Clinical CADD Gene Guide - ALPHA 1

UMCG RUG 5GPM
© 2014, Genomics Coordination Center, Department of Genetics, UMCG Groningen

How to use:

  1. Hit CTRL+F or CMD+F to enable your browser search and find your gene of interest.
  2. Check the Wilcoxon p-value find out if an association between CADD score and pathogenic vs. population variants has been detected:
    • If the p-value is
      green
      , the results are Bonferroni significant and usually quite meaningful.
    • If the p-value is
      yellow
      , the results are indicative, but not very convincing. Use with caution.
    • If the p-value is
      red
      , there is no proven association, usually due to low sample size.
  3. Open the plot by clicking on the gene name. Inspect the optimal group separation made by Youden's cutpoint.
  4. A high Youden's index make the cutpoint more reliable. Other properties (e.g. PPV and NPV at cutpoint) may also help you decide to trust it.
  5. You can always eyeball the plot to find a different (e.g. more stringent) cutpoint that you trust more.

Legend

Gene = The HGNC symbol of the gene being tested in this row. Click to view plot. more info
Wilcoxon p-val = Wilcoxon rank sum test with continuity correction. Probability of population variants being a different from pathogenic variants. more info
Wilcoxon stat = Sum of the ranks of the observations. more info
Youden's index = Point of optimal performance, measured as Sensitivity + Specificity − 1. more info
Youden's cutpoint = The CADD score cutoff at the index. more info
PPV = Positive Predictive Value, proportion of true positives over all positive calls. more info
NPV = Negative Predictive Value, proportion of negative positives over all negative calls. more info
AUC = Area Under Curve, probability a randomly chosen pathogenic variant CADD score ranks higher than a randomly chosen population variant CADD score. more info
nPatho = Number of pathogenic variants used (ClinVar). more info
nPop = Number of population variants used (GoNL+1000G). GoNL info, 1000G info
Raw data = Click link to download the pathogenic and population variants with their CADD scores used in the assessment. more info


GeneWilcoxon p-valWilcoxon statYouden's indexYouden's cutpointPPVNPVAUCnPathonPopRaw data
BRCA26.45630831985457e-6829640.773532615716.120.8565022421524660.9113475177304970.952518262206844289216download
BRCA13.13425295523501e-5028880.735052728615.830.6750.9685039370078740.935061722843073311143download
DMD1.93171968931571e-442408.50.7080291971360.86206896551724110.929678832116788137250download
COL4A51.43380312232735e-3019610.770444444413.450.6458333333333330.9715099715099720.9273703703703737572download
COL3A12.91921963309201e-3042890.667572463815.020.6607142857142860.93750.87859488224637736896download
F83.58722488113412e-295490.834722222213.620.8505747126436780.9562043795620440.9523437514480download
FBN11.73616610978887e-281357.50.757864421817.590.9674418604651160.6504854368932040.92481723526805574244download
MSH26.46789510465089e-27622.50.733799533817.560.7738095238095240.9253731343283580.94195804195804214375download
CFTR1.60705498719778e-2542980.549427043517.590.8287671232876710.7247191011235950.835828877005348154170download
GALT6.70218186755919e-259470.717295873611.080.8253968253968250.9214659685863870.92441535637321418767download
PAH2.97038486273244e-245000.781334841615.010.9389312977099240.8142857142857140.94343891402714965136download
MSH62.02711427725369e-23579.50.779361179416.590.9698795180722890.6756756756756760.94304668304668355185download
PTPN113.76270397577399e-231320.903528528515.790.9710144927536230.9350649350649350.9752252252252257472download
SMAD45.42094808895229e-221210.894664842714.070.9863013698630140.820.98160814713482343153download
ASPM2.5376104432836e-21302.50.899556541230.9861751152073730.8636363636363640.96646341463414641220download
HEXA5.29137673266868e-21209.50.88938580816.440.9864864864864860.8039215686274510.96876863446630943156download
PSEN11.36937984216138e-20111.50.964912280714.6910.8636363636363640.98284087411511238171download
GNPTAB3.92932806042343e-20840.50.685547785512.60.960396039603960.6526315789473690.90203962703962766130download
BTD1.81067452118823e-1910380.707357490113.780.7529411764705880.9196428571428570.88532920901458212473download
MLH13.14123607454472e-1914000.546587807125.30.5446428571428570.9217391304347830.87261146496815315770download
MYO7A3.89429051087995e-192700.810756399216.130.98750.5901639344262290.96117342536669538183download
