MPPED2

gene
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Also known as 239FBD11S302EHs.46638FAM1BdJ873F21.1dJ1024C24.1

Summary

MPPED2 (metallophosphoesterase domain containing 2, HGNC:1180) is a protein-coding gene on chromosome 11p14.1, encoding Metallophosphoesterase MPPED2 (Q15777). Displays low metallophosphoesterase activity (in vitro).

Predicted to enable manganese ion binding activity; phosphoric diester hydrolase activity; and purine ribonucleotide binding activity.

Source: NCBI Gene 744 — RefSeq curated summary.

At a glance

  • GWAS associations: 40
  • Clinical variants (ClinVar): 25 total
  • MANE Select transcript: NM_001584

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1180
Approved symbolMPPED2
Namemetallophosphoesterase domain containing 2
Location11p14.1
Locus typegene with protein product
StatusApproved
Aliases239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1
Ensembl geneENSG00000066382
Ensembl biotypeprotein_coding
OMIM600911
Entrez744

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000358117, ENST00000448418, ENST00000524636, ENST00000524667, ENST00000525519, ENST00000526437, ENST00000528686, ENST00000529220, ENST00000904183, ENST00000904184, ENST00000904185, ENST00000904186, ENST00000904187, ENST00000943646, ENST00000943647

RefSeq mRNA: 7 — MANE Select: NM_001584 NM_001145399, NM_001377952, NM_001377953, NM_001377954, NM_001377955, NM_001377956, NM_001584

CCDS: CCDS44560, CCDS7870

Canonical transcript exons

ENST00000358117 — 7 exons

ExonStartEnd
ENSE000007082113053599430536175
ENSE000014217703041022430411586
ENSE000017633483058024630580494
ENSE000035074883041751830417633
ENSE000035225243041422830414341
ENSE000036174363049529630495521
ENSE000039117713058604230586353

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 99.09.

FANTOM5 (CAGE): breadth broad, TPM avg 4.1439 / max 159.0528, expressed in 668 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
1191152.3939610
1191130.6204339
1191160.3665167
1191170.245999
1191140.1941120
1191180.114353
1191120.098034
1191110.066318
1191190.044522

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305399.09gold quality
ganglionic eminenceUBERON:000402398.78gold quality
cortical plateUBERON:000534396.48gold quality
buccal mucosa cellCL:000233693.86gold quality
thyroid glandUBERON:000204692.95gold quality
left lobe of thyroid glandUBERON:000112092.56gold quality
right lobe of thyroid glandUBERON:000111992.20gold quality
parotid glandUBERON:000183192.10gold quality
right uterine tubeUBERON:000130291.82gold quality
tibiaUBERON:000097988.15gold quality
adrenal tissueUBERON:001830387.65gold quality
nucleus accumbensUBERON:000188287.12gold quality
prostate glandUBERON:000236786.39gold quality
pigmented layer of retinaUBERON:000178286.29gold quality
embryoUBERON:000092285.82gold quality
ponsUBERON:000098885.38gold quality
endothelial cellCL:000011585.31gold quality
pituitary glandUBERON:000000785.16gold quality
caudate nucleusUBERON:000187385.05gold quality
putamenUBERON:000187485.03gold quality
descending thoracic aortaUBERON:000234584.44gold quality
prefrontal cortexUBERON:000045184.41gold quality
seminal vesicleUBERON:000099884.32gold quality
adenohypophysisUBERON:000219684.07gold quality
renal medullaUBERON:000036284.04gold quality
ascending aortaUBERON:000149683.94gold quality
thoracic aortaUBERON:000151583.93gold quality
dorsolateral prefrontal cortexUBERON:000983481.99gold quality
Brodmann (1909) area 9UBERON:001354081.42gold quality
telencephalonUBERON:000189381.05gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-CURD-119yes44.45
E-HCAD-5yes22.34
E-MTAB-7316yes21.00
E-ANND-3yes6.31
E-GEOD-100618no182.73

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, ESR1, EWSR1, NR3C2, PAX5, TP53, ZBTB7B

miRNA regulators (miRDB)

92 targeting MPPED2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5692A100.0074.406850
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-480399.9871.993117
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-9-3P99.9670.882068
HSA-MIR-570-3P99.9672.414910
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-552-5P99.9368.561583
HSA-MIR-338-5P99.9272.342951
HSA-MIR-10523-5P99.9169.222038

Literature-anchored findings (GeneRIF, showing 6)

