24075985).
- Miscellaneous:
-
- In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.
Protein Expression for SHMT1 Gene
Selected DME Specific Peptides for SHMT1 Gene
- P34896:
-
- KVAHFIHRGIELTLQIQ
- TGYINYDQLEENA
- LIASENF
- LVDLRSK
- LQGGPHNH
- GGHLTHG
- NKNTCPGD
- NSAVFPG
- ANFAVYTA
- TTHKTLRG
- LCQKRAL
- TTTTHKTL
- AVALKQA
- RYYGGTE
- VTTTTHK
- AVLEALGS
- IAGVAVALK
- NKYSEGYPG
- PKLIIAG
- SGSPANF
- SGLVAAGV
- YKVNPDTGYI
- NVQPYSGS
- DMAHISGLV
- LFPLPGLP
- IFYRKGV
- TDKKKISA
- LMADMAH
Post-translational modifications for SHMT1 Gene
Other Protein References for SHMT1 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibodies for research
- LifeSpan BioSciences SHMT / SHMT1 Monoclonal Antibody (LS-B4417) and SHMT / SHMT1 Monoclonal Antibody (LS-B16353)
- G Biosciences Immunotag™ SHMT1 Antibody
-
Custom Antibody ServicesOriGene Antibodies for SHMT1
- Novus Biologicals Antibodies for SHMT1
-
Abcam antibodies for SHMT1
- Invitrogen Antibodies for SHMT1 (AFLGC-Shmt1)
-
Santa Cruz Biotechnology (SCBT) Antibodies for SHMT1
- Sino Biological Antibodies for SHMT1
Protein products for research
- G Biosciences Human Serine hydroxymethyltransferase/SHMT1, Lyophilized
- Search Origene for MassSpec and Protein Over-expression Lysates for SHMT1
- Origene Custom Protein Services for SHMT1
- ProSpec Recombinant Proteins for SHMT1
-
ProSci Proteins for SHMT1
-
Abcam proteins for SHMT1
Assay products for research
- antibodies-online: Show 5 available SHMT1 Elisa Kits ranked by validation data
- Compare Top SHMT1 Elisa Kits
-
Quality Products:
Domains & Families for SHMT1 Gene
Gene Families for SHMT1 Gene
- HGNC:
- Human Protein Atlas (HPA):
-
- Enzymes
- FDA approved drug targets
- Plasma proteins
- Predicted intracellular proteins
Protein Domains for SHMT1 Gene
- InterPro:
- Blocks:
-
- Glycine hydroxymethyltransferase
- ProtoNet:
Suggested Antigen Peptide Sequences for SHMT1 Gene
- GenScript: Design optimal peptide antigens:
-
- Serine hydroxymethyltransferase (A8MYA6_HUMAN)
- Serine hydroxymethyltransferase (B4DPM9_HUMAN)
- Serine hydroxymethyltransferase (D3DXC9_HUMAN)
- Serine hydroxymethyltransferase (E7EW08_HUMAN)
- Serine methylase (GLYC_HUMAN)
Graphical View of Domain Structure for InterPro Entry
P34896- Family:
-
- Belongs to the SHMT family.
Function for SHMT1 Gene
Molecular function for SHMT1 Gene
- UniProtKB/Swiss-Prot Function:
- Interconversion of serine and glycine (PubMed:8505317, PubMed:24698160).
- 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:24698160, ECO:0000269|PubMed:8505317};.
- UniProtKB/Swiss-Prot BiophysicochemicalProperties:
- Kinetic parameters: KM=0.18 mM for L-serine {ECO:0000269|PubMed:24698160}; KM=5.2 uM for tetrahydrofolate {ECO:0000269|PubMed:24698160};
- UniProtKB/Swiss-Prot EnzymeRegulation:
- Inhibited by tetrahydrofolate concentrations above 40 uM.
