NREP

gene
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Also known as P311D4S114PRO1873PTZ17SEZ17

Summary

NREP (neuronal regeneration related protein, HGNC:16834) is a protein-coding gene on chromosome 5q22.1, encoding Neuronal regeneration-related protein (Q16612). May have roles in neural function.

Predicted to be involved in axon regeneration; regulation of neuron differentiation; and regulation of transforming growth factor beta receptor signaling pathway. Predicted to be located in cytoplasm.

Source: NCBI Gene 9315 — RefSeq curated summary.

At a glance

  • GWAS associations: 28
  • Clinical variants (ClinVar): 32 total
  • MANE Select transcript: NM_004772

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16834
Approved symbolNREP
Nameneuronal regeneration related protein
Location5q22.1
Locus typegene with protein product
StatusApproved
AliasesP311, D4S114, PRO1873, PTZ17, SEZ17
Ensembl geneENSG00000134986
Ensembl biotypeprotein_coding
OMIM607332
Entrez9315

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 28 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000257435, ENST00000379671, ENST00000395634, ENST00000419114, ENST00000446294, ENST00000447165, ENST00000450761, ENST00000453526, ENST00000455559, ENST00000503429, ENST00000504018, ENST00000505864, ENST00000507032, ENST00000507742, ENST00000508161, ENST00000508870, ENST00000509025, ENST00000509427, ENST00000509979, ENST00000513100, ENST00000513684, ENST00000514515, ENST00000515855, ENST00000875801, ENST00000875802, ENST00000875803, ENST00000875804, ENST00000920636, ENST00000920637, ENST00000920638, ENST00000920639, ENST00000920640, ENST00000920641, ENST00000920642

RefSeq mRNA: 11 — MANE Select: NM_004772 NM_001142474, NM_001142475, NM_001142476, NM_001142477, NM_001142478, NM_001142479, NM_001142480, NM_001142481, NM_001142482, NM_001142483, NM_004772

CCDS: CCDS4105, CCDS47255

Canonical transcript exons

ENST00000257435 — 4 exons

ExonStartEnd
ENSE00001770789111729303111731046
ENSE00002058117111757136111757194
ENSE00003586374111755770111755830
ENSE00003666801111735430111735507

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 54.3110 / max 1586.9318, expressed in 1656 samples.

FANTOM5 promoters (19 alternative TSS)

Promoter IDTPM avgSamples expressed
6292622.17161208
6292911.00811139
629286.5038992
629334.39881371
629324.18331227
629301.8474580
629271.4003632
629310.5781256
629250.5683185
629350.5483258

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534399.85gold quality
paraflocculusUBERON:000535199.76gold quality
ganglionic eminenceUBERON:000402399.73gold quality
embryoUBERON:000092299.63gold quality
cerebellar hemisphereUBERON:000224599.45gold quality
tibiaUBERON:000097999.44gold quality
ventricular zoneUBERON:000305399.42gold quality
cerebellumUBERON:000203799.41gold quality
cerebellar cortexUBERON:000212999.41gold quality
right hemisphere of cerebellumUBERON:001489099.37gold quality
adrenal tissueUBERON:001830398.56gold quality
ponsUBERON:000098898.14gold quality
Brodmann (1909) area 46UBERON:000648398.00gold quality
cartilage tissueUBERON:000241897.95gold quality
frontal poleUBERON:000279597.62gold quality
tendon of biceps brachiiUBERON:000818897.58gold quality
Brodmann (1909) area 10UBERON:001354197.54gold quality
biceps brachiiUBERON:000150797.53gold quality
prefrontal cortexUBERON:000045197.52gold quality
orbitofrontal cortexUBERON:000416797.28gold quality
endothelial cellCL:000011597.26gold quality
dorsolateral prefrontal cortexUBERON:000983497.14gold quality
adult organismUBERON:000702397.11gold quality
visceral pleuraUBERON:000240197.06gold quality
primary visual cortexUBERON:000243696.98gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450296.94gold quality
frontal cortexUBERON:000187096.90gold quality
secondary oocyteCL:000065596.88gold quality
Brodmann (1909) area 23UBERON:001355496.85gold quality
pigmented layer of retinaUBERON:000178296.82gold quality

Single-cell (SCXA)

Detected in 19 experiment(s), a significant marker in 12.

