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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PHGDH Gene

protein-coding GIFtS: 66
GCID: GC01P120202

phosphoglycerate dehydrogenase

Explore 25 diseases affiliated with
PHGDH 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

Aliases
Phosphoglycerate Dehydrogenase¹ ²		3PGDH²
PDG¹ ²		PGAD²
PGDH¹ ²		PGD²
SERA¹ ²		D-3-Phosphoglycerate Dehydrogenase²
3-PGDH² ³		PGDH3³
EC 1.1.1.95³ ⁸		EC 1.1.1⁸
3-Phosphoglycerate Dehydrogenase²

External Ids:	HGNC: 8923¹	Entrez Gene: 26227²	Ensembl: ENSG00000092621⁷	OMIM: 606879⁵	UniProtKB: O43175³

Export aliases for PHGDH gene to outside databases

Previous GC identifers: GC01P120701 GC01P119092 GC01P119401 GC01P119600 GC01P119966 GC01P120056 GC01P118112

(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 PHGDH:

This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is

required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms

homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly,

psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found,

however the full-length nature of most are not known. (provided by RefSeq, Aug 2011)

Gene Wiki entry for PHGDH (Phosphoglycerate dehydrogenase)

(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_000001.10 NC_018912.1 NT_032977.9

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PHGDH gene promoter:
GR Max1 IRF-1 CUTL1 PPAR-alpha Max NRF-2 GR-alpha c-Myc
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): PHGDH promoter sequence

Search SABiosciences Chromatin IP Primers for PHGDH

Epigenetics:

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

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

Entrez Gene cytogenetic band: 1p12 Ensembl cytogenetic band: 1p12 HGNC cytogenetic band: 1p12

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

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01P120202: view genomic region (about GC identifiers)

Start:	120,202,421 bp from pter	End:	120,286,849 bp from pter
Size:	84,429 bases	Orientation:	plus strand

(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: SERA_HUMAN, O43175 (See protein sequence)

Recommended Name: D-3-phosphoglycerate dehydrogenase

Size: 533 amino acids; 56651 Da

Subunit: Homotetramer (By similarity)

1 PDB 3D structure from and Proteopedia for PHGDH:

2G76 (3D)

Secondary accessions: B2RD08 Q5SZU3 Q9BQ01

Explore the universe of human proteins at neXtProt for PHGDH: NX_O43175

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_O43175

4/19 DME Specific Peptides for PHGDH (O43175) (see all 19)

PHLGAST

GREVATR

LLSYQTS

AWAGSPKG

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

REFSEQ proteins: NP_006614.2

ENSEMBL proteins:

ENSP00000358417 ENSP00000358415

Reactome Protein details: O43175
Human Recombinant Protein Products:

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	Uscn Proteins for PHGDH

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005829	cytosol	TAS	--

PHGDH for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for PHGDH

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

PHGDH for domains About GeneDecksing

4 InterPro domains/families:

IPR006236 D-3-Phosphoglycerate_DH

IPR006140 D-isomer_2_OHA_DH_NAD-bd

IPR006139 D-isomer_2_OHA_DH_cat_dom

IPR016040 NAD(P)-bd_dom

Graphical View of Domain Structure for InterPro Entry O43175

ProtoNet protein and cluster: O43175

2 Blocks protein families:

IPB001588 Casein

IPB006139 D-isomer specific 2-hydroxyacid dehydrogenase

UniProtKB/Swiss-Prot: SERA_HUMAN, O43175

Similarity: Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family

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

Function Summary:

UniProtKB/Swiss-Prot: SERA_HUMAN, O43175

Catalytic activity: 3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH

Catalytic activity: 2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH

Biophysicochemical properties: Kinetic parameters: KM=21.6 uM for 3-phosphohydroxypyruvate; Vmax=35 nmol/min/mg enzyme

with 3-phosphohydroxypyruvate as substrate (in patient-derived fibroblasts); Vmax=168 nmol/min/mg enzyme with

3-phosphohydroxypyruvate as substrate (in 3-PGDH overexpressed cells);

Induction: Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand).

Positively regulated by the transcription factors SP1 and NF-Y

Enzyme Numbers (IUBMB): EC 1.1.1.95¹ ² EC 1.1.1²

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		hsa-miR-128 hsa-miR-3681*
		SwitchGear 3'UTR luciferase reporter plasmid: PHGDH 3' UTR sequence

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHGDH

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000166	nucleotide binding	--	--
GO:0004617	phosphoglycerate dehydrogenase activity	TAS	--
GO:0009055	electron carrier activity	TAS	8758134
GO:0048037	cofactor binding	--	--
GO:0051287	NAD binding	IEA	--