- GENATLAS Biochemistry:
- serine hydroxy-methyltransferase,cytosolic,with several alternatively spliced isoforms,catalyzing serine synthesis,"one-carbone" metabolism,constantly deleted in Smith-Magenis syndrome,putative regulator of cell growth and proliferation
Enzyme Numbers (IUBMB) for SHMT1 Gene
Phenotypes From GWAS Catalog for SHMT1 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000900 | translation repressor activity, mRNA regulatory element binding | IDA | 10995219 |
| GO:0003824 | catalytic activity | IEA | -- |
| GO:0004372 | glycine hydroxymethyltransferase activity | IEA,IDA | 8505317 |
| GO:0004843 | thiol-dependent ubiquitin-specific protease activity | IEA | -- |
| GO:0005515 | protein binding | IPI | 25416956 |
Phenotypes for SHMT1 Gene
- MGI mutant phenotypes for SHMT1:
- inferred from 4 alleles
- GenomeRNAi human phenotypes for SHMT1:
Animal Models for SHMT1 Gene
Animal Models for research
-
Taconic Biosciences Mouse Models for SHMT1
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SHMT1 - Starting at $85 >
- * SHMT1 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
-
OriGene CRISPR knockouts for SHMT1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SHMT1
-
Santa Cruz Biotechnology (SCBT) CRISPR for SHMT1
miRNA for SHMT1 Gene
- miRTarBase miRNAs that target SHMT1
-
- mmu-miR-30e-5p (MIRT013348)
- hsa-miR-193b-3p (MIRT016266)
- hsa-miR-125b-5p (MIRT045899)
- hsa-let-7c-3p (MIRT489654)
- hsa-miR-6734-5p (MIRT489655)
- hsa-miR-921 (MIRT489656)
- hsa-miR-3177-5p (MIRT489657)
- hsa-miR-486-3p (MIRT489658)
- hsa-miR-449b-5p (MIRT489659)
- hsa-miR-449a (MIRT489660)
- hsa-miR-34c-5p (MIRT489661)
- hsa-miR-34a-5p (MIRT489662)
- hsa-miR-6499-3p (MIRT489663)
- hsa-miR-423-5p (MIRT489664)
- hsa-miR-3184-5p (MIRT489665)
- hsa-miR-7114-5p (MIRT489666)
- hsa-miR-4302 (MIRT489667)
- hsa-miR-3174 (MIRT489668)
- hsa-miR-6805-5p (MIRT489669)
- hsa-miR-4662a-3p (MIRT489670)
- hsa-miR-4477a (MIRT505647)
- hsa-miR-636 (MIRT505648)
- hsa-miR-4445-5p (MIRT505649)
- hsa-miR-6766-3p (MIRT505650)
- hsa-miR-4782-3p (MIRT505651)
- hsa-miR-219a-5p (MIRT505652)
- hsa-miR-508-3p (MIRT505653)
- hsa-miR-522-3p (MIRT505654)
- hsa-miR-224-3p (MIRT505655)
- hsa-miR-4282 (MIRT505656)
- hsa-miR-548c-3p (MIRT505657)
- hsa-miR-218-5p (MIRT505658)
- hsa-miR-6738-5p (MIRT530204)
- hsa-miR-5194 (MIRT530205)
- hsa-miR-1914-3p (MIRT530206)
- hsa-miR-1273g-5p (MIRT554314)
- hsa-miR-203a-5p (MIRT554315)
- hsa-miR-134-3p (MIRT554316)
- hsa-miR-4778-5p (MIRT554317)
- hsa-miR-4763-5p (MIRT573041)
- hsa-miR-6735-3p (MIRT573042)
- hsa-miR-4641 (MIRT573043)
- hsa-miR-20b-3p (MIRT573044)
- hsa-miR-1234-3p (MIRT573045)
- hsa-miR-7107-5p (MIRT573046)
- hsa-miR-122-3p (MIRT573047)
- hsa-miR-335-3p (MIRT666379)
- hsa-miR-1304-5p (MIRT666380)
- hsa-miR-664b-3p (MIRT666381)
- hsa-miR-5696 (MIRT666382)
- hsa-miR-579-3p (MIRT666383)
- hsa-miR-372-5p (MIRT666384)
- hsa-miR-371a-5p (MIRT666385)
- hsa-miR-616-5p (MIRT666386)
- hsa-miR-373-5p (MIRT666387)
- hsa-miR-371b-5p (MIRT666388)
- hsa-miR-3613-3p (MIRT666389)
- hsa-miR-548g-3p (MIRT666390)
- hsa-miR-548f-3p (MIRT666391)
- hsa-miR-548e-3p (MIRT666392)
- hsa-miR-548az-3p (MIRT666393)
- hsa-miR-548ar-3p (MIRT666394)
- hsa-miR-548a-3p (MIRT666395)
- hsa-miR-101-3p (MIRT761076)
- hsa-miR-1273e (MIRT761866)
- hsa-miR-1292-3p (MIRT762317)
