PRTG

gene
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Also known as FLJ25756IGDCC5

Summary

PRTG (protogenin, HGNC:26373) is a protein-coding gene on chromosome 15q21.3, encoding Protogenin (Q2VWP7). May play a role in anteroposterior axis elongation.

This gene encodes a member of the immunoglobulin superfamily. The encoded transmembrane protein has been associated with the development of various tissues, especially neurogenesis. It has been suggested that this gene may be associated with attention deficit hyperactivity disorder (ADHD).

Source: NCBI Gene 283659 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 160 total
  • MANE Select transcript: NM_173814

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26373
Approved symbolPRTG
Nameprotogenin
Location15q21.3
Locus typegene with protein product
StatusApproved
AliasesFLJ25756, IGDCC5
Ensembl geneENSG00000166450
Ensembl biotypeprotein_coding
OMIM613261
Entrez283659

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 TEC

ENST00000389286, ENST00000558349, ENST00000559842, ENST00000561292, ENST00000561465, ENST00000623053

RefSeq mRNA: 1 — MANE Select: NM_173814 NM_173814

CCDS: CCDS42040

Canonical transcript exons

ENST00000389286 — 20 exons

ExonStartEnd
ENSE000011030775563717055637340
ENSE000011030855562882255629004
ENSE000011030985563854955638676
ENSE000011844545562434255624507
ENSE000011844595562700855627128
ENSE000011844875562066355620767
ENSE000012530555561154455620266
ENSE000015053495563964255639828
ENSE000015053505564111355641208
ENSE000015053515567244555672633
ENSE000015053525567337155673676
ENSE000015053535567551955675683
ENSE000015053545567779755678044
ENSE000015053565567928655679445
ENSE000015053575568005455680212
ENSE000015053595568049155680628
ENSE000015053605568236455682497
ENSE000015367455568378755683931
ENSE000015367485574038255740684
ENSE000015367515574283855743152

Expression profiles

Bgee: expression breadth ubiquitous, 193 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.1884 / max 1561.5565, expressed in 1044 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter IDTPM avgSamples expressed
15013420.68741024
1501350.5722143
1501150.5438102
1501370.2905100
1501380.288789
1501360.210586
1501260.206862
1501390.182391
1501330.098152
1501240.058634

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233697.85gold quality
secondary oocyteCL:000065596.25gold quality
oocyteCL:000002394.23gold quality
spermCL:000001987.29gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.77gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.38gold quality
endothelial cellCL:000011582.83gold quality
thyroid glandUBERON:000204679.42gold quality
left lobe of thyroid glandUBERON:000112078.88gold quality
right lobe of thyroid glandUBERON:000111978.68gold quality
pancreatic ductal cellCL:000207977.93silver quality
tibiaUBERON:000097977.74gold quality
pigmented layer of retinaUBERON:000178277.36gold quality
calcaneal tendonUBERON:000370176.66gold quality
placentaUBERON:000198776.32gold quality
oviduct epitheliumUBERON:000480475.02gold quality
sural nerveUBERON:001548874.58gold quality
endometriumUBERON:000129573.10gold quality
tibialis anteriorUBERON:000138572.67silver quality
cauda epididymisUBERON:000436071.18gold quality
colonic epitheliumUBERON:000039771.04gold quality
adrenal tissueUBERON:001830369.75gold quality
visceral pleuraUBERON:000240168.92gold quality
uterusUBERON:000099568.50gold quality
body of uterusUBERON:000985368.30gold quality
lower lobe of lungUBERON:000894968.27silver quality
tendonUBERON:000004368.02gold quality
medial globus pallidusUBERON:000247767.96silver quality
testisUBERON:000047367.06gold quality
cartilage tissueUBERON:000241866.32gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-GEOD-75140yes860.27
E-MTAB-10018yes631.84
E-HCAD-56yes323.64
E-MTAB-9388yes10.15
E-ANND-3yes10.05
E-MTAB-8205no444.70
E-MTAB-8271no7.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

469 targeting PRTG, 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-190A-3P100.0080.355520
HSA-MIR-4262100.0073.263931
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-9-5P100.0072.282361
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692A100.0074.406850
HSA-MIR-12118100.0065.881270
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-3163100.0077.238605
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-4533100.0069.482758
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-8485100.0077.574731
HSA-MIR-126-5P100.0072.713180
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-4682100.0068.891258
HSA-MIR-4476100.0068.182030