AR5.56763582019025e-192820.815033161412.740.9561403508771930.820.94804716285924846118download
SPG118.33896805721615e-184380.779319041614.930.9870129870129870.5441176470588240.93862967633459439183download
BRAF1.5989246718618e-17146.50.870967741918.0410.6923076923076920.96718189964157736124download
THRB6.96219603491845e-17160.923563218413.830.9910714285714280.8529411764705880.99540229885057530116download
RB12.85837238049072e-16141.50.837118754116.430.9672131147540980.8461538461538460.9540882543802734667download
FLNB2.88166604623063e-167870.787043931521.30.9961389961389960.3626373626373630.9267498138495934316download
KCNQ26.61556131473467e-162110.834664300511.310.9833333333333330.8275862068965520.9375924282756584969download
USH2A6.89780356054093e-161694.50.693986254316.050.9921052631578950.2340425531914890.9029495990836236485download
SCN4A7.83327885559747e-16518.50.798815669615.340.9932432432432430.5373134328358210.92127239599149737178download
OTOF1.25835940925247e-151332.50.646420187817.470.9805194805194810.4205607476635510.86966940532081448213download
INSR2.12599268885929e-15142.50.862768031214.860.9888888888888890.6756756756756760.97222222222222227190download
CYP4V25.33490549991145e-15306.50.823736190211.370.9845360824742270.6341463414634150.94869434214931429206download
VHL5.35989978410831e-1553.50.916118421114.720.9863013698630140.8857142857142860.9780016447368423276download
CASR7.23659552119824e-15245.50.792270531415.230.9066666666666670.9069767441860460.9258756038647344672download
COL2A18.64265322384071e-152930.807004830916.050.9896907216494840.6481481481481480.92922705314009736115download
COL1A11.23952816274953e-141950.88603988615.970.9940828402366860.650.9603174603174627182download
RYR11.71484500641073e-1451200.515978914410.730.9641255605381170.3315789473684210.78914422205749171342download
RET2.04846133581627e-14963.50.733724340214.770.9615384615384620.680.85872434017595355124download
RRM2B3.16310770254747e-14550.95061728412.9610.8787878787878790.9765857811834822981download
FGFR23.29905710451976e-14170.50.869517241415.320.9912280701754390.70.95296551724137929125download
VWF8.74484942481644e-148100.714066496215.170.9941860465116280.3586956521739130.89641943734015434230download
F92.29873863015054e-1378.50.828598940811.930.8484848484848490.9538461538461540.9622051035146856731download
MECP23.48784702902791e-13900.908568443115.30.9940119760479040.7241379310344830.97648902821316622174download
APC5.09518856772373e-1382.50.8996598639350.9898477157360410.9500000000000010.97995626822157421196download
PMM25.88720065026305e-13140.50.934523809513.1510.6764705882352940.96363871635610823168download
GBA7.23594775464324e-132360.725623582812.870.8571428571428570.8723404255319150.9108087679516254954download
GALNS7.32818135493006e-131400.89166666678.44610.4468085106382980.97222222222222221240download
GLB17.74238212316317e-131210.817073170712.3110.6590909090909090.9491169049621532982download
GCK1.603808297312e-1260.966666666717.910.9230769230769230.9958333333333332460download
HMBS1.84339599393242e-12720.887323943715.8710.7714285714285710.9624413145539912771download
BEST12.41545907490244e-121150.890410958915.2310.5789473684210530.96419676214196822146download
TK24.26598632152891e-1243.50.888888888912.0210.68750.9780303030303032290download
RHO4.5946177396187e-12144.50.843137254914.7910.8297872340425530.9273504273504273951download
NIPBL6.50875325673661e-121180.839160839216.290.9913793103448280.5833333333333330.95874125874125922130download
PAX69.4066134353176e-12216.50.754815630215.450.9851851851851850.4565217391304350.94042377545404523158download
PROC1.17707140444537e-11350.806976744210.190.9512195121951220.8181818181818180.9593023255813952043download
TGM11.20117337111644e-112600.72474226816.820.9638554216867470.6136363636363640.9106529209621993097download
TERT1.42163794106459e-111670.7317972358.120.9508196721311470.70.9230414746543783170download
KCNA11.57005368898317e-1160.954545454513.4110.7826086956521740.99696969696969718110download
IDS1.96890454373159e-11360.923465423518.330.992907801418440.850.98601398601398618143download
OFD12.01229194344911e-111110.710253456214.410.921568627450980.750.9360599078341013156download
SLC22A52.09824057994234e-111880.852439024415.930.9946236559139780.4871794871794870.95414634146341520205download
CPT1A2.34816609637696e-11249.50.753198653211.030.9784946236559140.5681818181818180.91599326599326627110download
CDH233.0021468406772e-115500.749581706619.270.9927536231884060.2777777777777780.92331288343558322326download
