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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SHMT2 Gene

protein-coding GIFtS: 62
GCID: GC12P057623

serine hydroxymethyltransferase 2 (mitochondrial)

(Previous symbol: SHMT)

Explore 8 diseases affiliated with
SHMT2 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Serine Hydroxymethyltransferase 2 (Mitochondrial)¹ ²		GLY A+²
SHMT¹ ² ³		Glycine Auxotroph A, Human Complement For Hamster²
Glycine Hydroxymethyltransferase² ³		Serine Aldolase²
Serine Methylase² ³		Serine Hydroxymethylase²
EC 2.1.2.1³ ⁸		Serine Hydroxymethyltransferase, Mitochondrial²
GLYA² ⁵		Threonine Aldolase²

External Ids:	HGNC: 10852¹	Entrez Gene: 6472²	Ensembl: ENSG00000182199⁷	OMIM: 138450⁵	UniProtKB: P34897³

ORGUL members:
	NONCODE:n408345 n408346 n408344

Export aliases for SHMT2 gene to outside databases

Previous GC identifers: GC12U990093 GC12P057340 GC12P055909 GC12P055886 GC12P054662

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SHMT2:

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)

UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897

Function: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil

accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000012.11 NC_018923.1 NT_029419.12

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SHMT2 gene promoter:
E2F-3a E2F-1 Sp1 E2F-2 GATA-1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SHMT2 promoter sequence

Search SABiosciences Chromatin IP Primers for SHMT2

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SHMT2

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q12-q14 Ensembl cytogenetic band: 12q13.3 HGNC cytogenetic band: 12q12-q14

SHMT2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHMT2 gene location

GeneLoc information about chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12P057623: view genomic region (about GC identifiers)

Start:	57,623,110 bp from pter	End:	57,628,718 bp from pter
Size:	5,609 bases	Orientation:	plus strand

ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SHMT2

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897 (See protein sequence)

Recommended Name: Serine hydroxymethyltransferase, mitochondrial precursor

Size: 504 amino acids; 55993 Da

Cofactor: Pyridoxal phosphate

Subunit: Homotetramer

Subcellular location: Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid. Mitochondrion inner membrane

Miscellaneous: In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one

1 PDB 3D structure from and Proteopedia for SHMT2:

3OU5 (3D)

Secondary accessions: B7Z9F1 E7EQ19 E7EU43 O00740 Q8N1A5

Alternative splicing: 3 isoforms: P34897-1 P34897-2 P34897-3 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SHMT2: NX_P34897

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P34897

4/22 DME Specific Peptides for SHMT2 (P34897) (see all 22)

VTTTTHK

LIASENF

LVSGGTD

GGTDNHL

SHMT2 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (5 alternative transcripts):

NP_001159828.1 NP_001159829.1 NP_001159830.1 NP_001159831.1 NP_005403.2

ENSEMBL proteins:

ENSP00000333667 ENSP00000451169 ENSP00000452315 ENSP00000450930 ENSP00000452035

ENSP00000450594 ENSP00000451630 ENSP00000450610 ENSP00000406881 ENSP00000450927

ENSP00000450452 ENSP00000452161 ENSP00000450893 ENSP00000452045 ENSP00000452419

ENSP00000451968 ENSP00000452404 ENSP00000413770 ENSP00000451872 ENSP00000452339

ENSP00000451371 ENSP00000452163 ENSP00000451495 ENSP00000450490 ENSP00000377413

Human Recombinant Protein Products for SHMT2:

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	Browse Sino Biological Recombinant Proteins
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for SHMT2

Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005739	mitochondrion	IDA	--
GO:0005743	mitochondrial inner membrane	IDA	--
GO:0005758	mitochondrial intermembrane space	IEA	--
GO:0005759	mitochondrial matrix	IDA	--
GO:0015630	microtubule cytoskeleton	IDA	--

SHMT2 for ontologies About GeneDecksing

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Assay Products for SHMT2:

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	GenScript Custom Assay Services for SHMT2
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for SHMT2

