NBPF19

gene
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Summary

NBPF19 (NBPF member 19, HGNC:31999) is a protein-coding gene on chromosome 1q21.2, encoding NBPF family member NBPF19 (A0A087WUL8).

Predicted to be located in cytoplasm.

Source: NCBI Gene 101060226 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 1 total
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_001351365

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:31999
Approved symbolNBPF19
NameNBPF member 19
Location1q21.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000271383
Ensembl biotypeprotein_coding
OMIM614006
Entrez101060226

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000651566

RefSeq mRNA: 1 — MANE Select: NM_001351365 NM_001351365

CCDS: CCDS86016

Canonical transcript exons

ENST00000651566 — 94 exons

ExonStartEnd
ENSE00003841219149496789149496897
ENSE00003841256149526962149527013
ENSE00003841447149492768149492940
ENSE00003841577149540301149540473
ENSE00003841635149550667149550718
ENSE00003841657149522865149523037
ENSE00003841795149520575149520683
ENSE00003841974149475898149476107
ENSE00003842161149514936149515108
ENSE00003842416149545930149545981
ENSE00003842559149544300149544408
ENSE00003842560149531691149531742
ENSE00003842572149513356149513528
ENSE00003842672149498417149498468
ENSE00003842952149527614149527786
ENSE00003843015149534812149534920
ENSE00003843085149553774149553882
ENSE00003843156149539563149539671
ENSE00003843363149487332149487383
ENSE00003843380149508595149508767
ENSE00003843594149507939149507990
ENSE00003843673149547472149547523
ENSE00003843676149514238149514289
ENSE00003843742149495200149495251
ENSE00003843774149546590149546762
ENSE00003843934149554495149556361
ENSE00003844030149482175149482226
ENSE00003844346149545038149545210
ENSE00003844384149526070149526242
ENSE00003844404149551327149551499
ENSE00003844474149504716149504767
ENSE00003844498149503178149503229
ENSE00003844731149499955149500006
ENSE00003844903149538676149538848
ENSE00003844951149510179149510351
ENSE00003845027149541193149541244
ENSE00003845124149511808149511980
ENSE00003845132149524445149524617
ENSE00003845154149536446149536497
ENSE00003845210149549037149549145
ENSE00003845349149537982149538033
ENSE00003845377149512700149512751
ENSE00003845425149518992149519043
ENSE00003845577149500657149500829
ENSE00003845644149517456149517507
ENSE00003845659149491139149491311
ENSE00003845690149502286149502458
ENSE00003845805149497525149497697
ENSE00003845892149537100149537272
ENSE00003845927149492026149492134
ENSE00003846079149533925149534097
ENSE00003846259149530799149530971
ENSE00003846600149488013149488185
ENSE00003846733149477945149478047
ENSE00003846758149552887149553059
ENSE00003846830149493660149493711
ENSE00003846842149516564149516736
ENSE00003846873149511066149511174
ENSE00003846891149548150149548322
ENSE00003846969149478880149479094
ENSE00003846992149501544149501652
ENSE00003847057149529174149529346
ENSE00003847188149552209149552260
ENSE00003847336149518110149518282
ENSE00003847725149486130149486293
ENSE00003847782149503834149504006
ENSE00003847810149542735149542786
ENSE00003847919149507047149507219
ENSE00003847960149535554149535726
ENSE00003848002149480679149480884
ENSE00003848381149522211149522262
ENSE00003848659149549775149549947
ENSE00003848775149480142149480214
ENSE00003848806149505418149505590
ENSE00003848875149541853149542025
ENSE00003848885149475045149475795
ENSE00003849147149523747149523798
ENSE00003849215149499073149499245
ENSE00003849290149530061149530169
ENSE00003849341149488905149488956
ENSE00003849369149525332149525440
ENSE00003849586149509477149509528
ENSE00003849668149533227149533278
ENSE00003849741149495902149496074
ENSE00003849774149543413149543585
ENSE00003849922149490443149490494
ENSE00003850127149519688149519860
ENSE00003850623149489561149489733
ENSE00003850733149521319149521491
ENSE00003850807149494318149494490
ENSE00003850858149515822149515930
ENSE00003851030149528496149528547
ENSE00003851085149506305149506413
ENSE00003851207149532345149532517