- hsa-miR-1827 (MIRT763115)
- hsa-miR-1910-3p (MIRT763342)
- hsa-miR-2467-3p (MIRT764134)
- hsa-miR-34b-3p (MIRT765800)
- hsa-miR-3612 (MIRT765950)
- hsa-miR-3614-5p (MIRT766064)
- hsa-miR-3929 (MIRT767805)
- hsa-miR-4257 (MIRT768171)
- hsa-miR-4419b (MIRT768801)
- hsa-miR-4459 (MIRT769347)
- hsa-miR-4478 (MIRT769552)
- hsa-miR-4537 (MIRT770200)
- hsa-miR-4649-3p (MIRT770671)
- hsa-miR-4695-5p (MIRT771232)
- hsa-miR-4722-5p (MIRT771586)
- hsa-miR-4768-3p (MIRT772134)
- hsa-miR-485-5p (MIRT772647)
- hsa-miR-550b-3p (MIRT774624)
- hsa-miR-582-5p (MIRT775327)
- hsa-miR-6500-3p (MIRT776470)
- hsa-miR-650 (MIRT776708)
- hsa-miR-6511a-5p (MIRT776841)
- hsa-miR-655-5p (MIRT777309)
- hsa-miR-665 (MIRT777616)
- hsa-miR-6746-5p (MIRT778233)
- hsa-miR-6771-5p (MIRT778689)
- hsa-miR-6808-5p (MIRT779712)
- hsa-miR-6840-3p (MIRT780177)
- hsa-miR-6884-5p (MIRT781035)
- hsa-miR-6893-5p (MIRT781244)
- hsa-miR-7160-5p (MIRT781639)
- hsa-miR-940 (MIRT782938)
miRNA products for research
Inhibitory RNAs for research
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SHMT1
- Browse OriGene Inhibitory RNA Products For SHMT1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHMT1
Clone products for research
- Applied Biological Materials (abm): Clones for SHMT1 - Starting at $45 >
- * SHMT1 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
-
- MG207663
- MR207663
- MR207663L3
- MR207663L4
- RC203461
- RC203461L1
- RC203461L2
- RC203461L3
- RC203461L4
- RC205102
- RC205102L1
- RC205102L2
- RC205102L3
- RC205102L4
- RC237604
- RG203461
- RG205102
- RR203948
- RR203948L3
- RR203948L4
- MR207663L3V
- MR207663L4V
- RC203461L1V
- RC203461L2V
- RC203461L3V
- RC203461L4V
- RC205102L1V
- RC205102L2V
- RC205102L3V
- RC205102L4V
- RR203948L3V
- RR203948L4V
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Sino Biological Human cDNA Clone for SHMT1
- Addgene plasmids for SHMT1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SHMT1
Cell Lines for research
-
Horizon Cell Lines for SHMT1
No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHMT1 Gene
Localization for SHMT1 Gene
Subcellular locations from UniProtKB/Swiss-Prot for SHMT1 Gene
- Cytoplasm.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 5 |
| extracellular | 4 |
| mitochondrion | 3 |
| plasma membrane | 2 |
| peroxisome | 2 |
| cytoskeleton | 1 |
| endoplasmic reticulum | 1 |
| endosome | 1 |
| lysosome | 1 |
| golgi apparatus | 1 |
- Cytosol (3)
- Nucleoplasm (1)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IBA | 21873635 |
| GO:0005654 | nucleoplasm | IDA | -- |
| GO:0005737 | cytoplasm | IBA | 21873635 |
| GO:0005829 | cytosol | TAS | -- |
| GO:0070062 | extracellular exosome | HDA | 19056867 |
Pathways & Interactions for SHMT1 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | One carbon pool by folate | ||
| 2 | Metabolism of water-soluble vitamins and cofactors | ||
| 3 | Glycine, serine and threonine metabolism | ||
| 4 | Carbon metabolism | ||
| 5 | Metabolism |
.40
|
|
Pathways by source for SHMT1 Gene
10 BioSystems pathways for SHMT1 Gene
7 Reactome pathways for SHMT1 Gene
2 PharmGKB pathways for SHMT1 Gene
8 KEGG pathways for SHMT1 Gene
1 Cell Signaling Technology pathway for SHMT1 Gene
UniProtKB/Swiss-Prot P34896-GLYC_HUMAN
- Pathway: One-carbon metabolism; tetrahydrofolate interconversion.