ExperimentMarker?Max mean expression
E-HCAD-5yes1280.59
E-MTAB-8221yes1192.53
E-MTAB-9067yes837.68
E-CURD-112yes471.61
E-HCAD-10yes49.90
E-HCAD-31yes20.72
E-MTAB-7316yes12.52
E-MTAB-10042yes11.18
E-CURD-114yes10.94
E-GEOD-83139yes6.78
E-MTAB-9801yes5.95
E-GEOD-93593no2510.67
E-MTAB-8894no1692.38
E-MTAB-9154no1218.85
E-MTAB-11121no1061.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

154 targeting NREP, 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-3646100.0073.565283
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-3163100.0077.238605
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-4692100.0067.322066
HSA-MIR-607799.9968.042299
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872

Literature-anchored findings (GeneRIF, showing 16)

  • role for P311 in inducing TGF-beta1-independent myofibroblast transformation (PMID:12417574)
  • These results suggest a role for levels of P311 in regulating glioma motility and invasion through the reorganization of actin cytoskeleton at the cell periphery. (PMID:16229809)
  • P311 expression is tightly regulated during the critical periods of alveolar formation, and that under pathologic conditions, its relative absence may contribute to failure of alveolar regeneration and lead to the development of human emphysema. (PMID:16484684)
  • P311 may be involved in the pathogenesis of hypertrophic scar via induction of a myofibrobla (PMID:20404911)
  • P311 and ITGB4BP expression was elevated in non-small cell lung cancer, possibly indicative of a new signaling pathway. (PMID:21029697)
  • Protein HYI may closely bind with protein P311 by an alpha helix in hypertrophic scar fibroblasts. (PMID:22490543)
  • P311 may promote the migration of ESCs both in micewith superficial partial-thickness burns and in an injured cell model in vitro, and it may play an important role in wound healing. (PMID:22967977)
  • Novel RNA-binding protein P311 binds eIF3b to promote translation of TGF-beta1, TGF-beta2, TGF-beta3. (PMID:25336651)
  • P311 plays a key role in renal fibrosis via TGFbeta1/Smad signaling, which could be a novel target for the management of renal fibrosis. (PMID:26616407)
  • P311 is a novel TGFbeta1/Smad signaling-mediated regulator of transdifferentiation in epidermal stem cells during cutaneous wound healing. (PMID:27906099)
  • P311 could accelerate skin wound reepithelialization by promoting the migration of Epidermal Stem Cell through RhoA and Rac1 activation. (PMID:27927130)
  • These studies demonstrate that P311 is required for the production of normal cutaneous scars (PMID:27939132)
  • P311 expression in the in the lungs of patients with idiopathic pulmonary fibrosis. (PMID:30230348)
  • P311 Promotes IL-4 Receptor-Mediated M2 Polarization of Macrophages to Enhance Angiogenesis for Efficient Skin Wound Healing. (PMID:36309321)
  • NREP contributes to development of NAFLD by regulating one-carbon metabolism in primary human hepatocytes. (PMID:37354909)
  • H3K18 lactylation promotes the progression of arsenite-related idiopathic pulmonary fibrosis via YTHDF1/m6A/NREP. (PMID:37742376)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusNrepENSMUSG00000042834
rattus_norvegicusNrepENSRNOG00000068914

Protein

Protein identifiers

Neuronal regeneration-related proteinQ16612 (reviewed: Q16612)

Alternative names: Neuronal protein 3.1, Protein p311

All UniProt accessions (5): D6R982, Q16612, D6R9Y7, D6REJ5, D6RIC9

UniProt curated annotations — full annotation on UniProt →

Function. May have roles in neural function. Ectopic expression augments motility of gliomas. Also promotes axonal regeneration. May also have functions in cellular differentiation. Induces differentiation of fibroblast into myofibroblast and myofibroblast ameboid migration. Increases retinoic-acid regulation of lipid-droplet biogenesis. Down-regulates the expression of TGFB1 and TGFB2 but not of TGFB3. May play a role in the regulation of alveolar generation.