OAT3.1076178986736e-11890.852459016413.3110.750.9459623557984212761download
GLI33.58486068242685e-11146.50.875465838523.60.9933333333333330.6129032258064520.95450310559006220161download
BMPR23.74991396387671e-1165.50.887096774214.210.5757575757575760.97219864176570519124download
NPC13.77873240796805e-11197.50.842307692314.690.9942857142857140.4750.94935897435897420195download
GJB23.88342850165163e-113450.635560268616.830.8676470588235290.7619047619047620.8780487804878054169download
CP4.26011455821402e-113190.72296296312.880.9895833333333330.4642857142857140.90548148148148127125download
SOD14.64477434844366e-1112.50.870967741914.10.88571428571428610.9869927159209163131download
LRP54.65030860918743e-11259.50.784420289916.850.9913043478260870.489361702127660.92164855072463824138download
LMNA4.76863828568928e-11258.50.686720469615.940.9333333333333330.6969696969696970.9051724137931032994download
SLC26A45.26065143989211e-116120.559944559913.560.9615384615384620.4473684210526320.85862785862785937117download
LPL5.26483430868729e-112400.717551336711.420.9722222222222220.586956521739130.907012785741962989download
DYSF5.80799951682778e-1111200.606318681315.270.9857142857142860.3203883495145630.84615384615384635208download
ATM6.39136518792686e-11271.50.81130268219.130.9938080495356040.3720930232558140.95665708812260518348download
CSF1R6.64018400914555e-11970.848275862115.50.9821428571428570.750.95818965517241420116download
VPS13B7.09130213780267e-111690.783333333326.40.9870129870129870.5555555555555550.9608796296296318240download
MAPT7.21022508291556e-11322.50.814728682214.680.9915966386554620.450.937520258download
LHCGR8.19399651885196e-11132.50.829545454515.690.9891304347826090.6176470588235290.94208916083916122104download
CYP27A19.6299688718692e-11293.50.716.40.8823529411764710.81250.8792181069958854554download
ATRX1.05908596661368e-10770.828947368410.4210.6285714285714290.9539473684210532276download
DKC11.15245906069055e-1057.50.82521008412.890.8918918918918920.93750.9516806722689083435download
EDA1.17550869809215e-1052.50.881958417214.390.9850746268656720.80.9647887323943662171download
ABCC81.23000197392072e-102890.793333333315.540.9905660377358490.5333333333333330.90825396825396825126download
CLCN51.23078380397247e-10170.924050632915.5410.750.9880450070323491879download
KRAS1.56231193682436e-10170.936170212815.810.7391304347826090.989361702127661794download
SPAST1.87813285178383e-100117.12111949download
DHCR71.88642549193235e-10230.50.7964601779.85810.510638297872340.91500737463126824113download
ABCD12.280975902432e-101170.835045662112.040.9846153846153850.718750.9332191780821922473download
TP533.39041670425694e-10160.928571428613.6910.8260869565217390.9849624060150381956download
KCNJ113.61651357529498e-10161.50.722352941213.020.913043478260870.7894736842105260.9053450download
KRT53.64418946705867e-10620.8813.1510.60.96555555555555618100download
FLNA3.65210317438842e-10339.50.738625954210.290.9902912621359220.4528301886792450.89633587786259525131download
ALPL5.13127856072396e-1035.50.847069597114.130.960784313725490.8636363636363640.9674908424908422152download
TP635.83677286203122e-10740.868005738916.160.9913043478260870.640.96461023433763717123download
CYP17A16.64187651560541e-10380.91228070181310.80.9666666666666672057download
KCNQ17.01249503357076e-10820.861392405113.30.9863013698630140.7307692307692310.9481012658227852079download
ACADM7.37608488133009e-1038.50.873563218412.4310.6071428571428570.9739688979039891787download
SMPD17.51136401825608e-1068.50.876543209915.7110.6551724137931030.9554905782975961981download
CACNA1A8.28697418592417e-1077.50.8814.6610.4705882352941180.96770833333333316150download
BLM9.29222377950079e-101040.765550239215.280.987804878048780.50.9447102604997341999download
PKHD11.10284577113529e-09427.50.796296296313.0710.2142857142857140.92669753086419718324download
PMS21.15642561145572e-09430.823529411827.70.9655172413793110.9698879551820731784download
BCKDHA1.28898090198572e-0976.50.887515.8210.6785714285714280.9496710526315791980download
WFS11.32671992254101e-09229.50.815789473712.0710.3396226415094340.93289473684210518190download
SOS11.45598882142279e-09840.902654867315.4310.6071428571428570.95627277459656417113download
CBS1.7960743400387e-09960.917808219212.4810.5714285714285710.95890410958904116146download
MYH72.1347666091417e-094190.70136629814.010.9873417721518990.50.86369551073519829106download
BCKDHB2.22349688927805e-0959.50.893333333312.8610.6923076923076920.9559259259259261875download
