Gene info: ID 6470

Gene: SHMT1

GENE ID: 6470

Synonyms: CSHMT|SHMT

Description: serine hydroxymethyltransferase 1

Gene type: protein-coding

Location: 17p11.2

dbXrefs: Ensembl:ENSG00000176974 MIM:182144 Vega:OTTHUMG00000059094 UniprotKB:P34896

RefSeq: NG_017111.1

Retrived from: PubMed

SNPs: 0 ANCO-SNPs

Phenotype: ND

# Publications: 5

Sherlock p-value : NA (AD) NA (ND) (Frontal_Cortex)

Pascal p-value : 8.621e-1 (AD) 5.145e-1 (ND)

DNA Methylation

There is no related methylation information for this gene.

Gene Expression in Different Tissues

Temporal and Spatial Expressions (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes average value of the expressions.

Top Co-expressed Genes in Brain-Frontal Cortex (BA9) (GTEx v7)

Top 10 positively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
NPC2	0.808
CYP27A1	0.795
TMEM150A	0.795
MIF4GD	0.792
MVP	0.787
ASCC2	0.784
DERA	0.78
HAUS4	0.779
SERPINB6	0.779
AGTRAP	0.778

Top 10 negatively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
HS6ST3	-0.433
FREM3	-0.422
IGF1	-0.421
NXPH2	-0.417
HAPLN1	-0.411
PTHLH	-0.41
GPR26	-0.406
MARCH4	-0.404
OPRD1	-0.403
NPBWR1	-0.399

ID	Drug Name	Drug Type	CAS Num	Status	Role
DB00114	Pyridoxal Phosphate	Small Molecule	54-47-7	Approved\|Investigational\|Nutraceutical	Target
DB00116	Tetrahydrofolic acid	Small Molecule	135-16-0	Nutraceutical	Target
DB00145	Glycine	Small Molecule	56-40-6	Approved\|Nutraceutical	Target
DB01055	Mimosine	Small Molecule	500-44-7	Approved	Target
DB02067	Triglu-5-Formyl-Tetrahydrofolate	Small Molecule		Experimental	Target
DB02800	5-Hydroxymethylene-6-Hydrofolic Acid	Small Molecule		Experimental	Target
DB02824	N-Pyridoxyl-Glycine-5-Monophosphate	Small Molecule		Experimental	Target
DB00114	Pyridoxal Phosphate	Small Molecule	54-47-7	Approved\|Investigational\|Nutraceutical	Target
DB00142	Glutamic Acid	Small Molecule	56-86-0	Approved\|Nutraceutical	Target
DB00149	L-Leucine	Small Molecule	61-90-5	Approved\|Nutraceutical	Target
DB00161	L-Valine	Small Molecule	72-18-4	Approved\|Nutraceutical	Target
DB00167	L-Isoleucine	Small Molecule	73-32-5	Approved\|Investigational\|Nutraceutical	Target
DB07544	N'-(5-CHLOROBENZOFURAN-2-CARBONYL)-2-(TRIFLUOROMETHYL)BENZENESULFONOHYDRAZIDE	Small Molecule		Experimental	Target
DB01692	Dithioerythritol	Small Molecule	6892-68-8	Experimental	Target
DB02452	Thymidine-5'-Triphosphate	Small Molecule		Experimental	Target
DB01915	S-Hydroxycysteine	Small Molecule	-	Experimental	Target
DB01992	Coenzyme A	Small Molecule	85-61-0	Investigational\|Nutraceutical	Target

