GeneAssociated phenotypesInheritanceClinVarHGMD
ABCB11Cholestasis, Cholestasis, benign recurrent intrahepatic, 2AD/AR35299
ABCB4Gallbladder disease, Low phospholipid-associated cholelithiasis, CholestasisAD/AR27224
ABCC2Dubin-Johnson syndromeAD/AR2946
AKR1D1Bile acid synthesis defect, congenital, 2AR714
ATP8B1Intrahepatic cholestasis of pregnancy, Familial intrahepatic cholestasis, recurrent, Cholestasis, progressive familial intrahepatic, Benign recurrent intrahepatic cholestasisAD/AR18131
BAATHypercholanemia, familialAR37
CFTRCystic fibrosis, Congenital bilateral absence of the vas deferensAD/AR5181803
CREB3L3HypertriglyceridaemiaAD9
CYP7B1Bile acid synthesis defect, Spastic paraplegia 5A, autosomal recessiveAR1860
DCDC2Deafness, Nephronophthisis, Sclerosing cholangitis, neonatalAR139
DGUOKMitochondrial DNA depletion syndrome, Portal hypertension, noncirrhotic, Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 4AR2362
EPCAMDiarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposisAD/AR3880
FAHTyrosinemiaAR53102
HSD3B7Bile acid synthesis defect, congenital, 1AR825
JAG1Alagille syndromeAD131610
LCTLactase deficiencyAR1115
LMF1Combined lipase deficiencyAR414
MKS1Bardet-Biedl syndrome, Meckel syndromeAR5052
MYO5B*Diarrhea, with microvillus atrophyAR1480
NEUROG3Diarrhea, malabsorptive, congenitalAR38
NOTCH2*Alagille syndrome, Hajdu-Cheney syndromeAD3770
NPC1Niemann-Pick diseaseAR164472
NPC2Niemann-pick diseaseAR2127
NPHP1Nephronophthisis, Joubert syndrome, Senior-Loken syndromeAR1976
NPHP3Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndromeAR3875
NPHP4Nephronophthisis, Senior-Loken syndromeAR20113
NR1H4Cholestasis, progressive familial intrahepatic 5AR65
PEX1Heimler syndrome, Peroxisome biogenesis factor disorder 1A, Peroxisome biogenesis factor disorder 1BAR112134
PEX10Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder, AtaxiaAR3429
PEX12Zellweger syndrome, Peroxisome biogenesis disorderAR4337
PEX2Zellweger syndrome, Peroxisome biogenesis disorderAR1618
PEX26Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorderAR1327
PEX5Adrenoleukodystrophy, neonatal, Rhizomelic chondrodysplasia punctata, Zellweger syndrome, Peroxisome biogenesis disorderAR814
PEX6Heimler syndrome, Peroxisome biogenesis disorder 4A, Peroxisome biogenesis disorder 4BAR58107
SCYL1Spinocerebellar ataxia, autosomal recessive 21AR126
SERPINA1Alpha-1-antitrypsin deficiencyAR4980
SLC25A13Citrin deficiencyAR24113
SLC26A3Diarrhea, secretory chloride, congenitalAR5588
SMPD1Niemann-Pick diseaseAR110249
SPINT2Diarrhea, secretory sodium, congenitalAR612
TJP2Cholestasis, progressive familial intrahepatic, Hypercholanemia, familial, Deafness, autosomal dominant 51AD/AR2527
TMEM216Joubert syndrome, Meckel syndromeAR178
TRMULiver failure, infantile, Reversible infantile respiratory chain deficiencyAR2021
TTC37Trichohepatoenteric syndrome, Primary immunodeficiencyAR1264
UGT1A1Crigler-Najjar syndrome, Gilbert syndrome, Breast milk jaundiceAD/AR29144
VIPAS39Arthrogryposis, renal dysfunction, and cholestasis 2AR813
VPS33BArthrogryposis – renal dysfunction – cholestasisAD/AR1758
GeneAssociated phenotypesInheritanceClinVarHGMD
ADAM17Inflammatory skin and bowel disease, neonatal 1AR17
ALPIInflammatory bowel diseaseAR5
CYP27A1Cerebrotendinous xanthomatosisAR69110
DGAT1DiarrheaAR711
EPCAMDiarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposisAD/AR3880
FOXP3Immunodysregulation, polyendocrinopathy, and enteropathyXL2893
GUCY2CDiarrhea, Meconium ileusAD/AR710
IL10Graft vs. host diseaseAD15