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

SHMT2 for domains About GeneDecksing

5 InterPro domains/families:

IPR019798 Ser_HO-MeTrfase_PLP_BS

IPR001085 Ser_HO-MeTrfase

IPR015424 PyrdxlP-dep_Trfase

IPR015421 PyrdxlP-dep_Trfase_major_sub1

IPR015422 PyrdxlP-dep_Trfase_major_sub2

Graphical View of Domain Structure for InterPro Entry P34897

ProtoNet protein and cluster: P34897

1 Blocks protein family: IPB001085 Glycine hydroxymethyltransferase

UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897

Similarity: Belongs to the SHMT family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: GLYM_HUMAN, P34897

Function: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil

accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA

Catalytic activity: 5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine

Genatlas biochemistry entry for SHMT2:

serine hydroxy-methyltransferase,pyridoxal dependent,mitochondrial,catalyzing 5-10 methylene THF

synthesis,"one-carbone" metabolism,putative regulator of cell growth and proliferation

Enzyme Number (IUBMB): EC 2.1.2.1¹ ²

Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003682	chromatin binding	IDA	18063578
GO:0004372	glycine hydroxymethyltransferase activity	IDA	8505317
GO:0008168	methyltransferase activity	IEA	--
GO:0008732	L-allo-threonine aldolase activity	IEA	--
GO:0016597	amino acid binding	IEA	--

SHMT2 for ontologies About GeneDecksing

Animal Models:

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for SHMT2

miRNA Products:		OriGene 3'-UTR Clone: SHMT2 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SHMT2
		8/25 QIAGEN miScript miRNA Assays for microRNAs that regulate SHMT2 (see all 25):
		hsa-miR-579 hsa-miR-485-5p hsa-miR-495 hsa-miR-657 hsa-miR-4299 hsa-miR-4314 hsa-miR-183* hsa-miR-1184

		SwitchGear 3'UTR luciferase reporter plasmid: SHMT2 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHMT2

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/6 super-pathways (see all 6) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

glycine biosynthesis I

glycine biosynthesis I	1.00	folate polyglutamylation	0.50
superpathway of serine and glycine biosynthesis I	0.67	folate transformations I	0.33
dTMP de novo biosynthesis	0.50

One Carbon Metabolism

One Carbon Metabolism

1.00

One carbon pool by folate

0.52

glycine betaine degradation

glycine betaine degradation

1.00

Glycine, serine and threonine metabolism

Glycine, serine and threonine metabolism

1.00

Metabolism

Metabolic pathways

0.38

Pathway sources
See GeneCards unified pathways
Show all pathways

5/7 BioSystems Pathways for SHMT2 (see all 7)

	One Carbon Metabolism
	dTMP de novo biosynthesis
	folate transformations I
	folate polyglutamylation
	glycine biosynthesis I

4 Kegg Pathways (Kegg details for SHMT2):

	Glycine, serine and threonine metabolism
	Cyanoamino acid metabolism
	One carbon pool by folate
	Metabolic pathways

UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897

Pathway: One-carbon metabolism; tetrahydrofolate interconversion

SHMT2 for pathways About GeneDecksing

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for SHMT2

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

5/381 Interacting proteins for SHMT2 (P34897^{2, 3} ENSP00000333667⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 381)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TRMT10C	Q7L0Y3²^,³, ENSP00000312356⁴	MINT-8079030 I2D: score=1 STRING: ENSP00000312356
EEF1A1	P68104²^,³	MINT-8076236 I2D: score=1
KARS	Q15046²^,³	MINT-8079030 I2D: score=1
GNAS	P63092³, ENSP00000360141⁴	I2D: score=1 I2D: score=1 STRING: ENSP00000360141
ICT1	Q14197²^,³, ENSP00000301585⁴	MINT-8079030 I2D: score=1 STRING: ENSP00000301585

About this table

Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006544	glycine metabolic process	--	--
GO:0006545	glycine biosynthetic process	--	--
GO:0006563	L-serine metabolic process	--	--
GO:0006564	L-serine biosynthetic process	IEA	--
GO:0006730	one-carbon metabolic process	IDA	11516159