  • The structures of MPPED2 and two mutants show that the poor activity of MPPED2 is not only a consequence of the substitution of an active-site histidine residue by glycine but also due to binding of AMP or GMP to the active site. (PMID:21824479)
  • The overexpression of Mpped2 improves survival rate, substantially impairs tumor growth and induces neuronal differentiation. (PMID:22262177)
  • Findings indicate that epigenetic alterations of MPPED2 promoter region appear sequentially during the colorectal neoplastic progression. (PMID:30846004)
  • CTN2 (rs6655267) and MPPED2 (rs536007) are not associated with primary dentition caries. MPPED2 (rs11031093, G Allele) is marginally associated. (PMID:32040219)
  • MPPED2 is downregulated in glioblastoma, and its restoration inhibits proliferation and increases the sensitivity to temozolomide of glioblastoma cells. (PMID:33734003)
  • Association of MPPED2 gene variant rs10767873 with kidney function and risk of cardiovascular disease in patients with hypertension. (PMID:36797372)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriompped2aENSDARG00000006889
danio_reriompped2ENSDARG00000034443
mus_musculusMpped2ENSMUSG00000016386
rattus_norvegicusMpped2ENSRNOG00000004863
drosophila_melanogasterCG16717FBGN0036028
caenorhabditis_elegansWBGENE00011579
caenorhabditis_elegansWBGENE00016101
caenorhabditis_elegansWBGENE00019479

Paralogs (1): MPPED1 (ENSG00000186732)

Protein

Protein identifiers

Metallophosphoesterase MPPED2Q15777 (reviewed: Q15777)

Alternative names: Fetal brain protein 239, Metallophosphoesterase domain-containing protein 2

All UniProt accessions (3): Q15777, E9PQW8, F2Z346

UniProt curated annotations — full annotation on UniProt →

Function. Displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous system.

Subunit / interactions. Homodimer.

Tissue specificity. Expressed predominantly in fetal brain.

Activity regulation. Inhibited by nmolar levels of AMP and GMP.

Similarity. Belongs to the UPF0046 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q15777-11yes
Q15777-22

RefSeq proteins (7): NP_001138871, NP_001364881, NP_001364882, NP_001364883, NP_001364884, NP_001364885, NP_001575* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004843Calcineurin-like_PHPDomain
IPR024201Calcineurin-like_PesteraseFamily
IPR029052Metallo-depent_PP-likeHomologous_superfamily
IPR051693UPF0046_metallophosphoestFamily

Pfam: PF00149

UniProt features (13 total): binding site 10, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q15777-F195.430.92

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 (10): 65; 254; 67; 86; 86; 117–118; 117; 213; 225–226; 252–255

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 208 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, LEE_NEURAL_CREST_STEM_CELL_DN, YAATNRNNNYNATT_UNKNOWN, GCANCTGNY_MYOD_Q6, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOZGIT_ESR1_TARGETS_DN, TGACCTY_ERR1_Q2, AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, AGTCTTA_MIR499, CEBP_Q2, MORF_ZNF10, SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN

GO Biological Process (0):

GO Molecular Function (8): phosphoric diester hydrolase activity (GO:0008081), AMP binding (GO:0016208), GMP binding (GO:0019002), manganese ion binding (GO:0030145), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anion binding2
cation binding2
phosphoric ester hydrolase activity1
adenyl ribonucleotide binding1
guanyl ribonucleotide binding1
transition metal ion binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
catalytic activity1

Protein interactions and networks

STRING

680 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MPPED2DCDC1P59894905
MPPED2DNAJC24Q6P3W2888
MPPED2IMMP1LQ96LU5872
MPPED2ELP4Q96EB1855
MPPED2FSHBP01225707
MPPED2PAX6P26367699
MPPED2KRT12Q99456497
MPPED2D6RI10D6RI10454
MPPED2TBC1D30Q9Y2I9429
MPPED2EDARADDQ8WWZ3417
MPPED2ARL14EPQ8N8R7397
MPPED2WT1P19544372
MPPED2CCDC187A0A096LP49371
MPPED2AJAP1Q9UKB5370
MPPED2GPR149Q86SP6367

IntAct

55 interactions, top by confidence:

ABTypeScore
MPPED2TRIP13psi-mi:“MI:0915”(physical association)0.790
TRIP13MPPED2psi-mi:“MI:0915”(physical association)0.790
NCKAP1YWHAHpsi-mi:“MI:0914”(association)0.730
RXRGMPPED2psi-mi:“MI:0915”(physical association)0.720
VAC14MPPED2psi-mi:“MI:0915”(physical association)0.720
MPPED2RXRGpsi-mi:“MI:0915”(physical association)0.720
FAM72AMPPED2psi-mi:“MI:0915”(physical association)0.560
MPPED2CAGE1psi-mi:“MI:0915”(physical association)0.560
CAGE1MPPED2psi-mi:“MI:0915”(physical association)0.560
MPPED2FAM72Apsi-mi:“MI:0915”(physical association)0.560
MPPED2HOOK2psi-mi:“MI:0915”(physical association)0.560
MPPED2NUP93psi-mi:“MI:0915”(physical association)0.560
MPPED2RIBC1psi-mi:“MI:0915”(physical association)0.560
MPPED2POMPpsi-mi:“MI:0915”(physical association)0.560
MPPED2MBD3L1psi-mi:“MI:0915”(physical association)0.560
MPPED2BEX4psi-mi:“MI:0915”(physical association)0.560
MPPED2NR2F6psi-mi:“MI:0914”(association)0.530
MPPED2IKZF1psi-mi:“MI:0915”(physical association)0.370