IL10RAInflammatory bowel diseaseAR443
IL10RBInflammatory bowel diseaseAR219
IL21Immunodeficiency, common variable, 11AR11
LCTLactase deficiencyAR1115
LIPAWolman disease, Cholesterol ester storage diseaseAR2793
MVKMevalonic aciduria, Hyper-IgD syndrome, Porokeratosis 3, multiple typesAD/AR35181
MYO5B*Diarrhea, with microvillus atrophyAR1480
NCF2Chronic granulomatous diseaseAR1972
NEUROG3Diarrhea, malabsorptive, congenitalAR38
SAR1BChylomicron retention disease (Anderson disease)AR816
SISucrase-isomaltase deficiency, congenitalAR1223
SKIV2LTrichohepatoenteric syndrome 2AR633
SLC10A2Bile acid malabsorption, primaryAD24
SLC26A3Diarrhea, secretory chloride, congenitalAR5588
SLC5A1Glucose/galactose malabsorptionAR358
SLC9A3Diarrhea, secretory sodium, congenitalAR612
SPINT2Diarrhea, secretory sodium, congenitalAR612
STX3Microvillus inclusion diseaseAR3
TTC37Trichohepatoenteric syndrome, Primary immunodeficiencyAR1264
TTC7AGastrointestinal defects and immunodeficiency syndromeAR2146
XIAP*Lymphoproliferative syndromeXL1496
GeneAssociated phenotypesInheritanceClinVarHGMD
AHI1Joubert syndromeAR6293
ANKS6NephronophthisisAR912
ARL13BJoubert syndromeAR1110
ARL6Bardet-Biedl syndrome, Retinitis pigmentosaAR1421
B9D1Meckel syndromeAR710
B9D2Meckel syndromeAR84
BAATHypercholanemia, familialAR37
BBS1Bardet-Biedl syndromeAR66103
BBS10Bardet-Biedl syndromeAR90107
BBS12Bardet-Biedl syndromeAR3658
BBS2Bardet-Biedl syndrome, Retinitis pigmentosaAR5891
BBS4Bardet-Biedl syndromeAR2553
BBS5Bardet-Biedl syndromeAR1831
BBS7Bardet-Biedl syndromeAR1943
BBS9Bardet-Biedl syndromeAR2752
C5ORF42Orofaciodigital syndrome, Joubert syndromeAR97103
CC2D2A#COACH syndrome, Joubert syndrome, Meckel syndromeAR7691
CEP164NephronophthisisAR119
CEP290*Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndromeAR130289
CEP41Joubert syndromeAR/Digenic711
DCDC2Deafness, Nephronophthisis, Sclerosing cholangitis, neonatalAR139
GLIS2NephronophthisisAR33
INPP5EJoubert syndrome, Mental retardation, truncal obesity, retinal dystrophy, and micropenis (MORM syndrome)AR2550
INVSNephronophthisisAR1634
IQCB1Senior-Loken syndromeAR2441
KIF7Acrocallosal syndrome, Hydrolethalus syndrome, Al-Gazali-Bakalinova syndrome, Joubert syndromeAR/Digenic2444
LIPAWolman disease, Cholesterol ester storage diseaseAR2793
MKKSBardet-Biedl syndrome, McKusick-Kaufman syndromeAR2159
MKS1Bardet-Biedl syndrome, Meckel syndromeAR5052
NEK8NephronophthisisAR1618
NPHP1Nephronophthisis, Joubert syndrome, Senior-Loken syndromeAR1976
NPHP3Nephronophthisis, Renal-hepatic-pancreatic dysplasia, Meckel syndromeAR3875
NPHP4Nephronophthisis, Senior-Loken syndromeAR20113
NR1H4Cholestasis, progressive familial intrahepatic 5AR65
OFD1Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndromeXL153160
PKD2Polycystic kidney diseaseAD55333
PKHD1Polycystic kidney diseaseAR249557
RPGRIP1L#COACH syndrome, Joubert syndrome, Meckel syndrome, Retinal degeneration in ciliopathy, modifierAR3949
TCTN1#Joubert syndromeAR66
TCTN2Joubert syndrome, Meckel syndromeAR2015
TCTN3Orofaciodigital syndrome (Mohr-Majewski syndrome), Joubert syndromeAR912
TMEM138Joubert syndromeAR68
TMEM216Joubert syndrome, Meckel syndromeAR178
TMEM231Joubert syndrome, Meckel syndromeAR1219
TMEM237Joubert syndromeAR711
TMEM67Nephronophthisis, COACH syndrome, Joubert syndrome, Meckel syndromeAR87170
TRIM32Bardet-Biedl syndrome, Muscular dystrophy, limb-girdleAR1316
TTC21BShort-rib thoracic dysplasia, Nephronophthisis, Asphyxiating thoracic dysplasia (ATD; Jeune)AR2363
TTC8Bardet-Biedl syndrome, Retinitis pigmentosaAR516
