GDPGP1

Summary

GDPGP1 (GDP-D-glucose phosphorylase 1, HGNC:34360) is a protein-coding gene on chromosome 15q26.1, encoding GDP-D-glucose phosphorylase 1 (Q6ZNW5). Specific and highly efficient GDP-D-glucose phosphorylase regulating the levels of GDP-D-glucose in cells.

Enables GDP-D-glucose phosphorylase activity. Involved in glucose metabolic process. Predicted to be active in cytoplasm.

Source: NCBI Gene 390637 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_001013657

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34360
Approved symbol	GDPGP1
Name	GDP-D-glucose phosphorylase 1
Location	15q26.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000183208
Ensembl biotype	protein_coding
OMIM	619240
Entrez	390637

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000329600, ENST00000558017, ENST00000558291, ENST00000559204, ENST00000899066, ENST00000899067, ENST00000919183, ENST00000919184, ENST00000970464, ENST00000970465, ENST00000970466, ENST00000970467

RefSeq mRNA: 2 — MANE Select: NM_001013657 NM_001013657, NM_001322811

CCDS: CCDS32327

Canonical transcript exons

ENST00000329600 — 4 exons

Exon	Start	End
ENSE00002555539	90240900	90245811
ENSE00002560563	90234209	90234292
ENSE00002568505	90238492	90238548
ENSE00002571931	90234522	90234596

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 79.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0748 / max 50.0734, expressed in 1651 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
148424	5.0748	1651

Top tissues by expression

240 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.66	gold quality
mucosa of transverse colon	UBERON:0004991	79.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.36	silver quality
apex of heart	UBERON:0002098	76.23	gold quality
islet of Langerhans	UBERON:0000006	74.64	gold quality
rectum	UBERON:0001052	73.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.22	gold quality
granulocyte	CL:0000094	72.16	gold quality
right adrenal gland	UBERON:0001233	71.56	gold quality
right adrenal gland cortex	UBERON:0035827	70.81	gold quality
right lobe of liver	UBERON:0001114	70.74	gold quality
left adrenal gland	UBERON:0001234	70.71	gold quality
smooth muscle tissue	UBERON:0001135	70.70	gold quality
prefrontal cortex	UBERON:0000451	70.67	gold quality
transverse colon	UBERON:0001157	70.66	gold quality
heart left ventricle	UBERON:0002084	70.56	gold quality
left adrenal gland cortex	UBERON:0035825	70.34	gold quality
leukocyte	CL:0000738	69.92	gold quality
right atrium auricular region	UBERON:0006631	69.86	gold quality
cardiac ventricle	UBERON:0002082	69.54	gold quality
monocyte	CL:0000576	69.40	gold quality
stromal cell of endometrium	CL:0002255	69.37	gold quality
gall bladder	UBERON:0002110	69.27	gold quality
cardiac atrium	UBERON:0002081	69.10	gold quality
pancreas	UBERON:0001264	68.97	gold quality
small intestine Peyer’s patch	UBERON:0003454	68.89	gold quality
vermiform appendix	UBERON:0001154	68.60	gold quality
adrenal cortex	UBERON:0001235	68.34	gold quality
adrenal gland	UBERON:0002369	68.32	gold quality
heart	UBERON:0000948	68.26	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9543	yes	1518.88
E-ANND-3	yes	6.12
E-ENAD-17	no	161.79

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• C15orf58 in humans and C10F3.4 in C. elegans display GDP-hexose phosphorylase activity but the major reaction catalyzed by these enzymes is the phosphorolysis of GDP-D-glucose to GDP and D-glucose 1-phosphate (PMID:21507950)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gdpgp1	ENSDARG00000097155
mus_musculus	Gdpgp1	ENSMUSG00000050973
rattus_norvegicus	Gdpgp1	ENSRNOG00000064293
drosophila_melanogaster	CG3552	FBGN0035999
caenorhabditis_elegans		WBGENE00015678

Protein

Protein identifiers

GDP-D-glucose phosphorylase 1 — Q6ZNW5 (reviewed: Q6ZNW5)

All UniProt accessions (3): Q6ZNW5, A0A0G2JL98, H0YN11

UniProt curated annotations — full annotation on UniProt →

Function. Specific and highly efficient GDP-D-glucose phosphorylase regulating the levels of GDP-D-glucose in cells. Is involved in adaptive response to stress conditions, and plays a key role in neuronal stress resistance by modulating neuronal glycogen levels and maintaining glucose balance.

