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GPD2

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Summary

GPD2 (glycerol-3-phosphate dehydrogenase 2, HGNC:4456) is a protein-coding gene on chromosome 2q24.1, encoding Glycerol-3-phosphate dehydrogenase, mitochondrial (P43304). Calcium-responsive mitochondrial glycerol-3-phosphate dehydrogenase which seems to be a key component of the pancreatic beta-cell glucose-sensing device.

The protein encoded by this gene localizes to the inner mitochondrial membrane and catalyzes the conversion of glycerol-3-phosphate to dihydroxyacetone phosphate, using FAD as a cofactor. Along with GDP1, the encoded protein constitutes the glycerol phosphate shuttle, which reoxidizes NADH formed during glycolysis. Two transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 2820 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): diabetes mellitus, noninsulin-dependent (No Known Disease Relationship, GenCC)
  • GWAS associations: 18
  • Clinical variants (ClinVar): 131 total — 1 pathogenic, 1 likely-pathogenic
  • Regional missense constraint (gnomAD): 1 of 3 regions constrained (≈4% of expected missense variation)
  • GTEx eGene: eQTL in 24 tissues, sQTL in 5 (q < 0.05)
  • Phenotypes (HPO): 5
  • Drug target: yes — 1 curated mechanism-of-action drug
  • Approved drugs (ChEMBL mechanism of action): 1 — Metformin Hydrochloride
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.80 (unconstrained)
  • MANE Select transcript: NM_000408
  • Interaction hub: 1,814 STRING partners (top 9% of genes corpus-wide)
  • Notable: 131 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4456
Approved symbolGPD2
Nameglycerol-3-phosphate dehydrogenase 2
Location2q24.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000115159
Ensembl biotypeprotein_coding
OMIM138430
Entrez2820

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 18 protein_coding, 6 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000438166

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 2, TSL 3: 2, TSL 4: 3, TSL 5: 2

ENST00000438166, ENST00000310454, ENST00000409674, ENST00000409861, ENST00000415049, ENST00000416888, ENST00000430992, ENST00000464846, ENST00000492005, ENST00000495851, ENST00000496190, ENST00000540309, ENST00000893602, ENST00000893603, ENST00000893604, ENST00000893605, ENST00000893606, ENST00000893607, ENST00000893608, ENST00000893609, ENST00000893610, ENST00000893611, ENST00001003519, ENST00001063663, ENST00001110239, ENST00001114516, ENST00001118603, ENST00001138880

RefSeq mRNA: 2 — MANE Select: NM_000408 NM_000408, NM_001083112

CCDS: CCDS2202

Canonical transcript exons

ENST00000438166 — 17 exons

ExonStartEnd
ENSE00000778506156510796156510920
ENSE00001188495156582793156586403
ENSE00001581432156436379156436513
ENSE00001596519156513333156513496
ENSE00001655975156550602156550746
ENSE00001667537156512220156512317
ENSE00001669783156568825156568959
ENSE00001685130156570087156570218
ENSE00001689131156557389156557582
ENSE00001748838156569363156569538
ENSE00001768130156578889156579001
ENSE00001784164156571134156571292
ENSE00003488102156579086156579164
ENSE00003546640156496044156496215
ENSE00003554397156579690156579788
ENSE00003688248156476098156476207
ENSE00003745755156549608156549772

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 97.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.7097 / max 312.3710, expressed in 1758 samples.

Highest expression (Bgee): secondary oocyte, sperm, oocyte, esophagus squamous epithelium, buccal mucosa cell.

Genetic regulation across tissues (GTEx eQTL / sQTL)

GPD2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 24 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 29 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Testissqtl7.6e-35-1.102:156612298:C:T
Cells Cultured fibroblastseqtl7.8e-35+0.312:156437479:A:G
Nerve Tibialeqtl5.7e-24+0.322:156431846:T:C
Adipose Subcutaneouseqtl1.8e-18+0.282:156464828:C:G
Artery Tibialeqtl1.7e-16+0.232:156437479:A:G
Whole Bloodeqtl1.6e-11+0.182:156451296:A:AC
Cells Cultured fibroblastssqtl1.3e-07+1.392:156434467:T:TA
Thyroideqtl8.1e-06+0.572:156497991:C:G
Colon Transverseeqtl2.9e-05+0.102:156524067:G:A
Breast Mammary Tissueeqtl3.4e-05+0.232:156612032:C:A
Artery Coronaryeqtl4.0e-05+0.242:156431846:T:C
Brain Cerebellar Hemisphereeqtl3.2e-04-0.162:156573645:A:G
Cells EBV-transformed lymphocytessqtl1.3e-03+1.302:156434467:T:TA
Esophagus Gastroesophageal Junctioneqtl1.4e-03+0.172:156609646:G:C
Adipose Visceral Omentumeqtl1.5e-03+0.182:156442679:G:A
Heart Atrial Appendageeqtl1.5e-03+0.162:156484204:G:A
Small Intestine Terminal Ileumeqtl2.2e-03+0.162:156462379:G:A
Stomachsqtl3.0e-03+1.102:156723095:A:T
Colon Sigmoidsqtl6.3e-03+1.012:156256142:C:G
Esophagus Musculariseqtl8.5e-03+0.232:156359692:C:T