WDR19Retinitis pigmentosa, Nephronophthisis, Short -rib thoracic dysplasia with or without polydactyly, Senior-Loken syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Asphyxiating thoracic dysplasia (ATD; Jeune)AR3343
WDR35Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Short rib-polydactyly syndrome type 5AR2831
ZNF423Nephronophthisis, Joubert syndromeAD/AR107
GeneAssociated phenotypesInheritanceClinVarHGMD
CDK9AR1
CHD7Isolated gonadotropin-releasing hormone deficiency, CHARGE syndromeAD276860
CLMPCongenital short bowel syndromeAR613
DHCR7Smith-Lemli-Opitz syndromeAR88217
EFTUD2Mandibulofacial dysostosis with microcephaly, Esophageal atresia, syndromicAD4599
FANCBFanconi anemiaXL1121
FANCCFanconi anemiaAR9464
GLI3Acrocallosal syndrome, Pallister-Hall syndrome, Grieg cephalopolysndactyly syndrome, Postaxial polydactyly type A, Preaxial polydactyly type 3, Preaxial polydactyly type 4AD70235
MID1*Opitz GBBB syndromeXL3096
MNX1#Currarino syndromeAD1679
MYCNFeingold syndromeAD2741
PTF1APancreatic and cerebellar agenesis, Pancreatic agenesis 2AR416
RFX6Pancreatic hypoplasia, intestinal atresia, and gallbladder aplasia or hypoplasia, with or without tracheoesophageal fistula, Martinez-Frias syndrome, Mitchell-Riley syndromeAR1031
SOX2*Microphthalmia, syndromicAD34104
TTC7AGastrointestinal defects and immunodeficiency syndromeAR2146
GeneAssociated phenotypesInheritanceClinVarHGMD
BDNFCentral hypoventilation syndrome, congenitalAD123
CELSR3Hirschsprung diseaseAD25
EDN3Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndromeAD/AR721
EDNRBHirschsprung disease, ABCD syndrome, Waardenburg syndromeAD/AR1266
KIF1BPGoldberg-Shprintzen megacolon syndromeAR710
L1CAMMental retardation, aphasia, shuffling gait, and adducted thumbs (MASA) syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesisXL80292
MITFTietz albinism-deafness syndrome, Waardenburg syndrome, Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD)AD/AR3258
NRG1Nonsyndromic Hirschsprung diseaseAD/AR110
NRTNHirschsprung diseaseAD2
PAX3Craniofacial-deafness-hand syndrome, Waardenburg syndromeAD/AR54149
PHOX2BCentral hypoventilation syndrome, congenital, Neuroblastoma, susceptiblity to, Neuroblastoma with Hirschsprung diseaseAD1186
RETHirschsprung disease, Central hypoventilation syndrome, congenital, Pheochromocytoma, Medullary thyroid carcinoma, Multiple endocrine neoplasiaAD/AR122407
RMRPCartilage-hair hypoplasia, Metaphyseal dysplasia without hypotrichosis, Anauxetic dysplasiaAR87123
SOX10Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Kallmann syndromeAD56148
ZEB2*Mowat-Wilson syndromeAD154287
GeneAssociated phenotypesInheritanceClinVarHGMD
APOA5HyperchylomicronemiaAD/AR361
APOC2Hyperlipoproteinemia, type IbAR1322
CFTRCystic fibrosis, Congenital bilateral absence of the vas deferensAD/AR5181803
CPA1Hereditary chronic pancreatitisAD/AR41
CTRCHereditary chronic pancreatitis, Tropical pancreatitisAD/AR1144
GPIHBP1Hyperlipoproteinemia, type IDAR1031
PRSS1*Pancreatitis, hereditaryAD2362
SPINK1Pancreatitis, hereditaryAD1448
UBR1Johanson-Blizzard syndromeAR1171
GeneAssociated phenotypesInheritanceClinVarHGMD
GANABPolycystic kidney and/or polycystic liver disease 3AD712
LRP5*Van Buchem disease, Osteoporosis-pseudoglioma syndrome, Hyperostosis, endosteal, Osteosclerosis, Exudative vitreoretinopathy, Osteopetrosis late-onset form type 1, LRP5 primary osteoporosisAD/AR/Digenic57196
PKD1*Polycystic kidney diseaseAD2371923
PKD2Polycystic kidney diseaseAD55333
PRKCSHPolycystic liver diseaseAD928
SEC63Polycystic liver diseaseAD823