Subcellular location. Cytoplasm.

Miscellaneous. The orthologs in A.thaliana are GDP-L-galactose phosphorylases catalyzing the first reaction of the Smirnoff-Wheeler pathway, the major route to ascorbate biosynthesis in plants.

Similarity. Belongs to the GDPGP1 family.

RefSeq proteins (2): NP_001013679, NP_001309740 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026506	GDPGP	Family
IPR058865	GDPGP1_C	Domain
IPR058866	GDPGP1_N	Domain

Pfam: PF26216, PF26217

Enzyme classification (BRENDA):

• EC 2.7.7.78 — GDP-D-glucose phosphorylase (BRENDA: 3 organisms, 3 substrates, 0 inhibitors, 4 Km, 4 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
GDP-ALPHA-D-GLUCOSE	0.002–0.01	2
PHOSPHATE	1.2–2.9	2

Catalyzed reactions (Rhea), 1 shown:

• GDP-alpha-D-glucose + phosphate = alpha-D-glucose 1-phosphate + GDP + H(+) (RHEA:30387)

UniProt features (6 total): sequence variant 3, chain 1, active site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNW5-F1	91.29	0.78

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 218 (tele-gmp-histidine intermediate)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_GLUCOSE_METABOLIC_PROCESS, GOBP_MONOSACCHARIDE_METABOLIC_PROCESS, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY, GOMF_NUCLEOSIDE_TRIPHOSPHATASE_REGULATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, chr15q26, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOMF_GUANYLYLTRANSFERASE_ACTIVITY, ATF6_TARGET_GENES, DLX2_TARGET_GENES, E2F2_TARGET_GENES, GLI3_TARGET_GENES, HOXC6_TARGET_GENES, NAB2_TARGET_GENES

GO Biological Process (2): glucose metabolic process (GO:0006006), response to stress (GO:0006950)

GO Molecular Function (6): nucleotide binding (GO:0000166), guanyl-nucleotide exchange factor activity (GO:0005085), hydrolase activity (GO:0016787), GDP-D-glucose phosphorylase activity (GO:0080048), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
catalytic activity	2
hexose metabolic process	1
response to stimulus	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
guanylyltransferase activity	1
transferase activity, transferring phosphorus-containing groups	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

632 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GDPGP1	MIOX	Q9UGB7	717
GDPGP1	MPI	P34949	547
GDPGP1	GSR	P00390	456
GDPGP1	PSORS1C2	Q9UIG4	445
GDPGP1	UGDH	O60701	431
GDPGP1	SLC35D2	Q76EJ3	377
GDPGP1	GFOD2	Q3B7J2	369
GDPGP1	TGDS	O95455	355
GDPGP1	GGNBP2	Q9H3C7	352
GDPGP1	PMM2	O15305	346
GDPGP1	RGS22	Q8NE09	339
GDPGP1	MTCL2	O94964	337
GDPGP1	UGGT1	Q9NYU2	336
GDPGP1	C17orf58	Q2M2W7	336
GDPGP1	GPI	P06744	334

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CRKL	ARHGAP42	psi-mi:“MI:0914”(association)	0.350
ADNP2	GLI4	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), HDDC3 (Co-fractionation), LHPP (Co-fractionation), GDPGP1 (Affinity Capture-MS), GDPGP1 (Affinity Capture-MS), GDPGP1 (Co-fractionation), GDPGP1 (Co-fractionation), GDPGP1 (Affinity Capture-MS)

ESM2 similar proteins: A0JMS7, A2ARP1, A8E5Y3, B0X4N1, B3MF31, D3K0N9, O00329, O16216, O60678, O64876, O70467, O74429, P0C644, P22108, P42339, Q08CA1, Q0V9F1, Q14AI0, Q16NS8, Q1LXS2, Q2NL24, Q3TLS3, Q3V3E1, Q4R6F3, Q503I8, Q5BJ91, Q5XI55, Q5ZJM3, Q66I84, Q6DHQ3, Q6GMB0, Q6NTR1, Q6PFW1, Q6ZNW5, Q8C7R4, Q8HXE4, Q8IWV7, Q8K4F7, Q8NA58, Q922H1