FANTOM5 promoters

10 alternative TSS:

Promoter IDTPM avgSamples expressed
2317411.06711684
231732.63901084
231751.7138988
231690.5606268
231710.4588249
231680.3789206
231700.3123149
231720.2801156
231760.2764135
231770.02273

Top tissues by expression

showing 100 of 297 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065597.66gold quality
spermCL:000001996.21gold quality
oocyteCL:000002395.25gold quality
esophagus squamous epitheliumUBERON:000692094.81gold quality
buccal mucosa cellCL:000233693.90gold quality
mucosa of sigmoid colonUBERON:000499393.51gold quality
jejunal mucosaUBERON:000039993.42gold quality
colonic mucosaUBERON:000031793.10gold quality
male germ cellCL:000001592.71gold quality
calcaneal tendonUBERON:000370192.58gold quality
gingival epitheliumUBERON:000194992.44gold quality
cortical plateUBERON:000534392.09gold quality
oral cavityUBERON:000016791.80gold quality
gingivaUBERON:000182891.63gold quality
ventricular zoneUBERON:000305391.40gold quality
ganglionic eminenceUBERON:000402391.12gold quality
epithelium of nasopharynxUBERON:000195190.94gold quality
rectumUBERON:000105290.26gold quality
mucosa of paranasal sinusUBERON:000503090.19gold quality
biceps brachiiUBERON:000150789.69gold quality
upper leg skinUBERON:000426289.33gold quality
tendonUBERON:000004389.25gold quality
palpebral conjunctivaUBERON:000181289.01gold quality
jejunumUBERON:000211588.91gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450288.69gold quality
islet of LangerhansUBERON:000000688.66gold quality
esophagus mucosaUBERON:000246988.61gold quality
epithelium of esophagusUBERON:000197688.23gold quality
tonsilUBERON:000237288.13gold quality
monocyteCL:000057687.91gold quality
entorhinal cortexUBERON:000272887.90gold quality
squamous epitheliumUBERON:000691487.71gold quality
hindlimb stylopod muscleUBERON:000425287.18gold quality
mononuclear cellCL:000084287.11gold quality
skin of hipUBERON:000155486.75gold quality
muscle of legUBERON:000138386.73gold quality
nucleus accumbensUBERON:000188286.72gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451186.70gold quality
leukocyteCL:000073886.65gold quality
endothelial cellCL:000011586.60gold quality
gastrocnemiusUBERON:000138886.50gold quality
eyeUBERON:000097086.39gold quality
bronchial epithelial cellCL:000232886.38gold quality
lower lobe of lungUBERON:000894986.28gold quality
duodenumUBERON:000211486.21gold quality
lower esophagus mucosaUBERON:003583486.18gold quality
Ammon’s hornUBERON:000195485.97gold quality
amniotic fluidUBERON:000017385.90gold quality
postcentral gyrusUBERON:000258185.85gold quality
mouth mucosaUBERON:000372985.73gold quality
endometriumUBERON:000129585.69gold quality
right uterine tubeUBERON:000130285.67gold quality
temporal lobeUBERON:000187185.63gold quality
stromal cell of endometriumCL:000225585.61gold quality
caudate nucleusUBERON:000187385.58gold quality
minor salivary glandUBERON:000183085.56gold quality
amygdalaUBERON:000187685.54gold quality
medial globus pallidusUBERON:000247785.21gold quality
saliva-secreting glandUBERON:000104485.13gold quality
visceral pleuraUBERON:000240185.06gold quality
pharyngeal mucosaUBERON:000035584.81gold quality
nasal cavity mucosaUBERON:000182684.79gold quality
superior frontal gyrusUBERON:000266184.77gold quality
germinal epithelium of ovaryUBERON:000130484.76gold quality
parietal pleuraUBERON:000240084.54gold quality
seminal vesicleUBERON:000099884.46gold quality
parietal lobeUBERON:000187284.42gold quality
putamenUBERON:000187484.20gold quality
prefrontal cortexUBERON:000045184.12gold quality
mucosa of transverse colonUBERON:000499184.07gold quality
skeletal muscle organUBERON:001489284.02gold quality
muscle organUBERON:000163084.00gold quality
pleuraUBERON:000097783.89gold quality
globus pallidusUBERON:000187583.89gold quality
olfactory segment of nasal mucosaUBERON:000538683.80gold quality
cerebellar cortexUBERON:000212983.58gold quality
colonic epitheliumUBERON:000039783.57gold quality
telencephalonUBERON:000189383.56gold quality
thoracic mammary glandUBERON:000520083.45gold quality
mammary glandUBERON:000191183.43gold quality
cerebellar hemisphereUBERON:000224583.40gold quality
trabecular bone tissueUBERON:000248383.40gold quality
gall bladderUBERON:000211083.11gold quality
skin of abdomenUBERON:000141683.03gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.97gold quality
tendon of biceps brachiiUBERON:000818882.97gold quality
bone marrowUBERON:000237182.94gold quality
dorsolateral prefrontal cortexUBERON:000983482.84gold quality
cingulate cortexUBERON:000302782.82gold quality
cerebral cortexUBERON:000095682.80gold quality
cerebellumUBERON:000203782.73gold quality
tibial nerveUBERON:000132382.72gold quality
skin of legUBERON:000151182.69gold quality
vaginaUBERON:000099682.66gold quality
mammary ductUBERON:000176582.66gold quality
anterior cingulate cortexUBERON:000983582.58gold quality
esophagusUBERON:000104382.56gold quality
forebrainUBERON:000189082.46gold quality
zone of skinUBERON:000001482.43gold quality
trigeminal ganglionUBERON:000167582.35gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-100618yes260.58
E-ANND-3yes7.01