SHMT2 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

SHMT2 for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SHMT2

6 HMDB Compounds for SHMT2 About this table

Compound	Synonyms	CAS #	PubMed Ids
5,10-Methylene-THF	5,10-methylene-THF (see all 8)	31690-11-6	--
Glycine	2-Aminoacetate (see all 15)	56-40-6	--
L-Serine	(-)-Serine (see all 26)	56-45-1	--
Pyridoxal 5'-phosphate	Apolon B6 (see all 27)	54-47-7	--
Tetrahydrofolic acid	(6S)-Tetrahydrofolate (see all 10)	135-16-0	--
Water	Dihydrogen oxide (see all 2)	7732-18-5	--

3 DrugBank Compounds for SHMT2 About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
Glycine	2-Aminoacetic acid (see all 4)	56-40-6	target	--	17664250 16876889 17142057 16980404 17355947
Pyridoxal Phosphate	Codecarboxylase (see all 9)	54-47-7	target	cofactor	15865438 11877399 17482557 17651438 16980404
Tetrahydrofolic acid	5,6,7,8-tetrahydrofolate (see all 3)	135-16-0	target	cofactor	9449840 17142057 11386852 17651438 11737206

10/12 Novoseek chemical compound relationships for SHMT2 gene (see all 12) About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
4-deoxypyridoxine	88.7	1	7526359 (1)
tetrahydrofolate	86.8	3	8786078 (1), 19815026 (1), 15170323 (1)
pyridoxal 5-phosphate	79.8	14	12913008 (3), 10387080 (3), 19158217 (1), 8405393 (1) (see all 5)
5,10-methenyltetrahydrofolate	78.4	1	15170323 (1)
serine	73.2	44	18029478 (2), 8435385 (2), 2127307 (2), 11189372 (2) (see all 26)
vitamin b6	57.8	5	19158217 (2), 7526359 (1)
leucovorin	45.7	4	15170323 (2), 15888445 (1)
folate	44.6	5	15170323 (2), 16137637 (1), 10656824 (1)
aspartate	33.8	3	10493937 (1), 10656824 (1), 8405393 (1)
lysine	15.9	1	10387080 (1)

Search CenterWatch for drugs/clinical trials and news about SHMT2 / GLYM

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for SHMT2 gene (5 alternative transcripts):

NM_001166356.1 NM_001166357.1 NM_001166358.1 NM_001166359.1 NM_005412.5

Unigene Cluster for SHMT2:

Serine hydroxymethyltransferase 2 (mitochondrial)

Hs.741179 [show with all ESTs]

Unigene Representative Sequence: BC004189

18/36 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 36):

ENST00000328923(uc001snf.2 uc009zpk.2 uc001sng.2 uc001sni.2 uc010srh.2)

ENST00000556825(uc001snh.2 uc010srg.2 uc010srj.2) ENST00000557740

ENST00000554600 ENST00000553324 ENST00000554467 ENST00000557487 ENST00000553950

ENST00000555634 ENST00000556689 ENST00000557269 ENST00000555563 ENST00000557433

ENST00000414700 ENST00000557348 ENST00000557703 ENST00000553529 ENST00000554310

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		8/25 QIAGEN miScript miRNA Assays for microRNAs that regulate SHMT2 (see all 25):
		hsa-miR-579 hsa-miR-485-5p hsa-miR-495 hsa-miR-657 hsa-miR-4299 hsa-miR-4314 hsa-miR-183* hsa-miR-1184

		SwitchGear 3'UTR luciferase reporter plasmid: SHMT2 3' UTR sequence

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		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SHMT2

Additional cDNA sequence:

AK223555.1 AK295941.1 AK296183.1 AK297173.1 AK298231.1 AK301339.1 AK301443.1 AK303827.1

AK315916.1 BC004189.1 BC008066.2 BC008711.1 BC011911.2 BC013677.2 BC025355.1 BC032584.1

BC044211.1 BC091501.1 BT006866.1 BX647711.1 BX648847.1 L11932.1 NR_029415.1 NR_029416.1

NR_029417.1

24/62 DOTS entries (see all 62):