Interacting Proteins for SHMT1 Gene
Selected Interacting proteins:
P34896-GLYC_HUMAN
ENSP00000318868
for SHMT1 Gene via
UniProtKB
STRING
IID
GPS-Prot Interaction Network for SHMT1
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006508 | proteolysis | IEA | -- |
| GO:0006544 | glycine metabolic process | IDA | 24698160 |
| GO:0006545 | glycine biosynthetic process | IEA | -- |
| GO:0006563 | L-serine metabolic process | IDA | 24698160 |
| GO:0006565 | L-serine catabolic process | IBA,IDA | 17482557 |
No data available for SIGNOR curated interactions for SHMT1 Gene
Drugs & Compounds for SHMT1 Gene
| Name | Status | Disease Links | Group | Role | Mechanism of Action | Clinical Trials |
|---|---|---|---|---|---|---|
| Glycine | Approved, Vet_approved | Nutra | Target, product of | 202 | ||
| Pyridoxal Phosphate | Approved, Investigational | Nutra | Target, cofactor | 17 | ||
| Bevacizumab | Approved, Investigational | Pharma | VEGF antagonist, Therapeutic Antibodies, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors | 2478 | ||
| Fluorouracil | Approved | Pharma | RNA processing inhibitor and thymidylate synthase inhibitor | 2421 | ||
| Irinotecan | Approved, Investigational | Pharma | Topoisomerase I inhibitor, TOPO I inhibitor, Topoisomerase 1 Inhibitors | 1482 |
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| 5,10-Methylenetetrahydromethanopterin |
|
|
||||
| 5,10-Methylene-THF |
|
31690-11-6 |
|
|||
| 5,6,7,8-Tetrahydromethanopterin |
|
|
Drug products for research
- G Biosciences Human Serine hydroxymethyltransferase/SHMT1, Lyophilized
Transcripts for SHMT1 Gene
mRNA/cDNA for SHMT1 Gene
- 3 REFSEQ mRNAs :
- 15 NCBI additional mRNA sequence :
- 11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000316694 2527 nts (view in UCSC)
- ENST00000352886 2437 nts (view in UCSC)
- ENST00000354098 1656 nts (view in UCSC)
- ENST00000395682 570 nts (view in UCSC)
- ENST00000395684 2652 nts (view in UCSC)
CRISPR products for research
- Applied Biological Materials (abm): CRISPR Clones for SHMT1 - Starting at $85 >
- * SHMT1 CRISPR as ready-to-use vector or virus: Non-viral | Lenti- | Adeno- | AAV- | siRNA - Browse All
- * Cas9 Nucleases, Nickases, Null Mutants, and GFP tag also available.
-
OriGene CRISPR knockouts for SHMT1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SHMT1
-
Santa Cruz Biotechnology (SCBT) CRISPR for SHMT1
miRNA products for research
Inhibitory RNAs for research
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SHMT1
- Browse OriGene Inhibitory RNA Products For SHMT1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHMT1
Clone products for research
- Applied Biological Materials (abm): Clones for SHMT1 - Starting at $45 >
- * SHMT1 as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Retro- | Protein Vector - Browse All
- * Viral Packaging Services and High Titer Production Services also available.
-
- MG207663
- MR207663
- MR207663L3
- MR207663L4
- RC203461
- RC203461L1
- RC203461L2
- RC203461L3
- RC203461L4
- RC205102
- RC205102L1
- RC205102L2
- RC205102L3
- RC205102L4
- RC237604
- RG203461
- RG205102
- RR203948
- RR203948L3
- RR203948L4
- MR207663L3V
- MR207663L4V
- RC203461L1V
- RC203461L2V
- RC203461L3V
- RC203461L4V
- RC205102L1V
- RC205102L2V
- RC205102L3V
- RC205102L4V
- RR203948L3V
- RR203948L4V
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Sino Biological Human cDNA Clone for SHMT1
- Addgene plasmids for SHMT1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SHMT1
| ExUns: | 1a | · | 1b | · | 1c | · | 1d | ^ | 2 | ^ | 3 | ^ | 4a | · | 4b | ^ | 5 | ^ | 6 | ^ | 7a | · | 7b | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | - | ||||||||||||||||||||||||||||||||||
| SP2: | - | - | - | - | |||||||||||||||||||||||||||||||||
| SP3: | - | - | |||||||||||||||||||||||||||||||||||
| SP4: | - | - | |||||||||||||||||||||||||||||||||||
| SP5: | - |
Relevant External Links for SHMT1 Gene
- GeneLoc Exon Structure for
- SHMT1
Expression for SHMT1 Gene
mRNA differential expression in normal tissues according to GTEx for SHMT1 Gene
This gene is overexpressed in Liver (x15.6) and Kidney - Cortex (x6.6).