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Spinal cordtissue102.0
Hippocampal formationtissue93.2
Midbraintissue81.3
Cerebral cortextissue80.2medium
Motor cortextissue80.2
Medulla oblongatatissue79.8
Occipital cortextissue79.3
Somatosensory cortextissue76.8
Thalamustissue76.3
Prefrontal cortextissue74.8
Entorhinal cortextissue74.8
Ponstissue74.1
Insular cortextissue71.7
Retrosplenial cortextissue71.2
Amygdalatissue70.9
Periaqueductal graytissue70.9
Temporal cortextissue70.6
Retrosplenial and cingulate cortextissue70.3
Substantia nigratissue70.2
Putamentissue68.2
Cerebellumtissue65.0high
Superior colliculitissue63.8
Corpus callosumtissue62.0
Hypothalamustissue58.3
Frontal cortextissue53.2
Ventral forebraintissue50.9
Basal gangliatissue47.1medium
Septumtissue45.0
Olfactory bulbtissue42.4
Nucleus accumbenstissue32.8
Hippocampustissue32.5high
Caudate putamentissue31.2
Postcentral gyrustissue29.8
Locus coeruleustissue26.8
Skeletal muscletissue23.1medium
Parathyroid glandtissue19.3high
Colontissue17.4high
Fallopian tubetissue17.2high
Rectumtissue16.9high
Stomach 1tissue16.5high
Esophagustissue16.1high
Breasttissue15.1high
Small intestinetissue14.8high
Salivary glandtissue14.1high
Duodenumtissue13.6high
Choroid plexustissue13.5
Urinary bladdertissue13.4high
Tonguetissue13.3
Bone marrowtissue12.6medium
Skin 1tissue11.8high
Thyroid glandtissue11.5medium
Lungtissue10.8high
Prostatetissue10.3high
Cervixtissue9.6high
Vaginatissue9.1high
Retinatissue8.8
Gallbladdertissue8.4high
Tonsiltissue8.1high
Spleentissue8.0medium
Adipose tissuetissue7.7medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Ventral spinal cord (102.0), Dorsal hippocampus (93.2), Subiculum (80.2), Ventral hippocampus (79.6), Dorsal spinal cord (74.1).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXO1

miRNA regulators (miRDB)

Targeting GPD2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 220 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-3134100.0066.43777
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-340-5P100.0072.504437
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548N99.9871.944170
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-548P99.9872.253784
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AN99.9770.912817
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-568899.9673.234504
HSA-MIR-493-5P99.9672.472382
HSA-MIR-495-3P99.9672.814197

Functional genomics

gnomAD constraint: pLI 0.000127, LOEUF 0.796, missense Z 1.99 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000438166 splits into 3 regions with different missense tolerance; 1 is missense-constrained (≈4% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
2:156,476,106–156,579,697692 / 809.70.85no
2:156,579,698–156,582,80010 / 37.40.27yes (p 7.5e-06)
2:156,582,801–156,582,91546 / 49.10.94no

Literature-anchored findings (GeneRIF, showing 11)

  • testis-specific promoter of mitochondrial GPDH (PMID:15456763)
  • Overall, these data demonstrate that mGPDH is involved in maintaining a high rate of glycolysis and is an important site of electron leakage leading to ROS production in prostate cancer cells. (PMID:15967408)
  • the up-regulation of mGPDH, due to a highly glycolytic environment, contributes to the overall increase in ROS generation and may result in the progression of prostate cancer (PMID:17886033)
  • We report 3 additional patients with a de novo deletion encompassing NR4A2: 2 patients have deletions encompassing only NR4A2 gene and 1 patient has a deletion including NR4A2 and the first exon of GPD2 (PMID:29770430)
  • Here, the authors identify mGPDH as a critical regulator of skeletal muscle regeneration. Specifically, it regulates myogenic markers and myoblast differentiation by controlling mitochondrial biogenesis via CaMKKbeta/AMPK. (PMID:30389681)
  • mRNA and protein levels reduced in livers of patients with nonalcoholic fatty liver disease (PMID:30653687)
  • Deficiency of Mitochondrial Glycerol 3-Phosphate Dehydrogenase Exacerbates Podocyte Injury and the Progression of Diabetic Kidney Disease. (PMID:33741719)
  • mGPDH Deficiency leads to melanoma metastasis via induced NRF2. (PMID:33939274)
  • A ferroptosis defense mechanism mediated by glycerol-3-phosphate dehydrogenase 2 in mitochondria. (PMID:35749365)
  • GPD2: The relationship with cancer and neural stemness. (PMID:36592694)
  • Glycerol 3-phosphate dehydrogenases (1 and 2) in cancer and other diseases. (PMID:38689091)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriogpd2ENSDARG00000062430
mus_musculusGpd2ENSMUSG00000026827
rattus_norvegicusGpd2ENSRNOG00000033824
drosophila_melanogasterGpo1FBGN0022160
drosophila_melanogasterGpo2FBGN0033190
caenorhabditis_elegansgpdh-3WBGENE00012031

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:99778) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 23 distinct phenotype terms.