Diamond homologs: A8E5Y3, Q08CA1, Q0V9F1, Q3TLS3, Q5E9T1, Q5ZR76, Q6ZNW5, Q8HXE4, Q9FLP9, Q8RWE8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

8 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1175 predictions. Top by Δscore:

Variant	Effect	Δscore
15:90233662:CACTT:C	donor_loss	1.0000
15:90233663:ACTT:A	donor_loss	1.0000
15:90233664:CTTAC:C	donor_loss	1.0000
15:90233665:TTA:T	donor_loss	1.0000
15:90233666:TA:T	donor_loss	1.0000
15:90233667:A:AC	donor_gain	1.0000
15:90233668:C:CT	donor_gain	1.0000
15:90233668:CA:C	donor_gain	1.0000
15:90233668:CAG:C	donor_gain	1.0000
15:90233668:CAGG:C	donor_gain	1.0000
15:90238474:T:TA	acceptor_gain	1.0000
15:90238480:A:AG	acceptor_gain	1.0000
15:90238481:T:G	acceptor_gain	1.0000
15:90238483:A:AG	acceptor_gain	1.0000
15:90238483:AACAT:A	acceptor_gain	1.0000
15:90238484:A:G	acceptor_gain	1.0000
15:90238486:A:AG	acceptor_gain	1.0000
15:90238486:AT:A	acceptor_gain	1.0000
15:90238487:T:G	acceptor_gain	1.0000
15:90233668:CAGGA:C	donor_gain	0.9900
15:90234262:A:T	donor_gain	0.9900
15:90234293:G:GG	donor_gain	0.9900
15:90234593:CGAG:C	donor_loss	0.9900
15:90234595:AG:A	donor_loss	0.9900
15:90234596:GG:G	donor_loss	0.9900
15:90234597:G:GA	donor_loss	0.9900
15:90234598:TAGGT:T	donor_loss	0.9900
15:90238485:C:G	acceptor_gain	0.9900
15:90238487:T:TA	acceptor_gain	0.9900
15:90238490:A:AG	acceptor_gain	0.9900

AlphaMissense

2475 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:90241521:T:C	F205L	0.995
15:90241523:C:A	F205L	0.995
15:90241523:C:G	F205L	0.995
15:90241527:A:C	S207R	0.995
15:90241529:C:A	S207R	0.995
15:90241529:C:G	S207R	0.995
15:90241278:T:C	F124L	0.994
15:90241280:C:A	F124L	0.994
15:90241280:C:G	F124L	0.994
15:90241772:C:A	N288K	0.994
15:90241772:C:G	N288K	0.994
15:90241284:T:C	F126L	0.993
15:90241286:C:A	F126L	0.993
15:90241286:C:G	F126L	0.993
15:90241526:C:A	N206K	0.993
15:90241526:C:G	N206K	0.993
15:90241848:T:A	W314R	0.993
15:90241848:T:C	W314R	0.993
15:90241382:C:A	N158K	0.991
15:90241382:C:G	N158K	0.991
15:90241386:A:C	S160R	0.991
15:90241388:C:A	S160R	0.991
15:90241388:C:G	S160R	0.991
15:90241494:A:C	S196R	0.990
15:90241496:C:A	S196R	0.990
15:90241496:C:G	S196R	0.990
15:90241553:C:A	N215K	0.990
15:90241553:C:G	N215K	0.990
15:90241560:C:G	H218D	0.989
15:90241564:T:C	L219P	0.988

dbSNP variants (sampled 300 via entrez): RS1000076565 (15:90233564 C>G), RS1000472786 (15:90234979 A>G), RS1000868902 (15:90234174 G>A,C,T), RS1000884319 (15:90237821 A>C), RS1000915361 (15:90238042 G>A,C), RS1001092063 (15:90243918 G>T), RS1001438790 (15:90244336 G>A), RS1001472106 (15:90232877 C>T), RS1001620729 (15:90245488 GAAAA>G,GAAAAA), RS1001837679 (15:90232646 C>T), RS1002399572 (15:90240735 C>T), RS1002462281 (15:90236054 T>C), RS1002467825 (15:90242762 T>C), RS1002535925 (15:90236319 G>A), RS1002920933 (15:90235724 C>T)

Disease associations

OMIM: gene MIM:619240 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Niclosamide	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.