SCN1A2.27739609094157e-0994.50.817282665315.840.990.5333333333333330.95080687142113517113download
ATP7B2.65388827919018e-09345.50.704545454512.530.9910714285714290.3620689655172410.89388820638820622148download
KMT2D2.6636534037282e-09320.914634146313.7710.3823529411764710.98999374609130713246download
GUSB3.03511159015671e-09350.909090909114.3310.7391304347826090.9688057040998221766download
NR3C23.04432281044459e-09110.958762886616.510.7777777777777780.9918998527245951497download
SAMHD13.22845386523738e-0934.50.895022624413.330.9841269841269840.8421052631578950.9687782805429861765download
ADAR3.53002000576847e-0926.50.949152542416.1410.70.98395883777239714118download
GJA14.41908944406463e-09140.965517241415.6610.93750.9678160919540231529download
PRKAR1A4.43357426330853e-0959.50.863031914919.470.9886363636363640.6818181818181820.9604388297872341694download
GLA4.46761555378858e-09106.50.730884557712.120.8571428571428570.9166666666666670.9201649175412295823download
VDR4.6078712795037e-0930.50.930434782616.2710.6363636363636360.98105590062111814115download
GLRA15.03615399831371e-0972.50.76410730818.790.9523809523809520.750.9329324699352452347download
CLDN165.0442765880601e-09100.921568627514.510.80.9877450980392161651download
NF15.09682227058577e-09879.50.748986682114.760.989323843416370.3454545454545450.87268384481760322314download
PRKCG5.1851790436338e-09440.868421052612.6210.8214285714285720.9496567505720822338download
ABCC65.41202912024408e-092780.734243014915.620.9855072463768120.3953488372093020.90968161143599719162download
LYST6.01348770307708e-09910.886287625418.6610.2765957446808510.97658862876254213299download
IRF66.69266198116741e-0922.50.957746478915.1810.8333333333333330.978873239436621571download
COL7A16.7489814783816e-093420.698449612413.530.9841269841269840.3409090909090910.91162790697674418215download
MPZ6.81194327768014e-09220.875350140114.480.950.9428571428571430.9691876750700283421download
GDAP19.43418683528786e-09550.867647058813.230.9843750.7619047619047620.952422145328721768download
FGFR19.79361918926701e-0950.50.884393063615.3510.3939393939393940.97754557581147213173download
FKRP1.18566681715747e-0868.50.87692307699.69510.6923076923076920.9414529914529911865download
STAT11.29683809065533e-0840.947368421112.5910.7647058823529410.9959514170040491376download
PLP11.3070244527908e-08930.740322580612.890.980.593750.9252062download
NR0B11.36048932704579e-08260.831168831211.460.9666666666666670.8333333333333330.9624819624819622133download
SLC2A11.37279735971519e-0820.971830985914.0610.8666666666666670.997833152762731371download
MYBPC31.38812701223921e-08491.50.519607843115.780.7954545454545460.7377049180327870.8215323166303565451download
ABCA41.45777421562436e-086190.638936535217.880.9775280898876410.3214285714285720.86728130360205822212download
RS11.51093667584969e-08120.913043478312.3610.7142857142857140.9739130434782611046download
TAZ1.69448179717756e-080114.22111834download
UROS1.84148790027064e-08980.76315789478.23810.50.9283625730994151876download
FAH1.85381218393827e-081640.827155172410.150.9923076923076920.4838709677419350.92931034482758616145download
WT11.98121941428467e-0817.50.924528301915.3110.7894736842105260.9779874213836481553download
SHH2.03717499654071e-08145.50.809957924314.620.9384615384615380.950.897966339410942362download
BTK2.04836149112271e-08120.909090909112.2310.8571428571428570.979797979797981833download
ARSA2.119523588114e-081340.669696969715.030.920.6896551724137930.8984848484848482455download
PYGL2.29323542306693e-08129.50.853932584320.210.5806451612903230.919163545568041889download
SUMF12.46537331150262e-0870.50.924528301917.0110.520.9658925979680713159download
PCCB2.68089701532918e-08740.882352941215.5810.50.95558223289315714119download
GATA42.81623738067456e-08860.808333333313.910.9891304347826090.5185185185185180.94487179487179515104download
MYH93.90473721488644e-0894.50.895348837218.2210.4193548387096770.95773703041144913172download
F13A13.99672550600448e-08540.857142857114.0610.5185185185185180.9576138147566721491download
POLR3A4.11418260669224e-08213.50.79375220.9865771812080540.5185185185185180.916601562516160download
TRPV44.15388668637669e-082160.689485213613.170.9838709677419350.4883720930232560.881708652792992283download
OPA15.06820667422564e-08710.917293233117.7810.5416666666666670.95893580104106413133download
SCO25.18027083491979e-080114.07111829download
NOTCH25.30925387904478e-0885.50.829117191520.20.9926470588235290.4615384615384620.95585957666494613149download
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