ID	Drug Name	Action	PubMed
C576882	1-(2-trifluoromethoxyphenyl)-2-nitroethanone	1-(2-trifluoromethoxyphenyl)-2-nitroethanone results in increased expression of SHMT1 protein	22527513
C066841	2,3,7,8-tetrabromodibenzo-4-dioxin	"2,3,7,8-tetrabromodibenzo-4-dioxin results in increased expression of SHMT1 protein"	27604104
C029497	2,3-bis(3'-hydroxybenzyl)butyrolactone	"[Coumestrol co-treated with 2,3-bis(3'-hydroxybenzyl)butyrolactone] results in increased expression of SHMT1 mRNA"	19167446
D000082	Acetaminophen	Acetaminophen results in decreased expression of SHMT1 mRNA	29067470
D000082	Acetaminophen	Acetaminophen results in increased expression of SHMT1 mRNA	22230336
D000082	Acetaminophen	Acetaminophen affects the expression of SHMT1 mRNA	17562736
D016604	Aflatoxin B1	Aflatoxin B1 affects the expression of SHMT1 protein	20106945
D016604	Aflatoxin B1	Aflatoxin B1 results in decreased expression of SHMT1 mRNA	27153756
D016604	Aflatoxin B1	Aflatoxin B1 results in decreased expression of SHMT1 mRNA	19770486
D000393	Air Pollutants	Air Pollutants analog results in decreased expression of SHMT1 mRNA	21757418
D000517	alpha-Chlorohydrin	alpha-Chlorohydrin results in increased expression of SHMT1 mRNA	28522335
D001151	Arsenic	Arsenic results in increased expression of SHMT1 protein	19818359
C006632	arsenic trioxide	arsenic trioxide results in increased degradation of SHMT1 protein	28265077
C006632	arsenic trioxide	arsenic trioxide results in increased expression of SHMT1 mRNA	19417148\|2045855
D001379	Azathioprine	Azathioprine results in decreased expression of SHMT1 mRNA	22623647
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in decreased expression of SHMT1 mRNA	20064835\|2010694
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in decreased expression of SHMT1 mRNA	19770486\|2171566
C006780	bisphenol A	bisphenol A affects the expression of SHMT1 mRNA	21786754
C006780	bisphenol A	bisphenol A results in decreased expression of SHMT1 mRNA	29275510
D020122	tert-Butylhydroperoxide	tert-Butylhydroperoxide results in decreased expression of SHMT1 mRNA	15336504\|2750901
D020122	tert-Butylhydroperoxide	tert-Butylhydroperoxide results in decreased expression of SHMT1 mRNA	18804290
D019256	Cadmium Chloride	Cadmium Chloride results in decreased expression of SHMT1 mRNA	18804290
D002220	Carbamazepine	Carbamazepine affects the expression of SHMT1 mRNA	24752500
D002251	Carbon Tetrachloride	Carbon Tetrachloride affects the expression of SHMT1 mRNA	17484886
D002251	Carbon Tetrachloride	Carbon Tetrachloride results in decreased expression of SHMT1 mRNA	27339419
C074702	chromium hexavalent ion	chromium hexavalent ion affects the expression of SHMT1 mRNA	28472532
D002994	Clofibrate	Clofibrate results in decreased expression of SHMT1 protein	19952500
D002994	Clofibrate	Clofibrate results in decreased expression of SHMT1 mRNA	17585979
D003300	Copper	[NSC 689534 binds to Copper] which results in decreased expression of SHMT1 mRNA	20971185
D019327	Copper Sulfate	Copper Sulfate results in decreased expression of SHMT1 mRNA	19549813
D003375	Coumestrol	"[Coumestrol co-treated with 2,3-bis(3'-hydroxybenzyl)butyrolactone] results in increased expression of SHMT1 mRNA"	19167446
D003375	Coumestrol	[Coumestrol co-treated with resveratrol] results in increased expression of SHMT1 mRNA	19167446
D003375	Coumestrol	Coumestrol results in increased expression of SHMT1 mRNA	19167446
D003471	Cuprizone	Cuprizone results in increased expression of SHMT1 mRNA	27523638
D016572	Cyclosporine	Cyclosporine results in decreased expression of SHMT1 mRNA	20106945\|2163298
D003907	Dexamethasone	Dexamethasone inhibits the reaction [RX3 gene mutant form affects the expression of SHMT1 mRNA]	27941970