Subunit / interactions. Interacts with the latency-associated peptides (LAP) of TGFB1 and TGFB2; the interaction results in a decrease in TGFB autoinduction. Interacts with FLNA.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in lung (at protein level).

Post-translational modifications. Phosphorylated on Ser-59. Phosphorylation decreases stability and activity.

Induction. Down-regulated in emphysematous lung compared to normal lung.

Isoforms (2)

UniProt IDNamesCanonical?
Q16612-11yes
Q16612-22

RefSeq proteins (11): NP_001135946, NP_001135947, NP_001135948, NP_001135949, NP_001135950, NP_001135951, NP_001135952, NP_001135953, NP_001135954, NP_001135955, NP_004763* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR024417Neuronal_3.1Family

Pfam: PF11092

UniProt features (8 total): mutagenesis site 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16612-F167.600.00

Functional residue map

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

Post-translational modifications (1): 59

Mutagenesis-validated functional residues (2):

PositionPhenotype
59reduces protein degradation and induces glioma cell migration.
59accelerates protein degradation and reduces glioma cell migration.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 351 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, AAGCAAT_MIR137, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_REGENERATION, GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, MEF2_02, GOBP_RESPONSE_TO_AXON_INJURY, LHX3_01, GGGTGGRR_PAX4_03

GO Biological Process (3): regulation of transforming growth factor beta receptor signaling pathway (GO:0017015), axon regeneration (GO:0031103), regulation of neuron differentiation (GO:0045664)

GO Molecular Function (1): protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transforming growth factor beta receptor signaling pathway1
regulation of transmembrane receptor protein serine/threonine kinase signaling pathway1
regulation of cellular response to transforming growth factor beta stimulus1
neuron projection regeneration1
response to axon injury1
axon development1
neuron differentiation1
regulation of cell differentiation1
binding1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

448 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NREPMT2AP02795557
NREPEIF3BP55884529
NREPC1orf74Q96LT6495
NREPH3BSS0H3BSS0468
NREPRNF44Q7L0R7435
NREPRNF38Q9H0F5400
NREPPLXDC2Q6UX71400
NREPTGFBR2P37173380
NREPUSP54Q70EL1373
NREPC19orf67A6NJJ6371
NREPZSWIM8A7E2V4371
NREPPCNX2A6NKB5369
NREPPLSCR4Q9NRQ2352
NREPCRLS1Q9UJA2352
NREPEPB41L4AQ9HCS5349

IntAct

10 interactions, top by confidence:

ABTypeScore
EIF6NREPpsi-mi:“MI:0915”(physical association)0.630
NREPEIF6psi-mi:“MI:0915”(physical association)0.630
NREPEIF6psi-mi:“MI:0403”(colocalization)0.630
NREPEEF1A1psi-mi:“MI:0915”(physical association)0.370
KMT2BNREPpsi-mi:“MI:0915”(physical association)0.370
ATMNREPpsi-mi:“MI:0915”(physical association)0.370
NREPIGSF21psi-mi:“MI:0915”(physical association)0.000