Mouse phenotype (MP)Records
decreased body weight3
decreased body size1
abnormal eating behavior1
decreased white adipose tissue amount1
reduced fertility1
decreased litter size1
decreased circulating insulin level1
decreased insulin secretion1
increased circulating cholesterol level1
decreased oxygen consumption1
abnormal triiodothyronine level1
increased circulating thyroxine level1
increased circulating triiodothyronine level1
increased body temperature1
decreased body mass index1
decreased brown fat cell lipid droplet size1
decreased epididymal fat pad weight1
decreased parametrial fat pad weight1
decreased susceptibility to weight gain1
impaired adaptive thermogenesis1
postnatal lethality, incomplete penetrance1
prenatal lethality, incomplete penetrance1
decreased brown adipose tissue mass1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Streptococcus pyogenes MGAS315P0DB20100.0%Diamond
Streptococcus pyogenes SSI-1P0DB21100.0%Diamond
Mycobacterium tuberculosis variant bovis AF2122/97P64183100.0%Diamond
Mycobacterium tuberculosis CDC1551P9WN78100.0%Diamond
Mycobacterium tuberculosis H37RvP9WN79100.0%Diamond
Staphylococcus aureus subsp. aureus USA300Q2FHD8100.0%Diamond
Staphylococcus aureus subsp. aureus NCTC 8325Q2FYZ4100.0%Diamond
Staphylococcus aureus subsp. aureus COLQ5HGD1100.0%Diamond
Staphylococcus epidermidis RP62AQ5HPP0100.0%Diamond
Staphylococcus aureus subsp. aureus MSSA476Q6G9R2100.0%Diamond
Staphylococcus aureus subsp. aureus MW2Q7A105100.0%Diamond
Staphylococcus aureus subsp. aureus N315Q7A5V7100.0%Diamond
Staphylococcus epidermidis ATCC 12228Q8CPE6100.0%Diamond
Staphylococcus aureus subsp. aureus Mu50Q99UH2100.0%Diamond
Staphylococcus aureus RF122Q2YXR599.8%Diamond
Staphylococcus aureus subsp. aureus MRSA252Q6GHD499.8%Diamond
Streptococcus pyogenes serotype M1Q99YI899.5%Diamond
Streptococcus pyogenes MGAS8232Q8NZX099.2%Diamond
Macaca fascicularisQ4R75599.0%Diamond
Bos taurusA6QLU197.1%Diamond
Streptococcus pyogenes MGAS10394Q5XAK095.1%Diamond
Mesocricetus auratusA7DZP892.6%Diamond
Mycobacterium leprae TNP5343590.9%Diamond
Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292Q49X9481.1%Diamond
Staphylococcus haemolyticus JCSC1435Q4L60880.1%Diamond
Streptococcus pneumoniae TIGR4P3559675.8%Diamond
Bacillus subtilis subsp. subtilis str. 168P1815861.8%Diamond
Enterococcus casseliflavusO8696361.4%Diamond
Escherichia coli K-12P1303561.1%Diamond
Lactococcus lactis subsp. lactis Il1403Q9CG6559.9%Diamond
Schizosaccharomyces pombe 972h-O1440054.7%Diamond
Saccharomyces cerevisiae S288CP3219154.7%Diamond
Brucella abortus 2308Q2YIQ252.0%Diamond
Arabidopsis thalianaQ9SS4852.0%Diamond
Dictyostelium discoideumQ54QC149.4%Diamond
Encephalitozoon cuniculi GB-M1Q8SR4042.8%Diamond
Schistosoma mansoniQ0716742.4%Diamond
Synechocystis sp. PCC 6803 substr. KazusaP7425738.3%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
TRG-GCC2-2tRNA100189208
FLJ46875ncRNA440918
TRA-CGC3-1tRNA100189021
LINC01958ncRNA105373708
LINC03176ncRNA124907897
NR4A2protein-coding4929
LINC01876ncRNA101929378

Protein

Protein identifiers

Glycerol-3-phosphate dehydrogenase, mitochondrial — P43304 (reviewed: P43304)

Alternative names: mitochondrial glycerophosphate dehydrogenase gene, mtGPD

All UniProt accessions (4): E7EM56, E9PDK4, F5GYK7, P43304

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-responsive mitochondrial glycerol-3-phosphate dehydrogenase which seems to be a key component of the pancreatic beta-cell glucose-sensing device.

Subcellular location. Mitochondrion.

Activity regulation. Calcium-binding enhance the activity of the enzyme.

