oral cleft Gene Set

Dataset GWASdb SNP-Phenotype Associations
Category disease or phenotype associations
Type phenotype
Description The presence of a cleft in the oral cavity, the two main types of which are cleft lip and cleft palate. In cleft lip, there is the congenital failure of the maxillary and median nasal processes to fuse, forming a groove or fissure in the lip. In cleft palate, there is a congenital failure of the palate to fuse properly, forming a grooved depression or fissure in the roof of the mouth. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately. (Human Phenotype Ontology, HP_0000202)
External Link http://jjwanglab.org/gwasdb/gwasdb2/gwasdb2/go_trait/HP:0000202
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Genes

276 genes associated with the oral cleft phenotype in GWAS datasets from the GWASdb SNP-Phenotype Associations dataset.

Symbol Name Standardized Value
JAM3 junctional adhesion molecule 3 1.77312
ABCA4 ATP-binding cassette, sub-family A (ABC1), member 4 1.53903
IRF6 interferon regulatory factor 6 1.53903
KIAA1598 1.46277
DIEXF digestive organ expansion factor homolog (zebrafish) 1.4425
SYT14 synaptotagmin XIV 1.28732
PAX7 paired box 7 1.26545
TRAF3IP3 TRAF3 interacting protein 3 1.25755
THADA thyroid adenoma associated 1.24751
ADTRP androgen-dependent TFPI-regulating protein 1.18704
NTN1 netrin 1 1.18306
SEMA4D sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D 1.08774
ARHGAP29 Rho GTPase activating protein 29 1.07843
SH3BP4 SH3-domain binding protein 4 1.0674
TXNDC16 thioredoxin domain containing 16 1.05869
EPHA3 EPH receptor A3 1.05007
FILIP1L filamin A interacting protein 1-like 1.04365
ZIC2 Zic family member 2 1.04365
COL8A1 collagen, type VIII, alpha 1 1.02042
CSMD1 CUB and Sushi multiple domains 1 1.01962
TTC27 tetratricopeptide repeat domain 27 1.00697
BEST3 bestrophin 3 1.00059
ARHGAP8 Rho GTPase activating protein 8 1.00059
LINC00486 long intergenic non-protein coding RNA 486 0.994551
FMN1 formin 1 0.989013
PCDH7 protocadherin 7 0.977911
ACOT12 acyl-CoA thioesterase 12 0.969142
PAK1 p21 protein (Cdc42/Rac)-activated kinase 1 0.969142
LTBP1 latent transforming growth factor beta binding protein 1 0.955595
DOCK2 dedicator of cytokinesis 2 0.951336
RASGRF2 Ras protein-specific guanine nucleotide-releasing factor 2 0.942765
MTUS1 microtubule associated tumor suppressor 1 0.932469
LOC146880 Rho GTPase activating protein 27 pseudogene 0.931527
KCNK10 potassium channel, two pore domain subfamily K, member 10 0.93106
PLEKHM1P pleckstrin homology domain containing, family M (with RUN domain) member 1 pseudogene 0.929216
NKAIN3 Na+/K+ transporting ATPase interacting 3 0.925645
TTR transthyretin 0.923064
BMP6 bone morphogenetic protein 6 0.919744
CADM1 cell adhesion molecule 1 0.919744
CCDC38 coiled-coil domain containing 38 0.918332
SYT17 synaptotagmin XVII 0.913571
FAM49A family with sequence similarity 49, member A 0.912522
KLHL1 kelch-like family member 1 0.910053
NTRK2 neurotrophic tyrosine kinase, receptor, type 2 0.901553
ATXN3 ataxin 3 0.899912
PAX5 paired box 5 0.894147
NCKAP5 NCK-associated protein 5 0.889642
MAST4 microtubule associated serine/threonine kinase family member 4 0.887592
FHIT fragile histidine triad 0.882984
CHD1L chromodomain helicase DNA binding protein 1-like 0.872981
GRM7 glutamate receptor, metabotropic 7 0.868241
FGFR2 fibroblast growth factor receptor 2 0.852276
FRMD3 FERM domain containing 3 0.845086
C3ORF52 chromosome 3 open reading frame 52 0.844346
FER1L5 fer-1-like family member 5 0.842167
CACNA2D4 calcium channel, voltage-dependent, alpha 2/delta subunit 4 0.840142
CYLD cylindromatosis (turban tumor syndrome) 0.840142
PRSS23 protease, serine, 23 0.833415
