N4BP2L2

gene
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Also known as CG005PFAAP5

Summary

N4BP2L2 (NEDD4 binding protein 2 like 2, HGNC:26916) is a protein-coding gene on chromosome 13q13.1, encoding NEDD4-binding protein 2-like 2 (Q92802).

Enables enzyme binding activity. Involved in negative regulation of hematopoietic stem cell differentiation and positive regulation of hematopoietic stem cell proliferation. Located in nucleus. Part of transcription repressor complex.

Source: NCBI Gene 10443 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 42 total — 1 pathogenic
  • MANE Select transcript: NM_014887

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26916
Approved symbolN4BP2L2
NameNEDD4 binding protein 2 like 2
Location13q13.1
Locus typegene with protein product
StatusApproved
AliasesCG005, PFAAP5
Ensembl geneENSG00000244754
Ensembl biotypeprotein_coding
OMIM615788
Entrez10443

Gene structure

Transcript identifiers

Ensembl transcripts: 52 — 26 protein_coding, 13 retained_intron, 7 protein_coding_CDS_not_defined, 6 nonsense_mediated_decay

ENST00000267068, ENST00000357505, ENST00000380121, ENST00000399396, ENST00000446957, ENST00000473025, ENST00000475731, ENST00000483088, ENST00000503296, ENST00000503814, ENST00000504114, ENST00000505213, ENST00000509076, ENST00000511143, ENST00000512755, ENST00000674161, ENST00000674163, ENST00000674180, ENST00000674196, ENST00000674219, ENST00000674272, ENST00000674276, ENST00000674279, ENST00000674293, ENST00000674297, ENST00000674327, ENST00000674346, ENST00000674349, ENST00000674369, ENST00000674377, ENST00000674384, ENST00000674399, ENST00000674408, ENST00000674421, ENST00000674422, ENST00000674428, ENST00000674433, ENST00000674437, ENST00000674452, ENST00000674456, ENST00000674462, ENST00000674465, ENST00000674480, ENST00000674484, ENST00000674494, ENST00000884184, ENST00000884185, ENST00000884186, ENST00000884187, ENST00000884188, ENST00000946928, ENST00000946929

RefSeq mRNA: 35 — MANE Select: NM_014887 NM_001278432, NM_001320836, NM_001387001, NM_001387002, NM_001387008, NM_001387009, NM_001387015, NM_001387016, NM_001387018, NM_001387019, NM_001387020, NM_001387059, NM_001387060, NM_001387079, NM_001387080, NM_001387081, NM_001387082, NM_001387083, NM_001387099, NM_001387100, NM_001387101, NM_001387102, NM_001387103, NM_001387104, NM_001387105, NM_001387106, NM_001387107, NM_001387108, NM_001387165, NM_001387223, NM_001387224, NM_001387225, NM_001395224, NM_014887, NM_033111

CCDS: CCDS45024, CCDS61307, CCDS91796, CCDS91797, CCDS91798, CCDS91799, CCDS9346

Canonical transcript exons

ENST00000267068 — 6 exons

ExonStartEnd
ENSE000020390543252137332521449
ENSE000035000143252218232522270
ENSE000036284573252740832527532
ENSE000036673033251029232518003
ENSE000037559303253576932537027
ENSE000039781413253861832538795

Expression profiles

Bgee: expression breadth ubiquitous, 301 present calls, max score 99.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 60.5511 / max 1845.3212, expressed in 1812 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
13671551.86271801
1367145.32621474
1367162.1882909
1367130.8175428
1367120.3564126

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370199.48gold quality
choroid plexus epitheliumUBERON:000391199.14gold quality
nippleUBERON:000203098.76gold quality
tendonUBERON:000004398.74gold quality
cardia of stomachUBERON:000116298.42gold quality
renal medullaUBERON:000036298.22gold quality
colonic epitheliumUBERON:000039798.22gold quality
endothelial cellCL:000011598.17gold quality
germinal epithelium of ovaryUBERON:000130498.09gold quality
pylorusUBERON:000116698.05gold quality
parotid glandUBERON:000183197.99gold quality
urethraUBERON:000005797.92gold quality
visceral pleuraUBERON:000240197.74gold quality
seminal vesicleUBERON:000099897.71gold quality
sural nerveUBERON:001548897.70gold quality
tendon of biceps brachiiUBERON:000818897.66gold quality
penisUBERON:000098997.64gold quality
right uterine tubeUBERON:000130297.58gold quality
left ovaryUBERON:000211997.58gold quality
upper leg skinUBERON:000426297.51gold quality
superficial temporal arteryUBERON:000161497.49gold quality
right ovaryUBERON:000211897.44gold quality
tibiaUBERON:000097997.39gold quality
trabecular bone tissueUBERON:000248397.38gold quality
corpus callosumUBERON:000233697.36gold quality
monocyteCL:000057697.35gold quality
mononuclear cellCL:000084297.33gold quality
dorsal motor nucleus of vagus nerveUBERON:000287097.31gold quality
tonsilUBERON:000237297.21gold quality
adrenal tissueUBERON:001830397.21gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-1yes29.42
E-CURD-122yes20.28
E-MTAB-8142yes12.83
E-GEOD-125970yes6.65
E-MTAB-8381no1307.72
E-GEOD-70580no1216.88
E-HCAD-36no1124.22
E-CURD-46no945.35
E-MTAB-6386no717.05
E-HCAD-4no77.70
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting N4BP2L2, 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-3163100.0077.238605
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-539-5P99.9370.302855
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-3121-3P99.8271.963630