This gene is overexpressed in Liver, secretome (29.6), Kidney (8.5), and Liver (8.5).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHMT1 Gene
- Elite partner
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHMT1
SOURCE GeneReport for Unigene cluster for SHMT1 Gene:
Hs.513987Evidence on tissue expression from TISSUES for SHMT1 Gene
- Liver(4.7)
- Bone marrow(4.3)
- Nervous system(4)
- Kidney(3.9)
- Blood(2.5)
- Skin(2.5)
- Intestine(2.4)
- Heart(2)
- Thyroid gland(2)
Primer products for research
-
OriGene qPCR primer pairs for SHMT1
-
OriGene qPCR primer pairs and template standards for SHMT1
Gene Expression Assays for research
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 SHMT1 Gene
Orthologs for SHMT1 Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | SHMT1 30 31 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | SHMT1 30 31 |
|
OneToOne | |
| Platypus (Ornithorhynchus anatinus) |
Mammalia | SHMT1 31 |
|
OneToOne | |
| Cow (Bos Taurus) |
Mammalia | SHMT1 30 31 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Shmt1 30 17 31 |
|
OneToOne | |
| Rat (Rattus norvegicus) |
Mammalia | Shmt1 30 |
|
||
| Oppossum (Monodelphis domestica) |
Mammalia | SHMT1 31 |
|
OneToOne | |
| Chicken (Gallus gallus) |
Aves | SHMT1 30 31 |
|
OneToOne | |
| Lizard (Anolis carolinensis) |
Reptilia | SHMT1 31 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | shmt1 30 |
|
||
| Str.15846 30 |
|
||||
| African clawed frog (Xenopus laevis) |
Amphibia | shmt1-prov 30 |
|
||
| Zebrafish (Danio rerio) |
Actinopterygii | shmt1 30 31 |
|
OneToOne | |
| zgc66171 30 |
|
||||
| Fruit Fly (Drosophila melanogaster) |
Insecta | CG3011 30 31 32 |
|
OneToMany | |
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP001065 30 |
|
||
| Worm (Caenorhabditis elegans) |
Secernentea | mel-32 30 31 32 |
|
OneToMany | |
| A. gosspyii yeast (Eremothecium gossypii) |
Saccharomycetes | AGOS_ACR215C 30 |
|
||
| K. Lactis Yeast (Kluyveromyces lactis) |
Saccharomycetes | KLLA0F08921g 30 |
|
||
| Baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | SHM2 30 31 |
|
ManyToMany | |
| SHM1 31 |
|
ManyToMany | |||
| Thale Cress (Arabidopsis thaliana) |
eudicotyledons | SHM2 30 |
|
||
| Alicante grape (Vitis vinifera) |
eudicotyledons | Vvi.8061 30 |
|
||
| Barley (Hordeum vulgare) |
Liliopsida | Hv.2416 30 |
|
||
| Corn (Zea mays) |
Liliopsida | Zm.3136 30 |
|
||
| Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
OneToOne | |
| Bread mold (Neurospora crassa) |
Ascomycetes | NCU02274 30 |
|
||
| Fission Yeast (Schizosaccharomyces pombe) |
Schizosaccharomycetes | SPAC24C9.12c 30 |
|
||
| Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.4793 30 |
|
- Species where no ortholog for SHMT1 was found in the sources mined by GeneCards:
-
- Actinobacteria (Mycobacterium tuberculosis)
- Alpha proteobacteria (Wolbachia pipientis)
- Amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- Beta proteobacteria (Neisseria meningitidis)
- Chromalveolata (Phytophthora infestans)
- Common water flea (Daphnia pulex)
- 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)
- Orangutan (Pongo pygmaeus)
- Pig (Sus scrofa)
- Rainbow Trout (Oncorhynchus mykiss)
- Rice (Oryza sativa)
- Rice Blast Fungus (Magnaporthe grisea)
- Schistosome Parasite (Schistosoma mansoni)
- Sea Anemone (Nematostella vectensis)
- 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 SHMT1 Gene
- ENSEMBL:
- Gene Tree for SHMT1 (if available)
- TreeFam:
- Gene Tree for SHMT1 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for SHMT1: view image
Paralogs for SHMT1 Gene