OR5AR1 olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene) 0.832497
PARD6B par-6 family cell polarity regulator beta 0.831588
PRRT3 proline-rich transmembrane protein 3 0.828922
SMCO4 single-pass membrane protein with coiled-coil domains 4 0.82634
PRTG protogenin 0.824663
PPP2R5C protein phosphatase 2, regulatory subunit B', gamma 0.824663
PBX1 pre-B-cell leukemia homeobox 1 0.823837
NELL1 NEL-like 1 (chicken) 0.823837
NCOR2 nuclear receptor corepressor 2 0.819829
CACNA1D calcium channel, voltage-dependent, L type, alpha 1D subunit 0.816759
SLC8A1 solute carrier family 8 (sodium/calcium exchanger), member 1 0.813733
TRAPPC11 trafficking protein particle complex 11 0.806402
ZFHX3 zinc finger homeobox 3 0.804323
RGS6 regulator of G-protein signaling 6 0.804323
OR5R1 olfactory receptor, family 5, subfamily R, member 1 (gene/pseudogene) 0.798387
TRIO trio Rho guanine nucleotide exchange factor 0.794657
GABBR2 gamma-aminobutyric acid (GABA) B receptor, 2 0.792855
ALG14 ALG14, UDP-N-acetylglucosaminyltransferase subunit 0.792263
PTPRD protein tyrosine phosphatase, receptor type, D 0.789787
KLHL26 kelch-like family member 26 0.787244
NINJ2 ninjurin 2 0.785384
LVRN laeverin 0.784773
CD247 CD247 molecule 0.781779
ANKRD18CP ankyrin repeat domain 18C, pseudogene 0.78061
USP31 ubiquitin specific peptidase 31 0.780031
LAMA1 laminin, alpha 1 0.778318
A1CF APOBEC1 complementation factor 0.773909
NTNG1 netrin G1 0.772842
FAM227B family with sequence similarity 227, member B 0.769717
SEC16A SEC16 homolog A (S. cerevisiae) 0.764079
POU5F1 POU class 5 homeobox 1 0.762996
RBM20 RNA binding motif protein 20 0.760343
TCP11L2 t-complex 11, testis-specific-like 2 0.759822
GPR137C G protein-coupled receptor 137C 0.757765
ZNF608 zinc finger protein 608 0.757258
FGFBP1 fibroblast growth factor binding protein 1 0.757258
FHOD3 formin homology 2 domain containing 3 0.756753
SOX5 SRY (sex determining region Y)-box 5 0.755257
TKT transketolase 0.748581
RYR2 ryanodine receptor 2 (cardiac) 0.747666
CTNND2 catenin (cadherin-associated protein), delta 2 0.745419
NFRKB nuclear factor related to kappaB binding protein 0.744097
LINC00536 long intergenic non-protein coding RNA 536 0.74151
PPP4R4 protein phosphatase 4, regulatory subunit 4 0.740664
PALLD palladin, cytoskeletal associated protein 0.740245
NAALADL2 N-acetylated alpha-linked acidic dipeptidase-like 2 0.737224
KALRN kalirin, RhoGEF kinase 0.732349
CNTN6 contactin 6 0.728954
ENO4 enolase family member 4 0.7273
OR9G1 olfactory receptor, family 9, subfamily G, member 1 0.724872
HCG9 HLA complex group 9 (non-protein coding) 0.721729
PRICKLE1 prickle homolog 1 (Drosophila) 0.717942
DOCK8 dedicator of cytokinesis 8 0.717572
SCG5 secretogranin V 0.71538
NCOA2 nuclear receptor coactivator 2 0.708265
CLYBL citrate lyase beta like 0.70533
SKINTL Skint-like, pseudogene 0.704969
PMM2 phosphomannomutase 2 0.704969
TAP2 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) 0.704609
DLG2 discs, large homolog 2 (Drosophila) 0.701779
KIF6 kinesin family member 6 0.701084
PID1 phosphotyrosine interaction domain containing 1 0.700738
PTGER3 prostaglandin E receptor 3 (subtype EP3) 0.698689
ITGAV integrin, alpha V 0.697013
SUGP2 SURP and G patch domain containing 2 0.696351
SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 0.695366
RHPN2 rhophilin, Rho GTPase binding protein 2 0.695366
MACROD2 MACRO domain containing 2 0.694714
PTPRM protein tyrosine phosphatase, receptor type, M 0.694714
DLC1 DLC1 Rho GTPase activating protein 0.693105
TP63 tumor protein p63 0.690896
GIPC3 GIPC PDZ domain containing family, member 3 0.690896
ST6GALNAC3 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 0.690896