Literature-anchored findings (GeneRIF, showing 1)

  • Data suggest that expression of PFAAP5 allows neutrophil elastase to potentiate the repression of Gfi1 target genes. (PMID:19506020)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerion4bp2l2ENSDARG00000103507
mus_musculusN4bp2l2ENSMUSG00000029655
rattus_norvegicusN4bp2l2ENSRNOG00000001108

Paralogs (2): N4BP2 (ENSG00000078177), N4BP2L1 (ENSG00000139597)

Protein

Protein identifiers

NEDD4-binding protein 2-like 2Q92802 (reviewed: Q92802)

Alternative names: Phosphonoformate immuno-associated protein 5

All UniProt accessions (17): A0A6I8PL40, A0A6I8PL95, A0A6I8PRE0, A0A6I8PRI0, A0A6I8PRM1, A0A6I8PRP6, A0A6I8PRR0, A0A6I8PRR5, A0A6I8PRT3, A0A6I8PRV3, A0A6I8PRX5, A0A6I8PRY6, A0A6I8PS46, A0A6I8PU16, B4DPY1, D6R968, Q92802

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt IDNamesCanonical?
Q92802-11yes
Q92802-22
Q92802-33

RefSeq proteins (35): NP_001265361, NP_001307765, NP_001373930, NP_001373931, NP_001373937, NP_001373938, NP_001373944, NP_001373945, NP_001373947, NP_001373948, NP_001373949, NP_001373988, NP_001373989, NP_001374008, NP_001374009, NP_001374010, NP_001374011, NP_001374012, NP_001374028, NP_001374029, NP_001374030, NP_001374031, NP_001374032, NP_001374033, NP_001374034, NP_001374035, NP_001374036, NP_001374037, NP_001374094, NP_001374152, NP_001374153, NP_001374154, NP_001382153, NP_055702, NP_149102 (=MANE)

Domains & families (InterPro)

IDNameType
IPR026302NEDD4-bd_p2Family
IPR027417P-loop_NTPaseHomologous_superfamily

Pfam: PF13671

UniProt features (8 total): splice variant 4, chain 1, region of interest 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92802-F155.100.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 201 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, BASSO_B_LYMPHOCYTE_NETWORK, GOBP_NEGATIVE_REGULATION_OF_STEM_CELL_DIFFERENTIATION, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, chr13q13, YY1_Q6, GOBP_STEM_CELL_PROLIFERATION, GOBP_HEMATOPOIETIC_STEM_CELL_DIFFERENTIATION, GOBP_NEGATIVE_REGULATION_OF_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, LINDSTEDT_DENDRITIC_CELL_MATURATION_B, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, KOYAMA_SEMA3B_TARGETS_UP, YY1_02

GO Biological Process (5): negative regulation of transcription by RNA polymerase II (GO:0000122), blastocyst development (GO:0001824), positive regulation of hematopoietic stem cell proliferation (GO:1902035), negative regulation of hematopoietic stem cell differentiation (GO:1902037), in utero embryonic development (GO:0001701)

GO Molecular Function (3): transcription corepressor activity (GO:0003714), enzyme binding (GO:0019899), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), transcription repressor complex (GO:0017053), extracellular exosome (GO:0070062), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of DNA-templated transcription2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
in utero embryonic development1
anatomical structure development1
hematopoietic stem cell proliferation1
regulation of hematopoietic stem cell proliferation1
positive regulation of stem cell proliferation1
hematopoietic stem cell differentiation1
negative regulation of hematopoietic progenitor cell differentiation1
regulation of hematopoietic stem cell differentiation1
negative regulation of stem cell differentiation1
chordate embryonic development1
transcription coregulator activity1
protein binding1
binding1
intracellular membrane-bounded organelle1
transcription regulator complex1
extracellular vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