(3) SIMAP similar genes for SHMT1 Gene using alignment to 5 proteins:
- GLYC_HUMAN
- B4DPM9_HUMAN
- D3DXC9_HUMAN
- J3KRK5_HUMAN
- J3KRZ5_HUMAN
Pseudogenes.org Pseudogenes for SHMT1 Gene
Variants for SHMT1 Gene
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHMT1 Gene
| SNP ID | Clinical significance and condition | Chr 17 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| rs115185998 | Likely Benign: not provided | 18,340,220(-) |
G/A NM_004169.5(SHMT1):c.637C>T (p.Arg213Trp) |
MISSENSE | |
| rs115557642 | Benign: not provided | 18,335,678(-) |
G/A NM_004169.5(SHMT1):c.815-3C>T |
INTRON | |
| rs116100382 | Benign: not provided | 18,328,822(-) |
G/A NM_004169.5(SHMT1):c.1380C>T (p.Ala460=) |
SYNONYMOUS | |
| rs141575508 | Benign: not provided. Benign: not provided | 18,340,104(-) |
C/TC/G NM_004169.5(SHMT1):c.753G>A (p.Val251=) |
SYNONYMOUS | |
| rs143807950 | Likely Benign: not provided. Benign: not provided | 18,355,980(-) |
A/CA/T NM_004169.5(SHMT1):c.2T>G (p.Met1Arg) |
INITIATIOR_CODON_VARIANT,MISSENSE_VARIANT,FIVE_PRIME_UTR |
All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| esv1004827 | CNV | deletion | 20482838 |
| esv2758677 | CNV | gain+loss | 17122850 |
| esv3640147 | CNV | loss | 21293372 |
| nsv1129384 | OTHER | inversion | 24896259 |
| nsv155 | OTHER | inversion | 15895083 |
| nsv1998 | CNV | insertion | 18451855 |
| nsv428333 | CNV | gain | 18775914 |
| nsv481238 | CNV | novel sequence insertion | 20440878 |
| nsv499114 | OTHER | inversion | 21111241 |
| nsv509653 | CNV | insertion | 20534489 |
| nsv827913 | CNV | gain | 20364138 |
| nsv833386 | CNV | gain | 17160897 |
| nsv833387 | CNV | loss | 17160897 |
Residual Variation Intolerance Score:
39.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
6.06;
75.21% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for SHMT1 Gene
SNP Genotyping and Copy Number Assays for research
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHMT1 Gene
Disorders for SHMT1 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| adult acute lymphocytic leukemia |
|
|
| smith-magenis syndrome |
|
|
| neural tube defects |
|
|
| lacrimal gland carcinoma |
|
|
| pediatric osteosarcoma |
|
|
Search SHMT1 in MalaCards
View complete list of genes associated with diseases
Additional Disease Information for SHMT1
- Genetic Association Database
- (GAD)
- Human Genome Epidemiology Navigator
- (HuGE)
- Atlas
- ATLAS of Genetics and Cytogenetics in Oncology and Haematology
- Open Targets Platform
- Open Targets Platform
No data available for UniProtKB/Swiss-Prot and Genatlas for SHMT1 Gene
Publications for SHMT1 Gene
- 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) 2 3 4 23
- No association between cSHMT genotypes and the risk of breast cancer in the Nurses' Health Study. (PMID: 19707223) Bentley AR … Cassano PA (European journal of clinical nutrition 2010) 3 23 41
- Methotrexate in pediatric osteosarcoma: response and toxicity in relation to genetic polymorphisms and dihydrofolate reductase and reduced folate carrier 1 expression. (PMID: 19159907) Patiño-García A … Sierrasesúmaga L (The Journal of pediatrics 2009) 3 23 41
- A high frequency of the MTHFR 677C>T polymorphism in Scottish women with epilepsy: possible role in pathogenesis. (PMID: 17904392) Dean JC … Little J (Seizure 2008) 3 23 41
- Risk of colorectal cancer associated with the C677T polymorphism in 5,10-methylenetetrahydrofolate reductase in Portuguese patients depends on the intake of methyl-donor nutrients. (PMID: 18996879) Guerreiro CS … Cravo M (The American journal of clinical nutrition 2008) 3 23 41
ExternalLinks
Products for SHMT1 Gene