BioGRID (21): NREP (Two-hybrid), IGSF21 (Two-hybrid), MYH9 (Affinity Capture-MS), ACTB (Affinity Capture-MS), EIF3B (Affinity Capture-MS), FLNA (Affinity Capture-MS), GDI2 (Affinity Capture-MS), RAB7A (Affinity Capture-MS), EIF3G (Affinity Capture-MS), RPS13 (Affinity Capture-MS), RBMX (Affinity Capture-MS), NREP (Affinity Capture-Western), NREP (Reconstituted Complex), EIF3B (Reconstituted Complex), NREP (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GUQ0, A0A1B0GV22, A4WGH3, A5WBB8, A8A6G6, B1IX34, B1X9T3, B5BIL7, B5QUQ3, B5RFY4, B7L848, B7LK47, B7M557, B7MGC6, B7N2F0, B7NF22, B7NR07, B8MYS5, C0Q2L2, C4ZYY2, O71190, O83770, P03167, P03168, P05443, P0A8C8, P0A8C9, P0C304, P0C305, P12173, P12478, P20464, P53231, P61468, P61472, Q16612, Q1R4N0, Q31UV8, Q329B3, Q3SSW2

Diamond homologs: Q07475, Q16612, Q4R541, Q5NVD3, Q80Z34, Q90667

SIGNOR signaling

2 interactions.

AEffectBMechanism
PRKCE“down-regulates quantity by destabilization”NREPphosphorylation
PRKCZ“down-regulates quantity by destabilization”NREPphosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance23
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2385 predictions. Top by Δscore:

VariantEffectΔscore
5:111731065:C:CTacceptor_gain1.0000
5:111731065:C:Tacceptor_gain1.0000
5:111735423:ATCTT:Adonor_loss1.0000
5:111735424:TCTTA:Tdonor_loss1.0000
5:111735425:CTTAC:Cdonor_loss1.0000
5:111735426:TTAC:Tdonor_loss1.0000
5:111735427:TACCT:Tdonor_loss1.0000
5:111735428:A:AGdonor_loss1.0000
5:111735503:TAAAC:Tacceptor_gain1.0000
5:111735507:CCTA:Cacceptor_loss1.0000
5:111735508:C:CCacceptor_gain1.0000
5:111735509:T:Gacceptor_loss1.0000
5:111926540:T:TAdonor_gain1.0000
5:111731042:CTTCC:Cacceptor_gain0.9900
5:111731044:TCC:Tacceptor_gain0.9900
5:111731045:CCC:Cacceptor_gain0.9900
5:111731067:C:CTacceptor_gain0.9900
5:111731069:C:CTacceptor_gain0.9900
5:111731071:C:CTacceptor_gain0.9900
5:111732871:A:Cdonor_gain0.9900
5:111735428:A:ACdonor_gain0.9900
5:111735429:C:CCdonor_gain0.9900
5:111914107:A:ACdonor_gain0.9900
5:111914108:C:CCdonor_gain0.9900
5:111926541:C:Adonor_gain0.9900
5:111997320:ATAC:Adonor_loss0.9900
5:111997321:TACCT:Tdonor_loss0.9900
5:111997323:C:CAdonor_loss0.9900
5:111731043:TTCC:Tacceptor_gain0.9800
5:111731045:CC:Cacceptor_gain0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000006715 (5:111753265 C>T), RS1000008558 (5:111790622 G>A,T), RS1000031900 (5:111871070 G>GTGTC), RS1000044006 (5:111772797 T>C), RS1000055706 (5:111904009 C>G,T), RS1000062076 (5:111914990 T>C), RS1000066471 (5:111865896 A>G), RS1000086468 (5:111762171 A>G), RS1000091534 (5:111917364 C>T), RS1000091950 (5:111753706 G>A), RS1000116097 (5:111812227 C>A,T), RS1000119823 (5:111827869 A>AG), RS1000132966 (5:111910339 T>G), RS1000135139 (5:111945901 C>T), RS1000140056 (5:111865438 G>A,T)

Disease associations

OMIM: gene MIM:607332 | disease phenotypes: MIM:192350

GenCC curated gene-disease

Mondo (1): VACTERL/vater association (MONDO:0008642)