CYP4Z1 cytochrome P450, family 4, subfamily Z, polypeptide 1 0.690274
GPR39 G protein-coupled receptor 39 0.689042
DLG1 discs, large homolog 1 (Drosophila) 0.688736
BRINP3 bone morphogenetic protein/retinoic acid inducible neural-specific 3 0.688431
MSX2 msh homeobox 2 0.687222
KREMEN1 kringle containing transmembrane protein 1 0.686922
PDE10A phosphodiesterase 10A 0.686623
SCN10A sodium channel, voltage gated, type X alpha subunit 0.684265
SECISBP2L SECIS binding protein 2-like 0.682533
NRG1 neuregulin 1 0.67542
LIMCH1 LIM and calponin homology domains 1 0.674828
MVB12B multivesicular body subunit 12B 0.67249
SHROOM3 shroom family member 3 0.670205
SAP30BP SAP30 binding protein 0.667695
ZNF385B zinc finger protein 385B 0.667145
MIR31HG MIR31 host gene 0.666599
PHLDB2 pleckstrin homology-like domain, family B, member 2 0.666055
KCNE1 potassium channel, voltage gated subfamily E regulatory beta subunit 1 0.664442
RBFOX3 RNA binding protein, fox-1 homolog (C. elegans) 3 0.663645
SLC6A3 solute carrier family 6 (neurotransmitter transporter), member 3 0.662854
WDR46 WD repeat domain 46 0.662592
NFIB nuclear factor I/B 0.660006
PDE8B phosphodiesterase 8B 0.659752
IGSF11 immunoglobulin superfamily, member 11 0.658738
CCNY cyclin Y 0.658487
PDE1C phosphodiesterase 1C, calmodulin-dependent 70kDa 0.657487
OR8K1 olfactory receptor, family 8, subfamily K, member 1 0.657487
EML6 echinoderm microtubule associated protein like 6 0.656005
ASIC2 acid sensing (proton gated) ion channel 2 0.654787
CDH12 cadherin 12, type 2 (N-cadherin 2) 0.654787
PHF1 PHD finger protein 1 0.654545
MROH2A maestro heat-like repeat family member 2A 0.654545
TANC2 tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 0.654304
SHC4 SHC (Src homology 2 domain containing) family, member 4 0.653106
ABI3BP ABI family, member 3 (NESH) binding protein 0.650522
SGSM2 small G protein signaling modulator 2 0.650291
PTPRT protein tyrosine phosphatase, receptor type, T 0.649139
ZNF618 zinc finger protein 618 0.648884
FBXL17 F-box and leucine-rich repeat protein 17 0.648376
CDYL chromodomain protein, Y-like 0.648123
LOC100132891 0.646616
EXPH5 exophilin 5 0.645871
SLIT3 slit homolog 3 (Drosophila) 0.645624
FAXC failed axon connections homolog (Drosophila) 0.643909
LARP1 La ribonucleoprotein domain family, member 1 0.643425
FLT4 fms-related tyrosine kinase 4 0.643183
UBQLN1 ubiquilin 1 0.642942
INPP5E inositol polyphosphate-5-phosphatase, 72 kDa 0.641983
FRMD4B FERM domain containing 4B 0.641745
ASTN2 astrotactin 2 0.640092
APBA1 amyloid beta (A4) precursor protein-binding, family A, member 1 0.639624
GLP1R glucagon-like peptide 1 receptor 0.639391
TTL tubulin tyrosine ligase 0.639391
FAM187B family with sequence similarity 187, member B 0.637318
PON2 paraoxonase 2 0.636635
NLGN1 neuroligin 1 0.635508
KCNMA1 potassium channel, calcium activated large conductance subfamily M alpha, member 1 0.634172
AASS aminoadipate-semialdehyde synthase 0.634172
ENDOD1 endonuclease domain containing 1 0.63351
SPOCD1 SPOC domain containing 1 0.631765
MAP2K5 mitogen-activated protein kinase kinase 5 0.630049
DNAH11 dynein, axonemal, heavy chain 11 0.629837
HFE hemochromatosis 0.628991
KCNIP1 Kv channel interacting protein 1 0.628571
PRR16 proline rich 16 0.627736
ZNF839 zinc finger protein 839 0.626907
TMEFF2 transmembrane protein with EGF-like and two follistatin-like domains 2 0.625881
CNGB3 cyclic nucleotide gated channel beta 3 0.624865
SPOCK1 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1 0.62426
ECSIT ECSIT signalling integrator 0.622665
ZMYND8 zinc finger, MYND-type containing 8 0.622467
HABP2 hyaluronan binding protein 2 0.62168
DOK5 docking protein 5 0.6209
NR5A2 nuclear receptor subfamily 5, group A, member 2 0.616892