- Custom Antibody ServicesOriGene Antibodies for SHMT1
- Browse OriGene ELISA Kits
- Custom Assay Services
- Search Origene for MassSpec and Protein Over-expression Lysates for SHMT1
- Origene Custom Protein Services for SHMT1
- Origene shrna, sirna, and RNAi products in human, mouse, rat for SHMT1
- Browse OriGene Inhibitory RNA Products For SHMT1
- OriGene qPCR primer pairs for SHMT1
- OriGene qPCR primer pairs and template standards for SHMT1
- OriGene CRISPR knockouts for SHMT1
- MG207663
- MR207663
- MR207663L3
- MR207663L4
- RC203461
- RC203461L1
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- RC205102L1
- RC205102L2
- RC205102L3
- RC205102L4
- RC237604
- RG203461
- RG205102
- RR203948
- RR203948L3
- RR203948L4
- MR207663L3V
- MR207663L4V
- RC203461L1V
- RC203461L2V
- RC203461L3V
- RC203461L4V
- RC205102L1V
- RC205102L2V
- RC205102L3V
- RC205102L4V
- RR203948L3V
- RR203948L4V
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For SHMT1
- Sino Biological Human cDNA Clone for SHMT1
- Browse Sino Biological Recombinant Proteins
- Browse Sino Biological Cell Lysates
- Sino Biological Antibodies for SHMT1
- Browse Sino Biological Assays
- Browse Antibodies
- Browse cDNA Clones
- Browse ELISA Kits
- Browse CRO Services
- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Novus Biologicals Antibodies for SHMT1
- Novus Biologicals proteins and lysates for SHMT1
- Browse Antibodies
- Browse Peptides and Proteins
- Browse Lysates
- Browse ELISA Kits
- Abcam antibodies for SHMT1
- Abcam proteins for SHMT1
- Find your target
- Browse Primary Antibodies
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- Browse Proteins and Peptides
- Search Knockout (KO) Validated Antibodies
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- ProSpec Recombinant Proteins for SHMT1
- Taconic Biosciences Mouse Models for SHMT1
- Find your next knockout model in the Taconic Knockout Repository
- Genetically Engineered Models Available Immediately
- Humanized Mice
- Invitrogen Antibodies for SHMT1 (AFLGC-Shmt1)
- VectorBuilder Custom and pre-made DNA vectors for SHMT1 (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for SHMT1 (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for SHMT1 (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for SHMT1 CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for SHMT1
- Addgene plasmids for SHMT1
- antibodies-online: Show 19 available SHMT1 Antibodies ranked by validation data
- Compare Top SHMT1 Antibodies
- antibodies-online: Show 5 available SHMT1 Elisa Kits ranked by validation data
- Compare Top SHMT1 Elisa Kits
- Quality Products:
- antibodies-online: Show 14 available SHMT1 Proteins ranked by validation data
- Compare Top SHMT1 Proteins
- Santa Cruz Biotechnology (SCBT) Antibodies for SHMT1
- Search Santa Cruz Biotechnology (SCBT) for SHMT1 siRNA/shRNA
- Santa Cruz Biotechnology (SCBT) CRISPR for SHMT1
- Custom Antibody ServicesProSci Antibodies for SHMT1
- ProSci Proteins for SHMT1
- Horizon Cell Lines for SHMT1
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SHMT1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SHMT1
- Search GeneCopoeia for miRNA 3'UTR Target clone products for SHMT1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHMT1
Sources for SHMT1 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM® (Updated: 05-Mar-2021)
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) MedlinePlus Genetics
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNAcentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Open Targets Platform
- (175) 5SRRNADB
- (176) snoDB
- (177) MirGeneDB