DT.100803976 DT.91784496 DT.448610 DT.92057266 DT.92065933 DT.121193731 DT.100740502 DT.100886255

DT.121193641 DT.101985586 DT.100886226 DT.100886245 DT.91784339 DT.91712012 DT.100886251 DT.92407768

DT.121193660 DT.91784666 DT.91855748 DT.99981974 DT.100835452 DT.91784458 DT.91784410 DT.91784517

24/1296 AceView cDNA sequences (see all 1296):

AA243310 W73771 AI138694 AL560193 AA100409 AL552273 BQ709963 BE298849

BU147411 CF132149 AW976056 CR613033 BM787142 BG391570 AL557257 BE267512

BQ689256 BQ948999 AW264652 BQ639114 BQ056179 BI823409 AA313516 AA948010

GeneLoc Exon Structure

5/38 Alternative Splicing Database (ASD) splice patterns (SP) for SHMT2 (see all 38) About this scheme

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:															-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-		-				-

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:	-		-		-		-		-																						-										-

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:

ECgene alternative splicing isoforms for SHMT2

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SHMT2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ATCACAGTGT

About this image

SHMT2 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

3 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Eye

Inner Nuclear Layer

Mature Horizontal Cells

Horizontal, Retina

Limb

Forelimb Myotome

Limb Muscle Progenitor Cells

Skeletal Muscle

Bone

Mandibular Condyle

Bone

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Human multipotent adipose-derived (hMAD) stem cells (Adult Stem / Progenitor Cell)

Adipose

See SHMT2 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SHMT2

SOURCE GeneReport for Unigene cluster: Hs.741179

SABiosciences Expression via Pathway-Focused PCR Array including SHMT2:

Amino Acid Metabolism II in human mouse rat

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In Situ
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the last universal common ancestor (LUCA).

Orthologs for SHMT2 gene from 8/36 species (see all 36) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Shmt2^{1 , 5}	serine hydroxymethyltransferase 2 (mitochondrial)^{1, 5}	87.87(n)¹ 94.04(a)¹		10 (74.51 cM)⁵ 108037¹ NM_028230.4¹ NP_082506.1¹ 127517123⁵
lizard (Anolis carolinensis)	Reptilia	SHMT2⁶	--	82(a)	1 ↔ 1	GL343212.1(1740134-1764681)
African clawed frog (Xenopus laevis)	Amphibia	BX853756.1²	--	76.63(n)		BX853756.1
zebrafish (Danio rerio)	Actinopterygii	shmt2¹	serine hydroxymethyltransferase 2 (mitochondrial)	71.75(n) 78.05(a)		100144628 NM_001123374.1 NP_001116846.1
baker's yeast (Saccharomyces cerevisiae)	Saccharomycetes	SHM1(YBR263W)⁴ SHM2¹	Mitochondrial serine hydroxymethyltransferase, converts more⁴ Shm2p¹	56.75(n)¹ 56.6(a)¹		2(736264-737736)⁴ 850747¹ NP_013159.1¹ 852565⁴ NP_009822.2⁴
thale cress (Arabidopsis thaliana)	eudicotyledons	SHM2¹	serine hydroxymethyltransferase 2	57.52(n) 59.92(a)		832736 NM_180750.2 NP_851081.1
rice (Oryza sativa)	Liliopsida	Os.12148²	Oryza sativa (japonica cultivar-group) cDNA cloneJ more	74.3(n)		AK100404.1
E. coli (Escherichia coli)	Gamma proteobacteria	glyA⁶	serine hydroxymethyltransferase	47(a)	possible ortholog	Chromosome(2682276-2683529)

ENSEMBL Gene Tree for SHMT2 (if available)
TreeFam Gene Tree for SHMT2 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for SHMT2 gene