Literature-anchored findings (GeneRIF, showing 4)

  • Identified association of attention deficit hyperactivity disorder (ADHD) to Protogenin (PRTG), a gene that potentially plays a role in cell migration and axon growth. (PMID:19076634)
  • PRTG is regulated by miRNA9, plays an inhibitory action on survival of chondroblasts and articular chondrocytes during chondrogenesis and osteoarthritis pathogenesis. (PMID:24007463)
  • We found that a burden of low-frequency coding variants in N4BP2, CDSN, PRTG, and AHRR were associated with increased risk of Nonsyndromic cleft lip with or without cleft palate (NSCL/P) . Low-frequency variants in other genes were associated with decreased risk of NSCL/P. These results demonstrate that low-frequency variants contribute to the genetic etiology of NSCL/P (PMID:28425186)
  • The novel ZEB1-upregulated protein PRTG induced by Helicobacter pylori infection promotes gastric carcinogenesis through the cGMP/PKG signaling pathway. (PMID:33542225)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioprtgaENSDARG00000100044
mus_musculusPrtgENSMUSG00000036030
rattus_norvegicusPrtgENSRNOG00000055251

Paralogs (36): CNTN1 (ENSG00000018236), CDON (ENSG00000064309), NEO1 (ENSG00000067141), SDK2 (ENSG00000069188), IGSF9B (ENSG00000080854), IGSF9 (ENSG00000085552), NRCAM (ENSG00000091129), MXRA5 (ENSG00000101825), IGDCC4 (ENSG00000103742), CNTN3 (ENSG00000113805), IGSF21 (ENSG00000117154), CNTN6 (ENSG00000134115), CHL1 (ENSG00000134121), PTPRQ (ENSG00000139304), CNTN4 (ENSG00000144619), BOC (ENSG00000144857), SDK1 (ENSG00000146555), HMCN2 (ENSG00000148357), NCAM1 (ENSG00000149294), CNTN5 (ENSG00000149972), IGSF10 (ENSG00000152580), ROBO4 (ENSG00000154133), ROBO3 (ENSG00000154134), NCAM2 (ENSG00000154654), VCAM1 (ENSG00000162692), NFASC (ENSG00000163531), ROBO1 (ENSG00000169855), DSCAM (ENSG00000171587), IGDCC3 (ENSG00000174498), VSIG10 (ENSG00000176834), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), VSIG10L (ENSG00000186806), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

ProtogeninQ2VWP7 (reviewed: Q2VWP7)

Alternative names: Protein Shen-Dan

All UniProt accessions (4): Q2VWP7, H0YKD6, H0YLD1, H0YLT7

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in anteroposterior axis elongation.

Subcellular location. Membrane.

Similarity. Belongs to the immunoglobulin superfamily. DCC family.

RefSeq proteins (1): NP_776175* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR003961FN3_domDomain
IPR007110Ig-like_domDomain
IPR013098Ig_I-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily

Pfam: PF00041, PF07679, PF13927

UniProt features (30 total): domain 9, compositionally biased region 4, disulfide bond 4, glycosylation site 3, sequence variant 3, region of interest 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2VWP7-F174.180.29

Functional residue map

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

Disulfide bonds (4): 60–113, 156–205, 256–304, 348–395

Glycosylation sites (3): 90, 488, 630

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 186 (showing top): GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOBP_NEGATIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_CELL_CELL_ADHESION, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, TGTGTGA_MIR377, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP, GOBP_REGULATION_OF_CELL_DEVELOPMENT, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, ATGTTTC_MIR494

GO Biological Process (2): negative regulation of neurogenesis (GO:0050768), cell-cell adhesion (GO:0098609)

GO Molecular Function (3): signaling receptor activity (GO:0038023), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of cell development1
neurogenesis1
regulation of neurogenesis1
negative regulation of nervous system development1
cell adhesion1
molecular transducer activity1
protein binding1
binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

748 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PRTGLRFN2Q9ULH4540
PRTGDAZAP2Q15038480
PRTGERICH6BQ5W0A0413
PRTGLRRC63Q05C16387
PRTGN4BP2Q86UW6380
PRTGCHMP4BQ9H444368
PRTGNGFP01138359
PRTGAMOTL1Q8IY63353
PRTGKANSL3Q9P2N6349
PRTGLIN28BQ6ZN17344
PRTGCGNL1Q0VF96343
PRTGVWC2Q2TAL6339
PRTGIGSF11Q5DX21333
PRTGTAL2Q16559325
PRTGGUCY1A2P33402322