Pathway. Polyol metabolism; glycerol degradation via glycerol kinase pathway; glycerone phosphate from sn-glycerol 3-phosphate (anaerobic route): step 1/1.

Similarity. Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family.

Isoforms (2)

UniProt IDNamesCanonical?
P43304-11yes
P43304-22

RefSeq proteins (2): NP_000399, NP_001076581 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000447G3P_DH_FAD-depFamily
IPR002048EF_hand_domDomain
IPR006076FAD-dep_OxRdtaseDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR031656DAO_CDomain
IPR036188FAD/NAD-bd_sfHomologous_superfamily
IPR038299DAO_C_sfHomologous_superfamily

Pfam: PF01266, PF13499, PF16901

Enzyme classification (BRENDA)

  • EC 1.1.5.3 — glycerol-3-phosphate dehydrogenase (BRENDA: 17 organisms, 47 substrates, 82 inhibitors, 25 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

12 substrates with measured Km, best-characterized 12. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
GLYCEROL 3-PHOSPHATE0.1–3.25
SN-GLYCEROL 3-PHOSPHATE3.7–104
DL-GLYCEROL 3-PHOSPHATE0.8–10.23
2,6-DICHLOROPHENOLINDOPHENOL0.076–0.1252
COENZYME Q10.013–0.0522
COENZYME Q00.1251
COENZYME Q100.051
COENZYME Q20.0231
COENZYME Q60.111
DL-ALPHA-GLYCEROPHOSPHATE5.171
FERRICYANIDE0.551
PHENAZINE METHOSULFATE0.131

Catalyzed reactions (Rhea)

  • a quinone + sn-glycerol 3-phosphate = dihydroxyacetone phosphate + a quinol (RHEA:18977)

UniProt features (18 total): sequence variant 6, binding site 6, domain 2, transit peptide 1, chain 1, modified residue 1, splice variant 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P43304-F186.470.60

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Oxidoreductases, Metabolic proteins, Predicted intracellular proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): mitochondria

Antibody reliability (HPA): IH enhanced · IF supported

Functional residue map

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

Ligand- & substrate-binding residues (6)

PositionRole
71–99FAD
672Ca(2+)
674Ca(2+)
676Ca(2+)
678Ca(2+)
683Ca(2+)

Post-translational modifications (1)

TypePositions
Phosphotyrosine601

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 7; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

7 pathways:

IDPathwayEvidence
R-HSA-1483166Synthesis of PAcurated
R-HSA-163560Triglyceride catabolismcurated
R-HSA-1483206Glycerophospholipid biosynthesis—
R-HSA-1430728Metabolism—
R-HSA-556833Metabolism of lipids—
R-HSA-1483257Phospholipid metabolism—
R-HSA-8979227Triglyceride metabolism—

MSigDB gene sets: 339 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, REACTOME_TRIGLYCERIDE_CATABOLISM, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_POLYOL_METABOLIC_PROCESS, GOBP_GROWTH, GOBP_POLYOL_CATABOLIC_PROCESS, KYNG_DNA_DAMAGE_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, BROWNE_HCMV_INFECTION_12HR_UP, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NADPLUS_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, MODULE_205

GO Biological Process (3): glycerol-3-phosphate metabolic process (GO:0006072), glycerol-3-phosphate shuttle (GO:0006127), glycerol catabolic process (GO:0019563)

GO Molecular Function (4): glycerol-3-phosphate dehydrogenase (quinone) activity (GO:0004368), calcium ion binding (GO:0005509), oxidoreductase activity (GO:0016491), metal ion binding (GO:0046872)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743)

Reactome top-level categories

5 top-level categories:

CategoryPathways
Metabolism of lipids2
Glycerophospholipid biosynthesis1
Triglyceride metabolism1
Phospholipid metabolism1
Metabolism1

GO top-level categories

14 GO namespaces:

CategoryTerms
alditol phosphate metabolic process1
glycerol-3-phosphate dehydrogenase (quinone) activity1
NAD+ metabolic process1
glycerol-3-phosphate dehydrogenase (NAD+) activity1
glycerol metabolic process1
alditol catabolic process1
oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor1
metal ion binding1
catalytic activity1
cation binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO termNSEvidence
mitochondrionCCdirect assay
glycerol-3-phosphate dehydrogenase (quinone) activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 1,814 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPD2GPD1P21695960
GPD2GK2Q14410802
GPD2GKP32189794
GPD2NFYCQ13952744
GPD2NFYBP25208741
GPD2PCP11498738
GPD2NDE1Q9NXR1662
GPD2POLR2BP30876640
GPD2NDEL1Q9GZM8639
GPD2GAPDHP00354501
GPD2SLC2A2P11168500
GPD2GABPAQ06546491
GPD2KCNJ15Q99712487
GPD2MICOS10Q5TGZ0480
GPD2CAPN10Q9HC96463

IntAct

Human interaction partners of GPD2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

7 partners by confidence:

PartnerInteraction typeMIscoreRecords
PLEKHG7association0.3501
SFXN1association0.3501
SFXN3association0.3501
SLC8A3association0.3501
TRAPPC10association0.3501
TSPAN2association0.3501
TTC19association0.3501