1229 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
N4BP2L2EXOC6BQ9Y2D4482
N4BP2L2ZNF805Q5CZA5464
N4BP2L2REPS1Q96D71449
N4BP2L2IRGQQ8WZA9431
N4BP2L2DPAGT1Q9H3H5397
N4BP2L2KCTD20Q7Z5Y7391
N4BP2L2AATFQ9NY61385
N4BP2L2PRR22Q8IZ63372
N4BP2L2ADPGKQ9BRR6358
N4BP2L2GTF2IRD2BQ6EKJ0350
N4BP2L2GTF2IRD2Q86UP8349
N4BP2L2RUNDC3AQ59EK9337
N4BP2L2SPIRE1Q08AE8333
N4BP2L2ARFIP1P53367330
N4BP2L2RUNDC3BQ96NL0327

IntAct

105 interactions, top by confidence:

ABTypeScore
PRPF4PPIHpsi-mi:“MI:0914”(association)0.910
RFXANKRFXAPpsi-mi:“MI:0914”(association)0.780
PPIHN4BP2L2psi-mi:“MI:0915”(physical association)0.720
N4BP2L2PPIHpsi-mi:“MI:0915”(physical association)0.720
PRG2YPEL5psi-mi:“MI:0914”(association)0.640
Hoxa1N4BP2L2psi-mi:“MI:0915”(physical association)0.570
LMO2N4BP2L2psi-mi:“MI:0915”(physical association)0.560
N4BP2L2HOXA1psi-mi:“MI:0915”(physical association)0.560
N4BP2L2psi-mi:“MI:0915”(physical association)0.560
NAA38N4BP2L2psi-mi:“MI:0915”(physical association)0.560
HOXA1N4BP2L2psi-mi:“MI:0915”(physical association)0.560
N4BP2L2psi-mi:“MI:0915”(physical association)0.560
N4BP2L2NAA38psi-mi:“MI:0915”(physical association)0.560
N4BP2L2PPIL1psi-mi:“MI:0915”(physical association)0.560
MRPS18CMRPS14psi-mi:“MI:0914”(association)0.530
PIPTBKBP1psi-mi:“MI:0914”(association)0.530
N4BP2L2bipApsi-mi:“MI:0915”(physical association)0.370
N4BP2L2reppsi-mi:“MI:0915”(physical association)0.370
N4BP2L2psi-mi:“MI:0915”(physical association)0.370
EGLN3FAM168Bpsi-mi:“MI:0914”(association)0.350

BioGRID (103): N4BP2L2 (Two-hybrid), N4BP2L2 (Two-hybrid), PPIH (Two-hybrid), NAA38 (Two-hybrid), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS), Hoxa1 (Affinity Capture-Western), PPIA (Two-hybrid), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS), N4BP2L2 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LFM6, A0A2K1JJ00, A0JMD2, A4H824, A5WWA0, A9ZPC9, B0S6S9, D3ZJ47, H0WFA5, O70343, P15822, P24433, P31629, P48437, Q0P4S0, Q0VAV2, Q15468, Q1LV19, Q1LY84, Q4V7H1, Q5RD08, Q5SWW4, Q60988, Q62417, Q66H65, Q6DFV3, Q6ZPK7, Q71RC2, Q80TY4, Q80U59, Q865B6, Q865B7, Q8JZS6, Q8K3V7, Q8LFU0, Q8VY64, Q91018, Q92786, Q92802, Q93ZL5

Diamond homologs: Q29S05, Q3V2Q8, Q5TBK1, Q66H65, Q86UW6, Q8JZS6, Q92802, P13233, O64843, O74840, Q08954, Q9UTP4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance20
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
599575NM_001278432.2(N4BP2L2):c.1406dup (p.Asn469fs)Pathogenic

SpliceAI

1211 predictions. Top by Δscore:

VariantEffectΔscore
13:32517866:C:Adonor_gain1.0000
13:32521371:A:ACdonor_gain1.0000
13:32521372:C:CCdonor_gain1.0000
13:32521372:CTTTT:Cdonor_gain1.0000
13:32522163:T:Adonor_gain1.0000
13:32522181:CCA:Cdonor_gain1.0000
13:32522186:T:TAdonor_gain1.0000
13:32522268:TTG:Tacceptor_gain1.0000
13:32522271:C:CCacceptor_gain1.0000
13:32522281:A:Cacceptor_gain1.0000
13:32527394:AGC:Adonor_gain1.0000
13:32537025:CAT:Cacceptor_gain1.0000
13:32521372:CTT:Cdonor_gain0.9900
13:32521448:GCCTA:Gacceptor_loss0.9900
13:32521449:CCT:Cacceptor_loss0.9900
13:32522181:C:CTdonor_gain0.9900
13:32522266:TTTTG:Tacceptor_gain0.9900
13:32522267:TTTG:Tacceptor_gain0.9900
13:32522269:TG:Tacceptor_gain0.9900
13:32522269:TGC:Tacceptor_loss0.9900
13:32522271:C:Tacceptor_loss0.9900
13:32522272:T:Aacceptor_loss0.9900
13:32522281:A:ACacceptor_gain0.9900
13:32522283:A:Cacceptor_gain0.9900
13:32527394:AG:Adonor_gain0.9900
13:32527395:G:Cdonor_gain0.9900
13:32527531:TT:Tacceptor_gain0.9900
13:32527533:C:CCacceptor_gain0.9900
13:32537026:ATCT:Aacceptor_loss0.9900
13:32537027:TCTGA:Tacceptor_loss0.9900

AlphaMissense

3937 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:32521399:C:AW508C0.999
13:32521399:C:GW508C0.999
13:32521401:A:GW508R0.999
13:32521401:A:TW508R0.999
13:32522206:C:AW483C0.999
13:32522206:C:GW483C0.999
13:32522208:A:GW483R0.999
13:32522208:A:TW483R0.999
13:32522224:G:CN477K0.999
13:32522224:G:TN477K0.999
13:32522228:T:AD476V0.999
13:32522231:A:TI475K0.999
13:32522234:A:TI474K0.999
13:32522237:A:TV473D0.999
13:32527478:A:CF438L0.999
13:32527478:A:TF438L0.999
13:32527479:A:GF438S0.999
13:32527480:A:GF438L0.999
13:32535784:T:AK415I0.999
13:32517962:A:GM531T0.998
13:32521379:A:GL515S0.998
13:32521412:G:TP504H0.998
13:32521420:A:CF501L0.998
13:32521420:A:TF501L0.998
13:32521421:A:GF501S0.998
13:32521422:A:GF501L0.998
13:32521448:G:TA492D0.998
13:32522218:A:CN479K0.998
13:32522218:A:TN479K0.998
13:32522229:C:GD476H0.998

dbSNP variants (sampled 300 via entrez): RS1000012513 (13:32533947 G>T), RS1000023203 (13:32491377 A>G), RS1000033775 (13:32474407 C>T), RS1000034790 (13:32435189 CT>C), RS1000053451 (13:32484312 G>A,C), RS1000109786 (13:32446287 G>A,C,T), RS1000143571 (13:32517533 A>G), RS1000158592 (13:32534542 TTCA>T), RS1000171200 (13:32456271 C>T), RS1000228527 (13:32464377 A>G), RS1000241441 (13:32506745 A>G), RS1000247237 (13:32501120 G>A), RS1000265854 (13:32514668 G>A), RS1000277887 (13:32477470 C>A), RS1000302628 (13:32500863 TTC>T)

Disease associations

OMIM: gene MIM:615788 | 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
GCST001937_19Breast cancer5.000000e-08
GCST005196_74Coronary artery disease7.000000e-11
GCST006612_83LDL cholesterol2.000000e-14
GCST006979_1094Heel bone mineral density2.000000e-12
GCST007010_2Logical memory (delayed recall)1.000000e-06
GCST010866_102Coronary artery disease3.000000e-09
GCST010988_464Adult body size3.000000e-13
GCST011365_2Myocardial infarction4.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0009270heel bone mineral density
EFO:0004874memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases expression, decreases methylation5
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
mercuric bromideincreases expression, affects cotreatment2
Arsenicaffects cotreatment, increases abundance, decreases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression, increases expression2
Aflatoxin B1decreases methylation2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
aristolochic acid Idecreases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
testosterone enanthateaffects expression1
methylmercuric chlorideincreases expression, decreases expression1
trichostatin Aincreases expression1
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
tamibarotenedecreases expression1
pentabromodiphenyl etherincreases expression1
JP8 aviation fuelincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
dorsomorphinaffects cotreatment, increases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases response to substance, increases expression1
jinfukangdecreases expression1
NSC 689534affects binding, increases expression1
(+)-JQ1 compounddecreases expression1
PCI 5002affects cotreatment, increases expression1
Sunitinibincreases expression1
Vorinostatincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.