D003907	Dexamethasone	[INS protein co-treated with Dexamethasone co-treated with 1-Methyl-3-isobutylxanthine co-treated with Indomethacin] results in increased expression of SHMT1 mRNA	28628672
D003993	Dibutyl Phthalate	Dibutyl Phthalate results in decreased expression of SHMT1 mRNA	21266533
D003993	Dibutyl Phthalate	Dibutyl Phthalate results in decreased expression of SHMT1 mRNA	21266533
D004008	Diclofenac	Diclofenac affects the expression of SHMT1 mRNA	24752500
D004041	Dietary Fats	Dietary Fats results in increased expression of SHMT1 mRNA	21852083
D004041	Dietary Fats	resveratrol inhibits the reaction [Dietary Fats results in increased expression of SHMT1 mRNA]	21852083
C045651	epigallocatechin gallate	[potassium chromate(VI) co-treated with epigallocatechin gallate] results in decreased expression of SHMT1 mRNA	22079256
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in decreased expression of SHMT1 mRNA	17606305\|2022741
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in increased expression of SHMT1 mRNA	17942748
D004997	Ethinyl Estradiol	[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of SHMT1 mRNA	17942748
D005485	Flutamide	Flutamide results in decreased expression of SHMT1 mRNA	24793618
D005492	Folic Acid	Folic Acid affects the expression of SHMT1 mRNA	17311948
C069837	fullerene C60	fullerene C60 results in increased expression of SHMT1 mRNA	19167457
C056933	fumonisin B1	fumonisin B1 results in decreased expression of SHMT1 mRNA	16221962
D005947	Glucose	[INS protein co-treated with Glucose] results in decreased expression of SHMT1 mRNA	22634610
D007213	Indomethacin	[INS protein co-treated with Dexamethasone co-treated with 1-Methyl-3-isobutylxanthine co-treated with Indomethacin] results in increased expression of SHMT1 mRNA	28628672
D015056	1-Methyl-3-isobutylxanthine	[INS protein co-treated with Dexamethasone co-treated with 1-Methyl-3-isobutylxanthine co-treated with Indomethacin] results in increased expression of SHMT1 mRNA	28628672
C544151	jinfukang	jinfukang results in increased expression of SHMT1 mRNA	27392435
C561695	(+)-JQ1 compound	(+)-JQ1 compound results in decreased expression of SHMT1 mRNA	25982114
C410337	K 7174	K 7174 results in decreased expression of SHMT1 mRNA	24086573
C482199	lipopolysaccharide, E coli O55-B5	"lipopolysaccharide, E coli O55-B5 results in increased expression of SHMT1 mRNA"	24972896
D008727	Methotrexate	SHMT1 gene polymorphism affects the susceptibility to Methotrexate	21064136
D008748	Methylcholanthrene	Methylcholanthrene results in decreased expression of SHMT1 mRNA	18804290
D037742	Nanotubes, Carbon	"Nanotubes, Carbon analog results in increased expression of SHMT1 mRNA"	25554681
D037742	Nanotubes, Carbon	"Nanotubes, Carbon results in decreased expression of SHMT1 mRNA"	25620056
D037742	Nanotubes, Carbon	"Nanotubes, Carbon results in increased expression of SHMT1 mRNA"	25554681
C051752	nefazodone	nefazodone results in increased expression of SHMT1 mRNA	24136188
D009532	Nickel	Nickel results in decreased expression of SHMT1 mRNA	25583101
C558013	NSC 689534	[NSC 689534 binds to Copper] which results in decreased expression of SHMT1 mRNA	20971185
D010100	Oxygen	Oxygen deficiency results in increased expression of SHMT1 mRNA	24205000
C016030	pantogab	pantogab results in decreased expression of SHMT1 mRNA	17379144
C086401	pentabromodiphenyl ether	pentabromodiphenyl ether results in increased expression of SHMT1 mRNA	23948077
D010426	Pentosan Sulfuric Polyester	Pentosan Sulfuric Polyester results in increased expression of SHMT1 mRNA	28973697
C023036	perfluorooctanoic acid	perfluorooctanoic acid results in decreased expression of SHMT1 mRNA	23427857
C023036	perfluorooctanoic acid	perfluorooctanoic acid results in decreased expression of SHMT1 mRNA	18804290
D010634	Phenobarbital	Phenobarbital affects the expression of SHMT1 mRNA	23091169