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.90.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548898.90gold quality
bone marrow cellCL:000209297.48gold quality
monocyteCL:000057697.34gold quality
leukocyteCL:000073897.32gold quality
colonic epitheliumUBERON:000039796.36gold quality
ventricular zoneUBERON:000305396.22gold quality
granulocyteCL:000009496.16gold quality
calcaneal tendonUBERON:000370194.89gold quality
tonsilUBERON:000237294.03gold quality
mucosa of stomachUBERON:000119993.89gold quality
stromal cell of endometriumCL:000225593.69gold quality
skin of abdomenUBERON:000141692.65gold quality
zone of skinUBERON:000001492.40gold quality
smooth muscle tissueUBERON:000113592.32gold quality
skin of legUBERON:000151192.02gold quality
bone marrowUBERON:000237191.89gold quality
descending thoracic aortaUBERON:000234591.74gold quality
ganglionic eminenceUBERON:000402391.18gold quality
vermiform appendixUBERON:000115491.14gold quality
bloodUBERON:000017890.87gold quality
right coronary arteryUBERON:000162590.38gold quality
urinary bladderUBERON:000125590.15gold quality
subcutaneous adipose tissueUBERON:000219090.13gold quality
fallopian tubeUBERON:000388990.11gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.02gold quality
popliteal arteryUBERON:000225089.98gold quality
tibial arteryUBERON:000761089.97gold quality
endometriumUBERON:000129589.95gold quality
ovaryUBERON:000099289.94gold quality
body of uterusUBERON:000985389.62gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-125970yes21.96
E-CURD-135no620.90
E-MTAB-7316no460.69
E-GEOD-150728no435.54
E-ANND-3no1.56

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (14): NBPF3 (ENSG00000142794), NBPF20 (ENSG00000162825), NBPF6 (ENSG00000186086), NBPF4 (ENSG00000196427), NBPF1 (ENSG00000219481), NBPF11 (ENSG00000263956), NBPF15 (ENSG00000266338), NBPF12 (ENSG00000268043), NBPF9 (ENSG00000269713), NBPF8 (ENSG00000270231), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF19A0A087WUL8 (reviewed: A0A087WUL8)

Alternative names: Neuroblastoma breakpoint family member 19

All UniProt accessions (1): A0A087WUL8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Miscellaneous. Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the chromosome 1.

Similarity. Belongs to the NBPF family.

RefSeq proteins (1): NP_001338294* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010630Olduvai_domDomain
IPR055306NBPFFamily

Pfam: PF06758

UniProt features (79 total): domain 45, region of interest 16, compositionally biased region 16, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for A0A087WUL8 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): chr1q21, KLF14_TARGET_GENES, KLF7_TARGET_GENES, ZNF10_TARGET_GENES, ZNF391_TARGET_GENES, ZNF423_TARGET_GENES, ZNF660_TARGET_GENES, ZNF843_TARGET_GENES, ZSCAN21_TARGET_GENES, ZSCAN30_TARGET_GENES, HU_FETAL_RETINA_RPE, ZNF579_TARGET_GENES, ZSCAN4_TARGET_GENES, INSM2_TARGET_GENES, PRDM4_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

218 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NBPF19NOTCH2NLAQ7Z3S9667
NBPF19OR4L1Q8NH43580
NBPF19OR2T10Q8NGZ9571
NBPF19LRP12Q9Y561546
NBPF19NOTCH2NLBP0DPK3507
NBPF19HHIPL2Q6UWX4447
NBPF19NKAPLQ5M9Q1395
NBPF19CFAP46Q8IYW2391
NBPF19SCNN1DP51172348
NBPF19NOL4LQ96MY1348
NBPF19L1TD1Q5T7N2329
NBPF19TRIM15Q9C019313
NBPF19SMPD4Q9NXE4305
NBPF19PI4K2AQ9BTU6278
NBPF19MUC3AQ02505269

IntAct

0 interactions, top by confidence:

BioGRID (233): NBPF19 (Affinity Capture-RNA), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid), NBPF19 (Two-hybrid)