PHGDH for ontologies           About GeneDecksing

Animal Models:
     Mouse knock-out Phgdh^tm1.1Shfu for PHGDH
     9 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Phgdh):

cellular	craniofacial	embryogenesis	growth/size	homeostasis/metabolism
limbs/digits/tail	mortality/aging	nervous system	tumorigenesis

PHGDH for phenotypes About GeneDecksing

(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 About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Metabolism

Metabolism

1.00

Metabolic pathways

0.38

Amino acid synthesis and interconversion (transamination)

Amino acid synthesis and interconversion (transamination)

1.00

Metabolism of amino acids and derivatives

Metabolism of amino acids and derivatives

1.00

Serine biosynthesis

Serine biosynthesis

1.00

Glycine, serine and threonine metabolism

Glycine, serine and threonine metabolism

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

4 Reactome Pathways for PHGDH

	Metabolism
	Amino acid synthesis and interconversion (transamination)
	Metabolism of amino acids and derivatives
	Serine biosynthesis

2 Kegg Pathways (Kegg details for PHGDH):

	Glycine, serine and threonine metabolism
	Metabolic pathways

UniProtKB/Swiss-Prot: SERA_HUMAN, O43175

Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3

PHGDH for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for PHGDH

STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

5/853 Interacting proteins for PHGDH (O43175^{2, 3} ENSP00000358417⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 853)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
ETF1	P62495²^,³, ENSP00000353741⁴	MINT-7945693 MINT-7947479 I2D: score=6 STRING: ENSP00000353741
CHEK1	O14757²^,³	MINT-7945693 MINT-7947479 I2D: score=5
PSMC4	P43686²^,³	MINT-7945693 MINT-7947479 I2D: score=5
RBBP5	Q15291²^,³	MINT-7945693 MINT-7947479 I2D: score=5
ENSG00000258947	Q13509²^,³	MINT-7945693 I2D: score=4

About this table

Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006541	glutamine metabolic process	IEA	--
GO:0006544	glycine metabolic process	IEA	--
GO:0006564	L-serine biosynthetic process	TAS	--
GO:0006566	threonine metabolic process	IEA	--
GO:0007420	brain development	TAS	8758134

PHGDH 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

PHGDH for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PHGDH

5 HMDB Compounds for PHGDH About this table

Compound	Synonyms	CAS #	PubMed Ids
3-Phosphoglyceric acid	3-(dihydrogen phosphate)Glycerate (see all 21)	820-11-1	--
NAD	3-Carbamoyl-1-D-ribofuranosylpyridinium hydroxide 5'-ester with adenosine 5'-pyrophosphate (see all 28)	53-84-9	--
NADH	1,4-Dihydronicotinamide adenine dinucleotide (see all 17)	58-68-4	--
Oxoglutaric acid	2-Ketoglutarate (see all 9)	328-50-7	--
Phosphohydroxypyruvic acid	2-oxo-3-(phosphonooxy)-Propanoate (see all 8)	3913-50-6	--

1 DrugBank Compound for PHGDH About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
NADH	beta-DPNH (see all 18)	606-68-8	target	--	945314 17139284 17016423 2692566 12183470

8 Novoseek chemical compound relationships for PHGDH gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
3-phosphoglycerate	96.6	68	9163325 (4), 11034457 (3), 11571699 (3), 9708551 (2) (see all 32)
3-phosphohydroxypyruvate	94.7	2	18378410 (1)
serine	74	65	18296366 (5), 9708551 (3), 11055895 (3), 17068790 (2) (see all 27)
phosphoserine	56.8	3	16763900 (1), 10222452 (1), 8739971 (1)
5-methyltetrahydrofolate	53.1	1	11508546 (1)
alpha-ketoglutarate	47.1	2	9163325 (1), 8550422 (1)
nadh	38.7	1	19388702 (1)
purine	22	1	10222208 (1)

Search CenterWatch for drugs/clinical trials and news about PHGDH / SERA

(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, 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 PHGDH gene:

NM_006623.3

Unigene Cluster for PHGDH:

Phosphoglycerate dehydrogenase

Hs.487296 [show with all ESTs]

Unigene Representative Sequence: AK093306

7 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000493622 ENST00000496756 ENST00000369409(uc009whl.3 uc001ehz.3 uc009whm.3)

ENST00000462324 ENST00000369407(uc001eib.3) ENST00000469443 ENST00000482968

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		2 QIAGEN miScript miRNA Assays for microRNAs that regulate PHGDH:
		hsa-miR-128 hsa-miR-3681*
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Additional cDNA sequence:

AF171235.1 AF171236.1 AF171237.1 AK093306.1 AK129762.1 AK309662.1 AK310132.1 AK315360.1

BC000303.2 BC001349.2 BC011262.1 BC023235.1 BC032110.2 CR456795.1

24/46 DOTS entries (see all 46):