BioGRID (163 interactions; top human partners by supporting records): SLC39A4 (Affinity Capture-MS; 4 records), HAX1 (Affinity Capture-MS; 3 records), SLC39A8 (Affinity Capture-MS; 3 records), SLC8A3 (Affinity Capture-MS; 3 records), TRAPPC10 (Affinity Capture-MS; 3 records), WDFY2 (Affinity Capture-MS; 3 records), C12orf74 (Affinity Capture-MS; 2 records), GDPD5 (Affinity Capture-MS; 2 records), NUFIP1 (Affinity Capture-MS; 2 records), PARK2 (Affinity Capture-MS; 2 records), PHB (Cross-Linking-MS (XL-MS); 2 records), PVR (Affinity Capture-MS; 2 records), SFXN1 (Proximity Label-MS; 2 records), SLC25A51 (Proximity Label-MS; 2 records), ACO2 (Co-fractionation)

Disease & clinical

Genetic variants

Variant evidence for GPD2: 131 ClinVar records (2 pathogenic / likely pathogenic); 18 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance95
Likely benign8
Benign1

Top pathogenic / likely-pathogenic (2)

Showing all 2 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
1807710GRCh37/hg19 2q24.1(chr2:156996368-157372032)x1Likely pathogeniccriteria provided, single submitter1
16081NM_000408.5(GPD2):c.1904T>C (p.Phe635Ser)Pathogenicno assertion criteria provided1

Per-variant reference — Sugi Variant

Explore GPD2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 39 predictions of 1,646):

Position(s)EffectΔscoreSites
2:156436514–156436515donor_loss1.00003
2:156476085acceptor_gain1.0000
2:156476096–156476097acceptor_loss1.00006
2:156476208–156476209donor_loss1.00005
2:156510785acceptor_gain1.0000
2:156510793acceptor_gain1.0000
2:156510794–156510795acceptor_loss1.00005
2:156510921–156510922donor_loss1.00005
2:156512218–156512219acceptor_loss1.00006
2:156550600–156550601acceptor_loss1.00006

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

CancerPrognosticp-value
Kidney Renal Clear Cell Carcinoma (TCGA)favorable3.02e-06
Liver Hepatocellular Carcinoma (TCGA)unfavorable0.000294
Lung Adenocarcinoma (TCGA)unfavorable0.000805

Disease associations

OMIM: gene MIM:138430 | disease phenotypes: MIM:125853

GenCC curated gene-disease

1 curated gene-disease records:

DiseaseClassificationInheritanceRecords
diabetes mellitus, noninsulin-dependentNo Known Disease RelationshipAutosomal dominant

Mondo (2): type 2 diabetes mellitus (MONDO:0005148), (MONDO:0007455)

HPO phenotypes

5 phenotypes (HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000855Insulin resistance
HP:0003584Late onset
HP:0005978Type II diabetes mellitus
HP:0031819Increased waist to hip ratio

GWAS associations

18 associations:

StudyTraitp-value
GCST010002_401Refractive error1e-35
GCST002759_2Motion sickness2e-29
GCST006291_95Spherical equivalent or myopia (age of diagnosis)5e-15
GCST003997_10Myopia6e-13
GCST005316_115Intelligence (MTAG)8e-13
GCST005316_116Intelligence (MTAG)7e-10
GCST005141_68Cognitive ability (MTAG)1e-9
GCST005142_48Cognitive ability4e-9
GCST009640_20Urinary albumin-to-creatinine ratio1e-8
GCST005839_7Depression2e-8
GCST005316_117Intelligence (MTAG)3e-8
GCST005316_184Intelligence (MTAG)4e-8
GCST006269_645General cognitive ability4e-8
GCST002875_95Diisocyanate-induced asthma1e-6
GCST003963_3Possible neuropathic pain in post total joint replacement surgery for osteoarthritis3e-6
GCST006088_22Familial squamous cell lung carcinoma3e-6
GCST002548_3Ulcerative colitis6e-6
GCST000635_3Response to statin therapy9e-6

EFO canonical traits (from GWAS)

8 canonical traits:

EFO IDTrait name
EFO:0006928motion sickness
EFO:0006995response to diisocyanate
EFO:0005762neuropathic pain
EFO:0004337intelligence
EFO:0004784self reported educational attainment
EFO:0006953family history of lung cancer
EFO:0004847age at onset
EFO:0007778urinary albumin to creatinine ratio

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
D003924Diabetes Mellitus, Type 2C18.452.394.750.149; C19.246.300

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3391681 (SINGLE PROTEIN)

Drugs by curated mechanism of action (ChEMBL)

Drugs whose curated ChEMBL mechanism of action targets the GPD2 protein itself — single-protein targets only (drugs acting on a protein family or complex that merely includes it are excluded). Includes antibodies and oligonucleotides that bioactivity screening does not capture.