ESM2 similar proteins: A0A087WUL8, A0A0J9YWL9, A0A0U1RQI7, A0A1D9BZF0, A6NJU9, A6NKU9, A6NNC1, A6QL64, A8MRT5, B2SU53, B4DH59, B5DUH6, C9JG80, E5RHQ5, F8W0I5, P01068, P02895, P06916, P07907, P0DKL2, P0DPF3, P0DRJ4, P13208, P14417, P32072, P83060, Q26755, Q3BBV0, Q3BBV2, Q4ZJY7, Q4ZJZ0, Q4ZJZ1, Q4ZJZ3, Q5TAG4, Q5TI25, Q6P3W6, Q6RY98, Q7T3L1, Q86SG3, Q86T75

Diamond homologs: A0A087WUL8, B4DH59, P0C2Y1, P0DPF2, P0DPF3, Q32LC2, Q3BBV0, Q3BBV2, Q5TAG4, Q5TI25, Q5VU43, Q5VWK0, Q6P3W6, Q86T75, Q86XG9, Q8N660, Q96M43, Q9H094, A0A096LNW5, A2RUV0, G3I6Z6, O35516, P0DPK3, P0DPK4, P10040, P21783, P46530, P46531, Q01705, Q04721, Q04756, Q07008, Q20911, Q7Z3S9, Q80YT7, Q99466, Q9QW30, Q9UM47, Q19UN5, Q8K389

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2563 predictions. Top by Δscore:

VariantEffectΔscore
1:149475896:A:AGacceptor_gain1.0000
1:149475897:G:GGacceptor_gain1.0000
1:149475897:GTCC:Gacceptor_gain1.0000
1:149475897:GTCCC:Gacceptor_gain1.0000
1:149476103:ATACA:Adonor_gain1.0000
1:149476108:G:GGdonor_gain1.0000
1:149477943:A:AGacceptor_gain1.0000
1:149477944:G:GAacceptor_gain1.0000
1:149477944:GA:Gacceptor_gain1.0000
1:149480136:TTACA:Tacceptor_loss1.0000
1:149480138:ACAG:Aacceptor_loss1.0000
1:149480139:CA:Cacceptor_loss1.0000
1:149480140:A:AGacceptor_gain1.0000
1:149480140:AGAA:Aacceptor_loss1.0000
1:149480141:G:GGacceptor_gain1.0000
1:149480141:G:GTacceptor_loss1.0000
1:149480141:GA:Gacceptor_gain1.0000
1:149480141:GAA:Gacceptor_gain1.0000
1:149480141:GAAA:Gacceptor_gain1.0000
1:149480668:T:TAacceptor_gain1.0000
1:149482169:TTACA:Tacceptor_loss1.0000
1:149482170:TACAG:Tacceptor_loss1.0000
1:149482171:ACAG:Aacceptor_loss1.0000
1:149482172:CA:Cacceptor_loss1.0000
1:149482173:A:ACacceptor_loss1.0000
1:149482173:A:AGacceptor_gain1.0000
1:149482174:G:Aacceptor_loss1.0000
1:149482174:G:GGacceptor_gain1.0000
1:149487383:GGT:Gdonor_loss1.0000
1:149487384:GT:Gdonor_loss1.0000

AlphaMissense

25003 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:149500811:T:CF1037L0.998
1:149500813:T:AF1037L0.998
1:149500813:T:GF1037L0.998
1:149510333:T:CF1525L0.996
1:149510335:T:AF1525L0.996
1:149510335:T:GF1525L0.996
1:149496056:T:CF793L0.994
1:149496058:T:AF793L0.994
1:149496058:T:GF793L0.994
1:149500812:T:CF1037S0.994
1:149491293:T:CF549L0.993
1:149491295:T:AF549L0.993
1:149491295:T:GF549L0.993
1:149500781:T:CF1027L0.993
1:149500783:T:AF1027L0.993
1:149500783:T:GF1027L0.993
1:149501577:G:TR1054M0.992
1:149510334:T:CF1525S0.992
1:149491294:T:CF549S0.991
1:149495963:T:CC762R0.991
1:149500818:T:CL1039P0.991
1:149506354:G:CK1303N0.991
1:149506354:G:TK1303N0.991
1:149510303:T:CF1515L0.991
1:149510305:T:AF1515L0.991
1:149510305:T:GF1515L0.991
1:149500818:T:AL1039H0.990
1:149501575:A:CR1053S0.990
1:149501575:A:TR1053S0.990
1:149496057:T:CF793S0.989