DT.87017070 DT.92470699 DT.100689962 DT.100689953 DT.100689970 DT.121442379 DT.92470705 DT.95357891

DT.100689941 DT.100689969 DT.91985641 DT.95357924 DT.100689967 DT.121442325 DT.100689954 DT.101987501

DT.95357876 DT.100689976 DT.121442264 DT.92470724 DT.97861052 DT.100639300 DT.100639301 DT.121442309

24/1066 AceView cDNA sequences (see all 1066):

BQ685488 BM455208 AU143765 BM558946 D11962 BM745503 BM767353 BP359189

BQ217167 CR612347 BQ071223 BE794265 AL515759 BI761705 CN481718 BM770336

BC000303 BQ057413 BE259628 CB215385 BQ057953 BQ059624 BM773054 BG032955

GeneLoc Exon Structure

5/15 Alternative Splicing Database (ASD) splice patterns (SP) for PHGDH (see all 15) About this scheme

ExUns:	1a	·	1b	·	1c	^	2	^	3a	·	3b	^	4a	·	4b	·	4c	^	5a	·	5b	^	6	^	7	^	8a	·	8b	^	9a	·	9b	·	9c	^	10	^	11a	·	11b	·	11c	^	12a	·	12b	^	13a	·	13b	^
SP1:							-		-														-		-		-								-		-
SP2:																							-		-		-								-		-
SP3:							-		-		-												-		-		-								-		-
SP4:							-		-		-		-										-		-		-								-		-
SP5:							-		-														-		-		-								-

ExUns:	14a	·	14b	^	15	^	16a	·	16b	^	17a	·	17b	·	17c
SP1:	-						-
SP2:	-						-
SP3:
SP4:
SP5:

ECgene alternative splicing isoforms for PHGDH

(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

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

About this image

PHGDH expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Ovary

Antral Follicle

Secondary Oocyte

Female Gametocytes, Germ Cells

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 4 LifeMap Cells

Name

Category

PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)

Lateral Plate Mesoderm, Neural Crest

PureStem™ mesenchymal progenitor E15 (Embryonic Progenitor Cell)

Adipose, Bone, Cartilage

PureStem™ progenitor Z1 (Embryonic Progenitor Cell)

Mesenchymal Progenitor Cells - Passage 2 (Differentiation of ...)

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

SOURCE GeneReport for Unigene cluster: Hs.487296

SABiosciences Expression via Pathway-Focused PCR Arrays including PHGDH:

Multiple Sclerosis in human mouse rat

Amino Acid Metabolism II in human mouse rat

GABA & Glutamate in human mouse rat

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In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHGDH

(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 PHGDH gene from 9/33 species (see all 33) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	PHGDH¹	phosphoglycerate dehydrogenase	69.02(n) 68.7(a)		424381 XM_422226.3 XP_422226.2
lizard (Anolis carolinensis)	Reptilia	PHGDH⁶	--	69(a)	1 ↔ 1	GL343782.1(137291-158225)
tropical clawed frog (Xenopus tropicalis)	Amphibia	Str.20062²	Transcribed sequence with weak similarity to protein more	73.87(n)		CF785148.1
zebrafish (Danio rerio)	Actinopterygii	wufb38f06²	wufb38f06	76.52(n)		321928 BC056334.1
fruit fly (Drosophila melanogaster)	Insecta	CG6287^{1 , 3}	phosphoglycerate dehydrogenase³ CG6287¹	52(a)³ 57.1(n)¹ 54.26(a)¹		32D5³ 34554¹ NM_135652.2¹ NP_609496.1¹
worm (Caenorhabditis elegans)	Secernentea	C31C9.2³ CELE_C31C9.2¹	D-3-Phosphoglycerate dehydrogenase³ Protein C31C9.2¹	53(a)³ 57.67(n)¹ 54.29(a)¹		II(13636986-13638371)³ 175012¹ NM_064467.4¹ NP_496868.1¹
thale cress (Arabidopsis thaliana)	eudicotyledons	EDA9¹	D-3-phosphoglycerate dehydrogenase	50.14(n) 41.45(a)		829568 NM_119583.3 NP_195146.1
rice (Oryza sativa)	Liliopsida	Os04g0650800¹	hypothetical protein	51.35(n) 44.7(a)		4337230 NM_001060629.1 NP_001054094.1
E. coli (Escherichia coli)	Gamma proteobacteria	serA⁶	D-3-phosphoglycerate dehydrogenase	29(a)	1 ↔ 1	Chromosome(3055200-3056432)