USP45 ubiquitin specific peptidase 45 0.616892
ZFP57 ZFP57 zinc finger protein 0.615542
THEM5 thioesterase superfamily member 5 0.614589
LOC643542 uncharacterized LOC643542 0.6144
DSCAML1 Down syndrome cell adhesion molecule like 1 0.61421
RBFOX1 RNA binding protein, fox-1 homolog (C. elegans) 1 0.613833
PTGFR prostaglandin F receptor (FP) 0.613269
AXIN1 axin 1 0.612895
FUT2 fucosyltransferase 2 (secretor status included) 0.609951
PRKCB protein kinase C, beta 0.605862
ARHGEF18 Rho/Rac guanine nucleotide exchange factor (GEF) 18 0.605515
HS6ST3 heparan sulfate 6-O-sulfotransferase 3 0.605341
MINK1 misshapen-like kinase 1 0.603964
GRHL3 grainyhead-like 3 (Drosophila) 0.603793
PACRG PARK2 co-regulated 0.603622
TGM6 transglutaminase 6 0.60143
DOCK4 dedicator of cytokinesis 4 0.60027
SLC2A5 solute carrier family 2 (facilitated glucose/fructose transporter), member 5 0.599776
PPAPDC1A phosphatidic acid phosphatase type 2 domain containing 1A 0.599285
HS6ST1 heparan sulfate 6-O-sulfotransferase 1 0.597345
HSD11B1 hydroxysteroid (11-beta) dehydrogenase 1 0.597185
FAT1 FAT atypical cadherin 1 0.596389
APPL1 adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1 0.59466
C1S complement component 1, s subcomponent 0.593884
ANXA10 annexin A10 0.593884
OSBPL3 oxysterol binding protein-like 3 0.593884
FMN2 formin 2 0.593884
LOC284395 uncharacterized LOC284395 0.593575
LINGO2 leucine rich repeat and Ig domain containing 2 0.593113
PLEKHH2 pleckstrin homology domain containing, family H (with MyTH4 domain) member 2 0.592654
KCNH7 potassium channel, voltage gated eag related subfamily H, member 7 0.591138
ASCC3 activating signal cointegrator 1 complex subunit 3 0.590389
PHACTR2 phosphatase and actin regulator 2 0.590389
FRMD1 FERM domain containing 1 0.59024
ITPKB inositol-trisphosphate 3-kinase B 0.589942
PLXDC2 plexin domain containing 2 0.589942
KCNQ1 potassium channel, voltage gated KQT-like subfamily Q, member 1 0.588321
LRRIQ3 leucine-rich repeats and IQ motif containing 3 0.588029
LOC284294 uncharacterized LOC284294 0.587158
CHRM5 cholinergic receptor, muscarinic 5 0.586438
ABCB5 ATP-binding cassette, sub-family B (MDR/TAP), member 5 0.585756
CIDEA cell death-inducing DFFA-like effector a 0.585631
SYNGR1 synaptogyrin 1 0.585507
PARD3 par-3 family cell polarity regulator 0.585136
DYSF dysferlin 0.584889
ZNF831 zinc finger protein 831 0.583787
LOC285768 uncharacterized LOC285768 0.582939
PDZD2 PDZ domain containing 2 0.581742
TMEM30C transmembrane protein 30C 0.581504
C1ORF198 chromosome 1 open reading frame 198 0.581386
WWOX WW domain containing oxidoreductase 0.581149
NCAM1 neural cell adhesion molecule 1 0.580796
FMO5 flavin containing monooxygenase 5 0.58021
MMP16 matrix metallopeptidase 16 (membrane-inserted) 0.578934
HIVEP3 human immunodeficiency virus type I enhancer binding protein 3 0.578819
SH3GL3 SH3-domain GRB2-like 3 0.578704
LILRB2 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 0.578246
PKIB protein kinase (cAMP-dependent, catalytic) inhibitor beta 0.577224
MYO3B myosin IIIB 0.574995
FAM124A family with sequence similarity 124A 0.574556
ARHGEF26-AS1 ARHGEF26 antisense RNA 1 0.573685
LOC100505940 0.570703
PRKG1 protein kinase, cGMP-dependent, type I 0.569663
UNQ6494 uncharacterized LOC100129066 0.566616
C2ORF91 chromosome 2 open reading frame 91 0.554715
EPB41L4A erythrocyte membrane protein band 4.1 like 4A 0.545167
SMAP2 small ArfGAP2 0.525969
DAAM2 dishevelled associated activator of morphogenesis 2 0.49961
DGKG diacylglycerol kinase, gamma 90kDa 0.486856
TMCO4 transmembrane and coiled-coil domains 4 0.46966
SLC25A21 solute carrier family 25 (mitochondrial oxoadipate carrier), member 21 0.424616