BioGRID (31): RXRG (Two-hybrid), TRIP13 (Two-hybrid), VAC14 (Two-hybrid), CAGE1 (Two-hybrid), FAM72A (Two-hybrid), MPPED2 (Reconstituted Complex), NR2F6 (Affinity Capture-MS), MPPED2 (Affinity Capture-MS), MPPED2 (Two-hybrid), TRIP13 (Two-hybrid), NR2F6 (Affinity Capture-MS), SULT1A3 (Affinity Capture-MS), TRIP13 (Two-hybrid), HOOK2 (Two-hybrid), BEX4 (Two-hybrid)

ESM2 similar proteins: A0A067XMV3, A0A179HLJ8, A0A1L9WLF1, A0A2I1C3U0, A0A411PQM3, A0A4P8DJU1, A0A4V1E8I5, A0A5B8YUX5, A0A7R7ZLL0, A1D8J2, A2QX23, B1WBP0, C3K630, C5FM60, D4CZZ5, D7PHZ3, D7PHZ8, E1ACR1, E4V2N5, F2PWS8, F2S702, F2T0M3, G3KLH5, K3VFR8, M1WCF7, M3ANL0, P0CM88, P0CM89, P0CU68, P25170, P9WEG2, Q0CCY4, Q0CJ62, Q0CS61, Q0CS91, Q15777, Q26547, Q4W945, Q4WA58, Q4WAZ0

Diamond homologs: B1WBP0, O15442, Q15777, Q18161, Q21268, Q22306, Q5B5P1, Q5REB1, Q91ZG2, Q9CZJ0, A1D144, A5ABH4, B0XPA2, B8N5T6, Q0C7K7, Q2U5P7, Q2UDJ8, Q4WR79, Q5AZ85

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance14
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2180 predictions. Top by Δscore:

VariantEffectΔscore
11:30414222:TCTTA:Tdonor_loss1.0000
11:30414223:CTTA:Cdonor_loss1.0000
11:30414224:TTACC:Tdonor_loss1.0000
11:30414225:TAC:Tdonor_loss1.0000
11:30414226:A:Cdonor_loss1.0000
11:30414227:C:Adonor_loss1.0000
11:30423991:T:TAdonor_gain1.0000
11:30495294:A:ACdonor_gain1.0000
11:30495295:C:CCdonor_gain1.0000
11:30495295:CCAAG:Cdonor_gain1.0000
11:30495517:GTTTC:Gacceptor_gain1.0000
11:30495518:TTTC:Tacceptor_gain1.0000
11:30495519:TTC:Tacceptor_gain1.0000
11:30495520:TC:Tacceptor_gain1.0000
11:30495520:TCC:Tacceptor_loss1.0000
11:30495521:CC:Cacceptor_gain1.0000
11:30495522:C:CCacceptor_gain1.0000
11:30580244:A:ACdonor_gain1.0000
11:30580245:C:CAdonor_gain1.0000
11:30580245:CA:Cdonor_gain1.0000
11:30580245:CAT:Cdonor_gain1.0000
11:30580245:CATA:Cdonor_gain1.0000
11:30411438:C:Adonor_gain0.9900
11:30414341:CCTA:Cacceptor_loss0.9900
11:30414343:T:Gacceptor_loss0.9900
11:30423992:C:Adonor_gain0.9900
11:30442868:A:Cdonor_gain0.9900
11:30488565:A:ACdonor_gain0.9900
11:30488566:C:CCdonor_gain0.9900
11:30495294:AC:Adonor_gain0.9900