1 curated-mechanism drugs:

DrugModalityMax phase
METFORMIN HYDROCHLORIDESmall molecule4

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

47 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, increases methylation6
sodium arsenitedecreases expression, increases expression2
Benzo(a)pyreneaffects methylation, increases expression2
Aflatoxin B1affects expression, decreases methylation2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
pyrogallol 1,3-dimethyl etheraffects cotreatment, increases expression1
trichostatin Aaffects expression1
beta-lapachonedecreases expression1
cobaltous chloridedecreases expression1
perfluorooctane sulfonic aciddecreases expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression, increases expression1
bisphenol Sincreases expression1
LDN 193189affects cotreatment, increases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenic Trioxideincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Troglitazoneincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arbutinincreases expression1
Arsenicaffects methylation1
Clozapinedecreases expression1
Coaldecreases expression, increases abundance1
Coumestrolincreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E1FGAbcam A-431 GPD2 KOCancer cell lineFemale
CVCL_E1YDHAP1 GPD2 (-) 2Cancer cell lineMale
CVCL_E1YEHAP1 GPD2 (-) 3Cancer cell lineMale
CVCL_XP32HAP1 GPD2 (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 300 trials:

NCTPhaseStatusTitle
NCT00006163Phase 4COMPLETEDComputer-assisted Diabetes Self-management Interventions
NCT00036504Phase 4COMPLETEDEfficacy and Safety of Twice-Daily Insulin Lispro Low Mixture Compared to a Once-Daily Long Acting Insulin Comparator in Patients Who Have Been Using One or More Oral Antihyperglycemic Agents Without Insulin
NCT00044460Phase 4COMPLETEDEfficacy and Safety In Poorly Controlled Type 2 Diabetics
NCT00095446Phase 4COMPLETEDNovoLog Observation Trial in Subjects With Type 1 and Type 2 Diabetes
NCT00101751Phase 4COMPLETEDINITIATE Plus (INITiation of Insulin to Reach A1c TargEt) Study
NCT00110370Phase 4COMPLETEDComparing Pre-Mixed Insulin With Insulin Glargine Combined With Rapid-Acting Insulin in Patients With Type 2 Diabetes
NCT00110448Phase 4COMPLETEDJapanese Primary Prevention of Atherosclerosis With Aspirin for Diabetes (JPAD) Trial
NCT00118950Phase 4COMPLETEDEffect of Metformin Versus Repaglinide Treatment in Non-Obese Type 2 Diabetic Patients Uncontrolled by Diet
NCT00118963Phase 4COMPLETEDEffect of Repaglinide Versus Metformin Treatment in Non-Obese Patients With Type-2-Diabetes
NCT00121966Phase 4COMPLETEDSouth Danish Diabetes Study: Evaluation of the Antidiabetic Treatment of Type 2 Diabetes Mellitus
NCT00123604Phase 4COMPLETEDVascular Effects of Carvedilol Versus Metoprolol in Hypertensive Patients With Type 2 Diabetes
NCT00123643Phase 4COMPLETEDVascular Effects of Rosiglitazone Versus Glyburide in Type 2 Diabetic Patients
NCT00124397Phase 4COMPLETEDAtorvastatin and Endothelial Function in Type 2 Diabetes Mellitus (ATTEND-Study)
NCT00129233Phase 4COMPLETEDComparison of Valsartan With Amlodipine in Hypertensive Patients With Glucose Intolerance
NCT00133718Phase 4COMPLETEDA 2 Year Trial of Patients With Type 2 Diabetes Focusing on Cardiovascular Diagnostics and Metabolic Control
NCT00135070Phase 4TERMINATEDHospital In-Patient Insulin Study
NCT00141232Phase 4COMPLETEDEvaluating Atorvastatin With Omega-3 Fatty Acids in Cardiovascular Risk Reduction in Patients With Type 2 Diabetes
NCT00144144Phase 4UNKNOWNA Study on Ca Blocker Versus AII Antagonists in Hypertension With Type 2 Diabetes
NCT00149331Phase 4COMPLETEDThe Effects of Two Education Strategies About Insulin on Patient Preferences and Perceptions About Insulin Therapy
NCT00162357Phase 4COMPLETEDPost-PCI:Cardiac Imaging in Patients With Diabetes to Detect Coronary Artery Blockages Previously Opened by Angioplasty
NCT00174681Phase 4COMPLETEDTulip Study: Testing the Usefulness of Lantus When Initiated Prematurely In Patients With Type 2 Diabetes
NCT00174824Phase 4COMPLETEDComparison of Insulin Glargine and NPH Human Insulin in Progression of Diabetic Retinopathy in Type 2 Diabetic Patients
NCT00177398Phase 4COMPLETEDEffect of Glargine Insulin on Glucose Control in Hospitalized Patients Who Receive Tube Feedings
NCT00179400Phase 4COMPLETEDThe Role of Acute Combined PPAR Alpha and Gamma Stimulation on Insulin Action in Humans