SHMT1²

3 SIMAP similar genes for SHMT2 using alignment to 17 protein entries: GLYM_HUMAN (see all proteins):

DKFZp686P09201 SHMT1 SHMT

SHMT2 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 12 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs11615783^1,2	C,F,A,H	--	54661374(+)	`aaaaaT/Attttt`	8	--	us2k¹		2		NA EA	240
rs12319666^1,2	C,F,H	--	54663662(+)	`CCTCAG/TAGGTG`	13	E *	stg¹ ese³		7		NS EA NA	708
rs72159442^1,2	C	--	54663885(+)	`TGATC-/CCTT CCTTC`	1	--	int¹		0	--	--	--	--
rs76110172^1,2	F	--	54663953(+)	`TGAGGG/AGCCAC`	8	--	int¹		1		EA	120
rs2229715^1,2	C,F	--	54665444(+)	`CCCTCG/ACCTTT`	13	/S	nc-transcript-variantsyn¹ ese³		4		MN NA	4580
rs112928049^1,2	C	--	54665761(+)	`GCCCAG/AGTCCG`	8	--	int¹		1		WA	2
rs11557165^1,2	H	--	54666701(+)	`AGGATG/TACTTC`	13	D Y	mis¹ ese³		4		NS EA	406
rs2229718^1,2	F	--	54666739(+)	`GGGGTC/TAACAT`	13	V	syn¹ ese³		1		MN	54
rs11557170^1,2	C	--	54667101(-)	`AAATAG/AAAAGG`	8	--	ut3¹ nc-transcript-variant		2		NA	4
rs11557168^1,2	C,F,H	--	54667193(-)	`AAAAAG/AAAAAG`	8	--	ut3¹ nc-transcript-variant		2		NS NA	102

HapMap Linkage Disequilibrium report for SHMT2 (57623110 - 57628718 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SHMT2: --

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SHMT2

DNA2.0 Custom Variant and Variant Library Synthesis for SHMT2

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SHMT2 for disorders           About GeneDecksing

OMIM gene information: 138450    OMIM disorders: --

8 diseases for SHMT2:    About MalaCards

neural tube defect pyridoxine deficiency prostate cancer pneumonia

prostatitis tuberculosis malaria mycobacterium tuberculosis

Genetic Association Database (GAD): SHMT2
Human Genome Epidemiology (HuGE) Navigator: SHMT2 (9 documents)

Export disorders for SHMT2 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for SHMT2 gene, integrated from 9 sources (see all 92):
(articles sorted by number of sources associating them with SHMT2)

Utopia: connect your pdf to the dynamic
world of online information

Is mutated serine hydroxymethyltransferase (SHMT) involved in the etiology of neural tube defects? (PubMed id 11386852)^{1, 4, 7} Heil S.G....Blom H.J. (2001)
Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. (PubMed id 8999870)^{1, 2, 3} Stover P.J.... Shane B. (1997)
Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PubMed id 8505317)^{1, 2, 9} Garrow T.A.... Shane B. (1993)
The layered structure of human mitochondrial DNA nucleoids. (PubMed id 18063578)^{1, 2} Bogenhagen D.F....Burke S. (2008)
Effect of vitamin B6 availability on serine hydroxymethyltransferase in MCF-7 cells. (PubMed id 17482557)^{1, 7} Perry C....Stover P.J. (2007)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
The genetic organization and protein crystallographic structure of human serine hydroxymethyltransferase. (PubMed id 10828359)^{1, 2} Snell K.... Whitehouse S.K. (2000)
Affinity properties of phosvitin: interaction of phosvitin with serine hydroxymethyl transferase. (PubMed id 10549165)^{1, 9} Lakhey H.V....Ramadoss C.S. (1999)
Abnormal serine-glycine metabolism in the brains of schizophrenics. (PubMed id 8435385)^{1, 9} Waziri R....Sherman A.D. (1993)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 6472	HGNC: 10852	AceView: SHMT2andNXPH4	Ensembl:ENSG00000182199	euGenes: HUgn6472
ECgene: SHMT2	Kegg: 6472	H-InvDB: SHMT2

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for SHMT2	Pharmacogenomics, SNPs, Pathways

Intellectual Property for SHMT2 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for SHMT2 gene:
Search GeneIP for patents involving SHMT2

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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serine hydroxymethyltransferase 2 (mitochondrial)

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serine hydroxymethyltransferase 2 (mitochondrial)

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