D010634	Phenobarbital	Phenobarbital results in increased expression of SHMT1 mRNA	19270015
C014153	pirimiphos methyl	pirimiphos methyl results in increased expression of SHMT1 mRNA	27845199
C006253	pirinixic acid	[pirinixic acid binds to and results in increased activity of PPARA protein] which results in decreased expression of SHMT1 mRNA	19710929
C006253	pirinixic acid	pirinixic acid results in decreased expression of SHMT1 mRNA	18445702
C027373	potassium chromate(VI)	[potassium chromate(VI) co-treated with epigallocatechin gallate] results in decreased expression of SHMT1 mRNA	22079256
C027373	potassium chromate(VI)	potassium chromate(VI) results in decreased expression of SHMT1 mRNA	22079256
D011374	Progesterone	Progesterone results in increased expression of SHMT1 mRNA	18070364
D011441	Propylthiouracil	Propylthiouracil results in increased expression of SHMT1 mRNA	24780913
D011736	Pyridoxine	Pyridoxine affects the expression of and affects the activity of SHMT1 protein	17482557
D011794	Quercetin	Quercetin results in increased expression of SHMT1 mRNA	16455785
C059514	resveratrol	[Coumestrol co-treated with resveratrol] results in increased expression of SHMT1 mRNA	19167446
C059514	resveratrol	resveratrol inhibits the reaction [Dietary Fats results in increased expression of SHMT1 mRNA]	21852083
D015474	Isotretinoin	Isotretinoin results in decreased expression of SHMT1 mRNA	20436886
D012643	Selenium	Selenium results in increased expression of SHMT1 mRNA	28810182
D012822	Silicon Dioxide	Silicon Dioxide results in decreased expression of SHMT1 mRNA	23221170
C016104	sodium bichromate	sodium bichromate results in decreased expression of SHMT1 mRNA	24612858
D012969	Sodium Fluoride	Sodium Fluoride results in increased expression of SHMT1 protein	28918527
D013739	Testosterone	Testosterone results in decreased expression of SHMT1 mRNA	21669218
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of SHMT1 mRNA	22298810\|2257421
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in decreased expression of SHMT1 mRNA	20106945
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of SHMT1 mRNA	26377647
D013749	Tetrachlorodibenzodioxin	[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of SHMT1 mRNA	17942748
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in decreased expression of SHMT1 mRNA	19770486\|2629044
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in decreased expression of SHMT1 mRNA	21215274
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution results in decreased expression of SHMT1 mRNA	28065790
D014212	Tretinoin	Tretinoin results in decreased expression of SHMT1 mRNA	16604517
C012589	trichostatin A	trichostatin A affects the expression of SHMT1 mRNA	28542535
C015559	trimellitic anhydride	trimellitic anhydride results in increased expression of SHMT1 mRNA	19042947
C016805	tris(1,3-dichloro-2-propyl)phosphate	"tris(1,3-dichloro-2-propyl)phosphate results in decreased expression of SHMT1 mRNA"	26179874
C057693	troglitazone	troglitazone results in increased expression of SHMT1 mRNA	28973697
D014520	Urethane	Urethane results in decreased expression of SHMT1 mRNA	28818685
D014635	Valproic Acid	Valproic Acid results in decreased expression of SHMT1 mRNA	29154799
D014635	Valproic Acid	Valproic Acid results in increased expression of SHMT1 mRNA	23179753
D014640	Vancomycin	Vancomycin results in increased expression of SHMT1 mRNA	18930951
D001335	Vehicle Emissions	Vehicle Emissions results in decreased methylation of SHMT1 gene	25560391
C025643	vinclozolin	vinclozolin affects the expression of SHMT1 mRNA	19015723
C029297	vinylidene chloride	vinylidene chloride results in decreased expression of SHMT1 mRNA	26682919
D015032	Zinc	Zinc deficiency results in increased expression of SHMT1 mRNA	22171008