IntAct

24 interactions, top by confidence:

ABTypeScore
PRTGICAM5psi-mi:“MI:0915”(physical association)0.540
PRTGWFIKKN2psi-mi:“MI:0915”(physical association)0.540
ICAM5PRTGpsi-mi:“MI:0407”(direct interaction)0.540
PRTGWFIKKN2psi-mi:“MI:0407”(direct interaction)0.540
TMEM30BKLRG2psi-mi:“MI:0914”(association)0.530
FCGRTGOLIM4psi-mi:“MI:0914”(association)0.530
LGALS1PODXLpsi-mi:“MI:0914”(association)0.530
PRTGLTFpsi-mi:“MI:0407”(direct interaction)0.440
PRTGIGFBPL1psi-mi:“MI:0407”(direct interaction)0.440
PRTGIGFBP7psi-mi:“MI:0407”(direct interaction)0.440
HAPLN1PRTGpsi-mi:“MI:0915”(physical association)0.400
IL1RAPL2PRTGpsi-mi:“MI:0915”(physical association)0.400
LRRTM2PRTGpsi-mi:“MI:0915”(physical association)0.400
ISLR2PRTGpsi-mi:“MI:0915”(physical association)0.400
MICAPRTGpsi-mi:“MI:0915”(physical association)0.400
RIPK4VWA8psi-mi:“MI:0914”(association)0.350
DISC1AGRNpsi-mi:“MI:0914”(association)0.350
GDF11TSPY2psi-mi:“MI:0914”(association)0.350
NRSN1FAM171A2psi-mi:“MI:0914”(association)0.350
RYKTNFRSF10Bpsi-mi:“MI:0914”(association)0.350
MSTNGDF11psi-mi:“MI:0914”(association)0.350

BioGRID (13): PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-RNA), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), PRTG (Affinity Capture-MS), RRP9 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2A8L5, A4IFW2, A7MBJ4, B0V2N1, F1NWE3, O00533, O42414, O55005, O89026, O94856, O97394, P10586, P11627, P16621, P22063, P23468, P28685, P32004, P70232, P97685, P97686, Q02246, Q05695, Q13332, Q28902, Q2EY14, Q2EY15, Q2VWP7, Q2VWP9, Q3UH53, Q589G5, Q58EX2, Q61330, Q64487, Q64604, Q64605, Q6V4S5, Q7Z5N4, Q810U3, Q810U4

Diamond homologs: A2AAJ9, A2ABU4, O88599, P12960, P14781, P28685, P52179, P54296, P68500, P70402, P97527, P97528, Q02173, Q07409, Q12860, Q13203, Q14896, Q28106, Q2EY15, Q2VWP7, Q2VWP9, Q589G5, Q5PQM4, Q5VTT5, Q62234, Q62682, Q63198, Q7ZW34, Q86TB3, Q91ZB0, Q924C5, Q96JA1, Q96L96, Q98936, Q9P232, A0A452E9Y6, A1KZ92, A2ASS6, A4IGL7, A5JUY8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance138
Likely benign8
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3345 predictions. Top by Δscore:

VariantEffectΔscore
15:55625290:AAT:Adonor_gain1.0000
15:55625315:AAC:Adonor_gain1.0000
15:55627019:T:TAdonor_gain1.0000
15:55627129:C:CCacceptor_gain1.0000
15:55637165:TTTA:Tdonor_loss1.0000
15:55637166:TTA:Tdonor_loss1.0000
15:55637167:TAC:Tdonor_loss1.0000
15:55637169:C:CAdonor_loss1.0000
15:55637195:T:Adonor_gain1.0000
15:55637336:TGGTG:Tacceptor_gain1.0000
15:55637337:GGTG:Gacceptor_gain1.0000
15:55637338:GTG:Gacceptor_gain1.0000
15:55637339:TG:Tacceptor_gain1.0000
15:55637341:C:CCacceptor_gain1.0000
15:55637343:G:Cacceptor_gain1.0000
15:55637343:G:GCacceptor_gain1.0000
15:55637346:C:CTacceptor_gain1.0000
15:55637350:C:CTacceptor_gain1.0000
15:55638543:CTTTA:Cdonor_loss1.0000
15:55638544:TTTAC:Tdonor_loss1.0000
15:55638545:TTACC:Tdonor_loss1.0000
15:55638546:TACCT:Tdonor_loss1.0000
15:55638547:A:ATdonor_loss1.0000
15:55638548:CCTT:Cdonor_gain1.0000
15:55638548:CCTTC:Cdonor_loss1.0000
15:55638672:CTGAT:Cacceptor_gain1.0000
15:55638673:TGAT:Tacceptor_gain1.0000
15:55638675:ATC:Aacceptor_loss1.0000
15:55638676:TC:Tacceptor_loss1.0000
15:55638677:C:CAacceptor_loss1.0000