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

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for PHGDH gene

CTBP1² CTBP2² ENSG00000212884²

2 SIMAP similar genes for PHGDH using alignment to 3 protein entries: SERA_HUMAN (see all proteins):

PGDH3 GRHPR

PHGDH 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)
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SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs121907987^1,2	C,	pathogenic	118145069(+)	`CAGGCA/GTGCGG`	2	M V	mis¹		0	--	--	--	--
rs75735616^1,2	F,	--	118111472(+)	`AAGTTT/CGACTT`	1	--	us2k¹		1		EA	120
rs17024124^1,2	C,F,	--	118111779(+)	`AGGACA/TTTGTG`	1	--	us2k¹		5		NA WA	380
rs532782^1,2	C,F,O,H,	--	118112308(+)	`GTCTCA/GGAAAG`	1	--	us2k¹		7		NS NA WA	912
rs3790713^1,2	H	--	118113918(-)	`CCTTAC/GGAGGG`	1	--	int¹		4		NS EA	380
rs78621095^1,2	C,F,	--	118114320(+)	`TACCTC/TACCTG`	1	--	int¹		1		WA	118
rs77334960^1,2		--	118114483(+)	`CTGGAA/GACTGC`	1	--	int¹		1		WA	118
rs72988658^1,2	C,	--	118114492(+)	`GCCTCG/ACTCAC`	1	--	int¹		2		WA	120
rs76046580^1,2	F,	--	118116065(+)	`ACCCTG/CTCCCA`	1	--	int¹		1		WA	118
rs113589710^1,2		--	118117715(+)	`CCAAGG/AGAGTG`	1	--	int¹		2		CSA WA	119

HapMap Linkage Disequilibrium report for PHGDH (120202421 - 120286849 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 3 variations for PHGDH
3 CNVs: 4245 3309 4244
Human Gene Mutation Database (HGMD): PHGDH

SABiosciences Cancer Mutation PCR Assays

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

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

PHGDH for disorders           About GeneDecksing

OMIM gene information: 606879
OMIM disorders: 601815
UniProtKB/Swiss-Prot: SERA_HUMAN, O43175

Defects in PHGDH are the cause of phosphoglycerate dehydrogenase deficiency (PHGDH deficiency) [MIM:601815].

It is characterized by congenital microcephaly, psychomotor retardation, and seizures

20/25 diseases for PHGDH (see all 25): About MalaCards

2-hydroxyglutaric aciduria microcephaly serine deficiency phgdh deficiency

cerebral folate deficiency scarlet fever typhoid fever ornithosis

erysipelas anovulation mixed malaria west syndrome

autoimmune hepatitis keloids cerebritis seizures

tuberculosis astrocytoma breast cancer hepatitis

6 diseases from the University of Copenhagen DISEASES database for PHGDH:

Serine deficiency Mixed malaria Microcephaly Anovulation

Ornithosis Scarlet fever

3 Novoseek disease relationships for PHGDH gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
microcephaly	83.8	12	20196394 (2), 16763900 (1), 15610810 (1), 11055895 (1) (see all 8)
tuberculosis	19.9	11	15668250 (4), 19388702 (2), 17761677 (2), 18627175 (2)
shock	11.1	4	15606508 (1), 2115888 (1), 18310271 (1), 18334753 (1)

Human Genome Epidemiology (HuGE) Navigator: PHGDH (2 documents)

Export disorders for PHGDH 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)
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PubMed articles for PHGDH gene, integrated from 9 sources (see all 98):
(articles sorted by number of sources associating them with PHGDH)

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

Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. (PubMed id 19235232)^{1, 2, 9} Tabatabaie L.... Klomp L.W.J. (2009)
Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L- serine biosynthesis. (PubMed id 11055895)^{1, 2, 9} Klomp L.W.J.... Berger R. (2000)
V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. (PubMed id 11751922)^{1, 2, 9} Pind S.... Natowicz M.R. (2002)
Nucleotide sequence and differential expression of the human 3- phosphoglycerate dehydrogenase gene. (PubMed id 10713460)^{1, 2, 9} Cho H.M.... Kim Y.H. (2000)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{1, 2} Gregory S.G.... Bentley D.R. (2006)
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)
3-Phosphoglycerate dehydrogenase expression is regula ted by HOXA10 in murine endometrium and human endometrial cells. (PubMed id 19778996)^{1, 9} Du H....Taylor H.S. (2010)
[Cloning and expression of 3-phosphoglycerate dehydro genase gene and its correlative antibodies in diagnosis of autoimmune hepatitis ] (PubMed id 19497206)^{1, 9} XIANG D.J....YANG J.X. (2009)
Positive regulation of promoter activity of human 3-phosphoglycerate dehydrogenase (PHGDH) gene is mediated by transcription factors Sp1 and NF-Y. (PubMed id 18378410)^{2, 9} Jun D.Y....Kim Y.H. (2008)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
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)
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Entrez Gene: 26227	HGNC: 8923	AceView: PHGDH	Ensembl:ENSG00000092621	euGenes: HUgn26227
ECgene: PHGDH	Kegg: 26227	H-InvDB: PHGDH

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for PHGDH	Pharmacogenomics, SNPs, Pathways

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

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

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

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