AlphaMissense

1938 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:30417572:A:GW200R0.999
11:30417572:A:TW200R0.999
11:30417606:A:CF188L0.999
11:30417606:A:TF188L0.999
11:30417608:A:GF188L0.999
11:30536072:C:AG78W0.999
11:30536122:A:TV61D0.999
11:30580296:G:CF26L0.999
11:30580296:G:TF26L0.999
11:30580298:A:GF26L0.999
11:30411541:G:CS271W0.998
11:30414332:T:AD221V0.998
11:30414333:C:GD221H0.998
11:30495305:C:TG176D0.998
11:30495486:C:AG116W0.998
11:30495488:G:TA115D0.998
11:30536032:C:TG91E0.998
11:30536033:C:GG91R0.998
11:30536033:C:TG91R0.998
11:30536128:C:GR59P0.998
11:30411546:A:CN269K0.997
11:30411546:A:TN269K0.997
11:30414260:G:TP245H0.997
11:30414278:A:TV239D0.997
11:30414290:A:GL235P0.997
11:30414303:C:GG231R0.997
11:30414332:T:GD221A0.997
11:30417541:A:GL210P0.997
11:30417614:A:GW186R0.997
11:30417614:A:TW186R0.997

dbSNP variants (sampled 300 via entrez): RS1000036617 (11:30402018 C>T), RS1000064042 (11:30526016 T>C), RS1000078325 (11:30464022 A>G), RS1000093482 (11:30567734 C>T), RS1000094070 (11:30463645 C>G), RS1000098552 (11:30482764 T>C), RS1000107496 (11:30546778 G>A,C), RS1000120667 (11:30447660 C>A,T), RS1000129689 (11:30505977 A>G), RS1000168300 (11:30513107 T>C), RS1000172656 (11:30574335 T>A), RS1000178475 (11:30532317 G>A,T), RS1000181056 (11:30415932 T>C), RS1000194963 (11:30457015 G>A,T), RS1000229572 (11:30447235 C>A)

Disease associations

OMIM: gene MIM:600911 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

40 associations (top):

StudyTraitp-value
GCST001244_1Dental caries8.000000e-06
GCST001466_1Chronic kidney disease8.000000e-18
GCST001606_1Renal function-related traits (sCR)3.000000e-09
GCST001607_2Renal function-related traits (eGRFcrea)1.000000e-09
GCST002358_14Pit-and-Fissure caries7.000000e-06
GCST003372_24Glomerular filtration rate (creatinine)6.000000e-18
GCST003374_8Chronic kidney disease9.000000e-08
GCST003401_37Glomerular filtration rate in non diabetics (creatinine)5.000000e-16
GCST003720_12Migraine4.000000e-08
GCST003790_23Glomerular filtration rate4.000000e-09
GCST003831_23Asthma9.000000e-07
GCST004292_27Glomerular filtration rate (creatinine)2.000000e-16
GCST005983_38Serum uric acid levels1.000000e-08
GCST005984_34Glomerular filtration rate8.000000e-22
GCST005985_52Creatinine levels3.000000e-21
GCST005986_38Blood urea nitrogen levels2.000000e-26
GCST006041_20Major depressive disorder8.000000e-08
GCST006291_22Spherical equivalent or myopia (age of diagnosis)4.000000e-08
GCST007267_120Systolic blood pressure1.000000e-10
GCST007324_78Adventurousness3.000000e-09
GCST007329_35Automobile speeding propensity1.000000e-14
GCST007344_19Estimated glomerular filtration rate9.000000e-36
GCST007344_65Estimated glomerular filtration rate5.000000e-07
GCST007565_37Morning person2.000000e-14
GCST007576_84Chronotype2.000000e-14
GCST007725_18Serum uric acid levels8.000000e-10
GCST007733_31Serum uric acid levels8.000000e-07
GCST007876_27Estimated glomerular filtration rate2.000000e-43
GCST007928_38Medication use (diuretics)4.000000e-08
GCST008971_43Urate levels6.000000e-08

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0004761uric acid measurement
EFO:0004847age at onset
EFO:0006335systolic blood pressure
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0009928Diuretic use measurement
EFO:0004531urate measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004615apolipoprotein B measurement
EFO:0004530triglyceride measurement
EFO:0004462PR interval
EFO:0004980appendicular lean mass
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression, decreases expression, decreases methylation5
Estradioldecreases reaction, increases expression, affects cotreatment, decreases expression4
methylmercuric chloridedecreases expression3
sodium arseniteaffects methylation, decreases expression2
entinostatdecreases expression, affects cotreatment2
belinostatdecreases expression, affects cotreatment2
Panobinostataffects cotreatment, decreases expression2
Benzo(a)pyreneaffects methylation, increases methylation2
Nickeldecreases expression2
Tretinoinincreases expression2
aflatoxin B2increases methylation1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenic Trioxidedecreases expression1
Air Pollutantsincreases abundance, decreases expression1
Coumestrolincreases expression, affects cotreatment1
Doxorubicindecreases expression1
Rotenonedecreases expression1
Tamoxifenaffects cotreatment, decreases expression1
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression, increases expression1
Tobacco Smoke Pollutiondecreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsincreases expression1
Okadaic Aciddecreases expression1
Raloxifene Hydrochlorideaffects cotreatment, decreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

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