NCT00184561Phase 4COMPLETEDEffectiveness and Safety of Biphasic Insulin Aspart 70/30 in Subjects With Type 2 Diabetes
NCT00184626Phase 4COMPLETEDComparison of Insulin Glargine Versus Biphasic Insulin Aspart 30/70 or Biphasic Insulin Aspart 30/70 in Combination With Metformin in Subjects With Type 2 Diabetes.
NCT00191178Phase 4COMPLETEDEffects of Insulin in Perceived Mood Symptoms in Patients With Type 2 Diabetes
NCT00191282Phase 4COMPLETEDHyperglycemia and Cardiovascular Outcomes With Type 2 Diabetes
NCT00191464Phase 4COMPLETEDLong-Term Effects of Insulin Plus Metformin Regimens on the Overall and Postprandial Glycemic Control of Patients With Type 2 Diabetes
NCT00192803Phase 4UNKNOWNNon-Insulin Dependent Diabetes Mellitus (NIDDM) and Angiotensin Converting Enzyme 2 (ACE2): Diabetic Patients Treated With Antihypertensive Drugs
NCT00202033Phase 4COMPLETEDImpact of Self-Monitoring Blood Glucose Frequency on Glycemic Control in Patients With Type 2 Diabetes
NCT00205660Phase 4COMPLETEDChanges in Adiposity, Metabolic Measures From Atypicals to Aripiprazole
NCT00212290Phase 4COMPLETEDInsulin Resistance and Central Nervous System (CNS) Function in Type 2 Diabetes
NCT00212303Phase 4COMPLETEDExercise Training in Type 2 Diabetes and Hypertension
NCT00225342Phase 4WITHDRAWNStudy Protocol for Rosiglitazone Versus Gliclazide in Diabetics With Angina
NCT00238472Phase 4COMPLETEDA Pilot Study to Evaluate the Effects of Nateglinide vs. Glibenclamide on Renal Hemodynamics and Albumin Excretion
NCT00239538Phase 4COMPLETEDSMOOTH - Blood Pressure Control in Diabetic/Obese Patients
NCT00240253Phase 4COMPLETEDA Study Evaluating the Efficacy and Safety of Adding Symlin® to Lantus® (Insulin Glargine) in Subjects With Type 2 Diabetes
NCT00240422Phase 4COMPLETEDTrial to Compare the Effects of Either Telmisartan (40-80 mg PO Once Daily) or Ramipril (5-10 mg PO Once Daily) on Renal Endothelial Dysfunction in Hypertensive Patients With Type 2 Diabetes
NCT00241085Phase 4COMPLETEDEffect of Valsartan on Proteinuria in Patients With Hypertension and Diabetes Mellitus
NCT00241605Phase 4COMPLETEDAVANDAMET Versus Metformin For Type 2 Diabetes Mellitus
NCT00254085Phase 4UNKNOWNSubstitution of First Phase Insulin Response in Patient With Type 2 Diabetes.
NCT00258804Phase 4COMPLETEDInsulin Glargine During and After the Period of Fasting in Ramadan
NCT00262548Phase 4COMPLETEDC-Reactive Protein (CRP) in Obese Diabetic Women
NCT00264589Phase 4COMPLETEDExercise Training and Cardiovascular Function in Obesity and in Type 2 Diabetes
NCT00264901Phase 4COMPLETEDComparison of Self Adjustment Versus Standard of Care Treatment in Subjects With Type 2 Diabetes
NCT00265746Phase 4WITHDRAWNPrevention of Diabetes Mellitus Development in Women Who Had Already Experienced A Gestational Diabetes
NCT00268645Phase 4COMPLETEDInsulin Glargine in Type 2 Diabetes
NCT00272077Phase 4COMPLETEDInsulin Glargine in Type 2 Diabetes Mellitus
NCT00272831Phase 4COMPLETEDThe Use of Cilostazol in Patients With Diabetic Nephropathy
NCT00274274Phase 4COMPLETEDEfficacy and Safety of a Fixed or a Flexible Supplementary Insulin Therapy in Type 2 Diabetes
NCT00279201Phase 4COMPLETEDThe DURABLE Trial: Evaluating the Durability of Starter Insulin Regimens in Patients With Type 2 Diabetes (IOOV)
NCT00282360Phase 4COMPLETEDEffect of Metabolic Therapy in Patients With Chronic Ischemic Heart Disease
NCT00282451Phase 4COMPLETEDEffect of Biphasic Insulin Compared to Biphasic Insulin Combined With Insulin Aspart, With or Without Metformin in Type 2 Diabetes
NCT00283049Phase 4TERMINATEDInsulin Glargine Injection Treatment in Place of Thiazolidinedione (TZD), Sulfonylurea, or Metformin in Triple Agent Therapy for Type 2 Diabetes Mellitus (T2DM) Adult Subjects With Unsatisfactory Control
NCT00283777Phase 4COMPLETEDChromium and Insulin Action
NCT00290394Phase 4COMPLETEDAmbulatory Blood Pressure Reduction After Rosiglitazone Treatment In Normotensive Type 2 Diabetic Patients
NCT00296296Phase 4COMPLETEDImmunosuppression Impact on the Metabolic Control of Kidney Transplant With Pre-Existing Type 2 Diabetes (DM)
NCT00300911Phase 4COMPLETEDEffects of Rosiglitazone on Plasma BNP Levels and Left Ventricular Dysfunction
NCT00306176Phase 4COMPLETEDRosiglitazone and Exercise in Patients With Type 2 Diabetes Mellitus