Orphanet (1): VACTERL/VATER association (Orphanet:887)

HPO phenotypes

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

GWAS associations

28 associations (top):

StudyTraitp-value
GCST001762_458Obesity-related traits8.000000e-06
GCST002875_171Diisocyanate-induced asthma2.000000e-06
GCST003542_54Night sleep phenotypes4.000000e-06
GCST004144_8Thyroid cancer3.000000e-10
GCST004603_6Platelet count1.000000e-15
GCST004607_236Plateletcrit4.000000e-30
GCST004862_143Itch intensity from mosquito bite adjusted by bite size5.000000e-06
GCST004862_190Itch intensity from mosquito bite adjusted by bite size4.000000e-06
GCST004862_218Itch intensity from mosquito bite adjusted by bite size3.000000e-06
GCST004988_635Breast cancer4.000000e-09
GCST005993_5Mean corpuscular hemoglobin8.000000e-13
GCST005996_46Red blood cell count1.000000e-09
GCST006268_507Reaction time2.000000e-08
GCST009375_9Mosaic loss of chromosome Y (Y chromosome dosage)3.000000e-15
GCST010241_340Apolipoprotein A1 levels4.000000e-08
GCST012032_4Platelet count1.000000e-07
GCST90002383_211Hematocrit9.000000e-10
GCST90002383_212Hematocrit6.000000e-11
GCST90002390_137Mean corpuscular hemoglobin8.000000e-16
GCST90002392_636Mean corpuscular volume8.000000e-17
GCST90002395_456Mean platelet volume1.000000e-13
GCST90002396_309Mean reticulocyte volume1.000000e-14
GCST90002397_46Mean spheric corpuscular volume4.000000e-16
GCST90002400_647Plateletcrit8.000000e-65
GCST90002402_780Platelet count2.000000e-32
GCST90002403_409Red blood cell count2.000000e-12
GCST90002403_410Red blood cell count5.000000e-10
GCST90007007_5Gut microbiota relative abundance (Sutterella)9.000000e-06

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate
EFO:0004309platelet count
EFO:0007985platelet crit
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0004305erythrocyte count
EFO:0008393reaction time measurement
EFO:0007783mosaic loss of chromosome Y measurement
EFO:0004614apolipoprotein A 1 measurement
EFO:0004348hematocrit
EFO:0010701mean reticulocyte volume
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, decreases expression, affects cotreatment4
bisphenol Aaffects expression, affects cotreatment, decreases methylation, decreases expression3
cobaltous chloridedecreases expression3
nickel sulfatedecreases expression3
Estradiolaffects expression, affects cotreatment, increases expression, decreases expression3
Silicon Dioxidedecreases expression3
Cyclosporinedecreases expression, decreases methylation3
sulforaphanedecreases expression2
potassium chromate(VI)affects cotreatment, decreases expression2
Zoledronic Acidincreases expression2
Acetaminophendecreases expression2
Arsenicincreases abundance, decreases expression2
Benzo(a)pyreneincreases methylation, decreases expression2
Doxorubicinaffects response to substance, decreases expression2
Nickeldecreases expression2
Tobacco Smoke Pollutiondecreases expression2
Asbestos, Crocidolitedecreases expression2
Cadmium Chlorideaffects expression, decreases expression, increases abundance2
aristolochic acid Idecreases expression1
sotorasibaffects cotreatment, decreases expression1
chloroacetaldehydedecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
sodium arsenatedecreases expression, increases abundance1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arsenitedecreases expression, increases abundance1
butyraldehydedecreases expression1
tobacco tardecreases expression, decreases reaction1
didecyldimethylammoniumdecreases expression1
periodate-oxidized adenosineaffects expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03799705Not specifiedCOMPLETEDGenetic Variants in Nicotinamide Adenine Dinucleotide (NAD) Synthesis Pathway