AlphaMissense

7450 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:55628950:A:TV893D1.000
15:55637275:A:GW840R1.000
15:55637275:A:TW840R1.000
15:55677861:C:AW439C1.000
15:55677861:C:GW439C1.000
15:55677863:A:GW439R1.000
15:55677863:A:TW439R1.000
15:55680117:A:GC304R1.000
15:55680161:A:GL289P1.000
15:55680501:C:AW268C1.000
15:55680501:C:GW268C1.000
15:55680503:A:GW268R1.000
15:55680503:A:TW268R1.000
15:55682433:A:CY203D1.000
15:55683825:C:AW168C1.000
15:55683825:C:GW168C1.000
15:55683827:A:GW168R1.000
15:55683827:A:TW168R1.000
15:55628944:A:CI895R0.999
15:55628944:A:TI895K0.999
15:55637273:C:AW840C0.999
15:55637273:C:GW840C0.999
15:55637274:C:GW840S0.999
15:55637280:A:TV838D0.999
15:55638617:A:TV795D0.999
15:55638623:A:GF793S0.999
15:55639742:A:GW742R0.999
15:55639742:A:TW742R0.999
15:55672528:A:GL653P0.999
15:55672574:A:GW638R0.999

dbSNP variants (sampled 300 via entrez): RS1000016155 (15:55671456 G>A), RS1000016587 (15:55691273 G>T), RS1000030533 (15:55624107 A>G), RS1000061945 (15:55659608 T>C), RS1000085823 (15:55708232 C>A), RS1000100251 (15:55666673 A>G), RS1000155601 (15:55655742 T>C), RS1000177001 (15:55734129 G>A), RS1000197404 (15:55695937 C>G,T), RS1000229965 (15:55679128 C>T), RS1000304954 (15:55684782 G>A,C), RS1000318428 (15:55618467 C>A,T), RS1000359475 (15:55673035 T>C), RS1000371672 (15:55612590 T>G), RS1000403122 (15:55690550 T>A,C)

Disease associations

OMIM: gene MIM:613261 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST002004_4Adverse response to chemotherapy (neutropenia/leucopenia) (carboplatin)9.000000e-07
GCST003998_13Joint mobility (Beighton score)1.000000e-08
GCST004713_7Testicular germ cell tumor1.000000e-11
GCST005580_89Intraocular pressure4.000000e-11
GCST007325_18General risk tolerance (MTAG)3.000000e-08
GCST007401_22Factor VII activity2.000000e-06
GCST010703_182Brain morphology (MOSTest)5.000000e-11
GCST012489_44Heel bone mineral density x serum urate levels interaction1.000000e-11

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0007905joint hypermobility measurement
EFO:0004695intraocular pressure measurement
EFO:0008579risk-taking behaviour
EFO:0004619factor VII measurement
EFO:0004346neuroimaging measurement
EFO:0004531urate measurement
EFO:0009270heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, increases expression, affects expression4
Ethanolaffects cotreatment, increases expression, decreases expression3
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
trichostatin Aincreases expression1
sodium arsenitedecreases expression1
perfluorooctanoic acidincreases expression1
aflatoxin B2decreases methylation1
nickel sulfateincreases expression1
CGP 52608increases reaction, affects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrinedecreases expression1
LDN 193189affects cotreatment, increases expression1
Fulvestrantincreases methylation, affects cotreatment1
Leflunomideincreases expression1
Air Pollutantsincreases abundance, increases expression1
Carbamazepineaffects expression1
Doxorubicindecreases expression1
Estradiolincreases expression1
Folic Acidaffects cotreatment, increases expression1
Leadaffects methylation1
Nickeldecreases expression1
Phthalic Acidsdecreases methylation1
Urethaneincreases expression1
Vanadatesdecreases expression1
Cyclosporinedecreases expression1
Cadmium Chloridedecreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): testicular germ cell tumor