dbSNP variants (sampled 300 via entrez): RS1043866 (1:149556114 C>A,G), RS111884557 (1:149514755 T>A), RS112466911 (1:149509929 T>A), RS112542840 (1:149521084 C>G), RS112637520 (1:149525218 G>C), RS113072215 (1:149524185 G>A), RS113202683 (1:149531329 A>G), RS113249690 (1:149508837 A>C), RS113337668 (1:149525425 A>C), RS113721966 (1:149530673 A>C), RS11485704 (1:149483838 A>C), RS11488536 (1:149485303 C>T), RS11488537 (1:149480744 A>G,T), RS1156260337 (1:149487487 A>G), RS1156312702 (1:149555601 A>C)

Disease associations

OMIM: gene MIM:614006 | disease phenotypes: MIM:148300

GenCC curated gene-disease

Mondo (1): keratoconus (MONDO:0015486)

Orphanet (2): OBSOLETE: Keratoconus (Orphanet:156071), NON RARE IN EUROPE: Isolated keratoconus (Orphanet:2335)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000563Keratoconus

GWAS associations

3 associations (top):

StudyTraitp-value
GCST007725_40Serum uric acid levels6.000000e-14
GCST007733_48Serum uric acid levels6.000000e-14
GCST007733_68Serum uric acid levels1.000000e-29

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004761uric acid measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D007640KeratoconusC11.204.627