GO/Pathway

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0000900	translation repressor activity, mRNA regulatory element binding	-	IDA	10995219
GO:0004372	glycine hydroxymethyltransferase activity	-	EXP	627563
GO:0004372	glycine hydroxymethyltransferase activity	-	IDA	8505317 10995219 17482557 24698160
GO:0005515	protein binding	-	IPI	25416956
GO:0008732	L-allo-threonine aldolase activity	-	IEA	-
GO:0030170	pyridoxal phosphate binding	-	IDA	17482557 24698160
GO:0042802	identical protein binding	-	IPI	25416956
GO:0042803	protein homodimerization activity	-	IDA	9753690
GO:0048027	mRNA 5'-UTR binding	-	IDA	10995219
GO:0070905	serine binding	-	IDA	24698160

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0006231	dTMP biosynthetic process	-	IEA	-
GO:0006544	glycine metabolic process	-	IDA	24698160
GO:0006563	L-serine metabolic process	-	IDA	24698160
GO:0006565	L-serine catabolic process	-	IDA	17482557
GO:0009113	purine nucleobase biosynthetic process	-	IDA	11516159
GO:0017148	negative regulation of translation	-	IDA	10995219
GO:0019264	glycine biosynthetic process from serine	-	IEA	-
GO:0035999	tetrahydrofolate interconversion	-	IDA	24698160
GO:0035999	tetrahydrofolate interconversion	-	IEA	-
GO:0045329	carnitine biosynthetic process	-	TAS	-
GO:0046653	tetrahydrofolate metabolic process	-	IDA	24698160
GO:0046655	folic acid metabolic process	-	IDA	11278996
GO:0046655	folic acid metabolic process	-	TAS	-
GO:0051262	protein tetramerization	-	IDA	9753690
GO:0051289	protein homotetramerization	-	IDA	24698160
GO:1904482	cellular response to tetrahydrofolate	-	IDA	24698160
GO:1990830	cellular response to leukemia inhibitory factor	-	IEA	-

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0005634	nucleus	-	IDA	-
GO:0005829	cytosol	-	IDA	17482557
GO:0005829	cytosol	-	TAS	-
GO:0070062	extracellular exosome	-	HDA	19056867 23533145

KEGG ID	KEGG Term
hsa00260	Glycine, serine and threonine metabolism
hsa00460	Cyanoamino acid metabolism
hsa00670	One carbon pool by folate
hsa01100	Metabolic pathways

Reactome ID	Reactome Term	Evidence
R-HSA-1430728	Metabolism	TAS
R-HSA-196757	Metabolism of folate and pterines	TAS
R-HSA-196849	Metabolism of water-soluble vitamins and cofactors	TAS
R-HSA-196854	Metabolism of vitamins and cofactors	TAS
R-HSA-70895	Branched-chain amino acid catabolism	TAS
R-HSA-71262	Carnitine synthesis	TAS
R-HSA-71291	Metabolism of amino acids and derivatives	TAS

Interactions (STRING v10.5, Interaction Score >= 0.400)

Publications (Co-occurrence of gene symbol strings and ANCO-Dependence terms)

PMID	Title (Year)	Author	Journal
24278388	One-carbon metabolism pathway gene variants and risk of clear cell renal cell carcinoma in a Chinese population. (2013)	Zhang L	PLoS One
23372658	Investigating multiple candidate genes and nutrients in the folate metabolism pathway to detect genetic and nutritional risk factors for lung cancer. (2013)	Swartz MD	PLoS One
16536979	[Correlations between serine hydroxymethyltransferase1 C1420T polymorphisms and susceptibilities to esophageal squamous cell carcinoma and gastric cardiac adenocarcinoma]. (2006 Mar)	Wang YM	Ai Zheng
22649255	Folate network genetic variation predicts cardiovascular disease risk in non-Hispanic white males. (2012 Jul)	Wernimont SM	J Nutr
18635682	Genetic analysis of 56 polymorphisms in 17 genes involved in methionine metabolism in patients with abdominal aortic aneurysm. (2008 Nov)	Giusti B	J Med Genet