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
securinineincreases expression1
sodium arsenitedecreases expression, increases abundance1
zinc chromateincreases abundance, increases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent ionincreases abundance, increases expression1
abrineincreases expression1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases abundance, increases expression1
Lipopolysaccharidesincreases expression, affects response to substance, affects cotreatment1
Methapyrileneincreases methylation1
Tretinoinincreases expression1
Aflatoxin B1increases methylation1
Cadmium Chlorideincreases abundance, increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01485211PHASE4COMPLETEDCorneal Thickness Changes During Corneal Collagen Cross-linking With Ultraviolet-A Irradiation and Riboflavin
NCT02119039PHASE4COMPLETEDEffect of CACICOL20 on Corneal Epithelial Healing After Cross-linking in Patients With Keratoconus
NCT03245853PHASE4COMPLETEDEpi-On Corneal Crosslinking for Keratoconus
NCT03429569PHASE4UNKNOWNCross-Linking ACcéléré Iontophorèse Confocal kératocONE
NCT04427956PHASE4COMPLETEDCorneal Crosslinking Treatment Study
NCT07474870PHASE4NOT_YET_RECRUITINGOutcomes of CTAK Surgery
NCT00371202PHASE3UNKNOWNComparison of Penetrating Keratoplasty and Deep Lamellar Keratoplasty With the Big Bubble Technique for Keratoconus
NCT00647699PHASE3COMPLETEDCorneal Collagen Cross-linking for Progressive Keratoconus
NCT00815256PHASE3UNKNOWNSafety and Effectiveness of Collagen Cross Linking in Progressive Mild and Moderate Keratoconus
NCT00887900PHASE3COMPLETEDDeep Anterior Lamellar Keratoplasty (DALK)
NCT01112072PHASE3UNKNOWNCorneal Collagen Crosslinking and Intacs for Keratoconus and Ectasia
NCT01152541PHASE3UNKNOWNCorneal Collagen Crosslinking for Progressive Keratoconus and Ectasia Using Riboflavin/Dextran and Hypotonic Riboflavin
NCT01190306PHASE3TERMINATEDSafety Study of the VEGA UV-A System to Treat Keratoconus
NCT01344187PHASE3COMPLETEDSafety and Efficacy Study of Corneal Collagen Cross-Linking in Eyes With Keratoconus
NCT01459679PHASE3TERMINATEDSafety & Efficacy of Corneal Collagen Cross-Linking in Eyes With Keratoconus or Corneal Ectasia After Refractive Surgery
NCT01464268PHASE3UNKNOWNTransepithelial Corneal Collagen Crosslinking for Keratoconus and Corneal Ectasia
NCT01604135PHASE3ACTIVE_NOT_RECRUITINGCollagen Crosslinking for Keratoconus - a Randomized Controlled Clinical Trial
NCT01643226PHASE3COMPLETEDSafety and Efficacy Study of Corneal Collagen Cross-Linking in Eyes With Keratoconus
NCT01672814PHASE3COMPLETEDMicrowave Treatment and Corneal Collagen Crosslinking for Keratoconus
NCT01682993PHASE3TERMINATEDCorneal Cross Linking and Topography Guided Excimer Laser Treatment
NCT01972854PHASE3TERMINATEDSafety and Efficacy of Corneal Collagen Cross-Linking in Eyes With Keratoconus
NCT02613780PHASE3UNKNOWNRefractive Treatment of Early Keratoconus
NCT02638376PHASE3UNKNOWNEvaluating the Safety and Efficacy of the KXL System for Corneal Collagen Cross-Linking in Eyes Having Keratoconus
NCT03080077PHASE3UNKNOWNSafety and Effectiveness of Corneal Crosslinking (CXL): Keratoconus and Post-Refractive Ectasia
NCT03187912PHASE3COMPLETEDAccelerated Corneal Cross-linking With Different Riboflavin Solutions
NCT03442751PHASE3COMPLETEDStudy to Evaluate the Safety and Efficacy of Epi-on Corneal Cross-linking in Eyes With Progressive Keratoconus
NCT03858036PHASE3UNKNOWNCorneal Collagen Cross-Linking (CXL) Performed With Epi-ON Versus Epi-OFF in Eyes With Keratoconus and Other Corneal Ectatic Disorders
NCT04897503PHASE3UNKNOWNCorneal Collagen Crosslinking for Keratoconus and Ectasia Using Riboflavin/Dextran or Riboflavin/Methylcellulose
NCT04905108PHASE3UNKNOWNTransepithelial (Epi-on) Corneal Collagen Crosslinking to Treat Keratoconus and Corneal Ectasia
NCT05027295PHASE3UNKNOWNAccelerated Corneal Collagen Crosslinking for Keratoconus and Ectasia Using Pulse or Continuous UV-A Light
NCT06100939PHASE3ACTIVE_NOT_RECRUITINGEpithelium-On Corneal Cross-linking in Subjects 8 to 45 Years of Age With Keratoconus
NCT06100952PHASE3ACTIVE_NOT_RECRUITINGEpithelium-On Corneal Cross-linking in Subjects 8 to 45 Years of Age with Keratoconus
NCT06450470PHASE3RECRUITINGUse of a Freeze-dried Amniotic Membrane Post Crosslinking in Subjects With Progressive Keratoconus
NCT06601101PHASE3RECRUITINGEffects of Topical Insulin on Corneal Epithelium Healing After Corneal Crosslinking in Patients With Keratoconus
NCT07124910PHASE3RECRUITINGComparison of Epi-ON Corneal Collagen Crosslinking Performed Using an 18-Minute UVA Exposure vs. a 24-Minute UVA Exposure on Eyes With Ectatic Corneal Diseases
NCT07135167PHASE3RECRUITINGCompassionate Use Study of Epi-ON Corneal Collagen Crosslinking Performed Using UVA Exposure on Eyes With Ectatic Corneal Diseases for Subjects With Down Syndrome
NCT00409955PHASE2COMPLETEDLamellar Transplant With Lyophilized Corneas
NCT00925327PHASE2UNKNOWNSafety and Effectiveness of the UV-X System for Corneal Collagen Cross-Linking for Compassionate Treatment in Pediatric Patients With Progressive Keratoconus
NCT01143389PHASE2COMPLETEDCorneal Crosslinking in Patients With Keratoconus and Post-Refractive Ectasia
NCT01181219PHASE2COMPLETEDTransepithelial Corneal Collagen Cross-linking (CXL) in Treatment of Keratoconus
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): keratoconus