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encyclopedia of Rare Disease Annotation for Precision Medicine



   meckel syndrome
  

Disease ID 762
Disease meckel syndrome
Definition
Meckel syndrome (also known as Meckel–Gruber Syndrome, Gruber Syndrome, Dysencephalia Splanchnocystica) is a rare, lethal, ciliopathic, genetic disorder, characterized by renal cystic dysplasia, central nervous system malformations (occipital encephalocele), polydactyly (post axial), hepatic developmental defects, and pulmonary hypoplasia due to oligohydramnios. - Wikipedia
Reference: https://en.wikipedia.org/wiki/meckel syndrome
Synonym
dysencephalia splachnocystica
gruber syndrome
meckel syndrome type 1
meckel syndrome type1
meckel-gruber syndrome, type 1
Orphanet
OMIM
DOID
UMLS
C3714506
Comorbidity
UMLS | Disease | Sentences' Count(Total Sentences:2)
C0158699  |  renal agenesis  |  1
C0162510  |  caroli disease  |  1
Curated Gene
Entrez_id | Symbol | Resource(Total Genes:9)
51259  |  TMEM216  |  GHR
23322  |  RPGRIP1L  |  GHR;UNIPROT
54903  |  MKS1  |  CLINVAR;CTD_human;GHR;UNIPROT
80184  |  CEP290  |  GHR;UNIPROT
57096  |  RPGRIP1  |  UNIPROT
91147  |  TMEM67  |  GHR;UNIPROT
80776  |  B9D2  |  GHR
27077  |  B9D1  |  GHR
57545  |  CC2D2A  |  GHR;UNIPROT
Inferring Gene
Entrez_id | Symbol | Resource(Total Genes:1)
54903  |  MKS1  |  CIPHER;CTD_human
Text Mined Gene
Entrez_id | Symbol | Score | Resource(Total Genes:68)
174  |  AFP  |  2.62  |  DISEASES
257  |  ALX3  |  1.63  |  DISEASES
392509  |  ARL13A  |  4.802  |  DISEASES
200894  |  ARL13B  |  5.141  |  DISEASES
50807  |  ASAP1  |  2.512  |  DISEASES
26005  |  C2CD3  |  3.597  |  DISEASES
65250  |  C5orf42  |  3.741  |  DISEASES
800  |  CALD1  |  1.95  |  DISEASES
57545  |  CC2D2A  |  6.175  |  DISEASES
387707  |  CC2D2B  |  4.595  |  DISEASES
8814  |  CDKL1  |  3.276  |  DISEASES
8999  |  CDKL2  |  3.526  |  DISEASES
80184  |  CEP290  |  6.033  |  DISEASES
55165  |  CEP55  |  2.388  |  DISEASES
23059  |  CLUAP1  |  3.426  |  DISEASES
54875  |  CNTLN  |  4.277  |  DISEASES
51473  |  DCDC2  |  2.21  |  DISEASES
1855  |  DVL1  |  1.607  |  DISEASES
79659  |  DYNC2H1  |  2.615  |  DISEASES
2108  |  ETFA  |  1.969  |  DISEASES
132884  |  EVC2  |  1.743  |  DISEASES
2673  |  GFPT1  |  1.123  |  DISEASES
2736  |  GLI2  |  1.042  |  DISEASES
2737  |  GLI3  |  2.726  |  DISEASES
2804  |  GOLGB1  |  1.592  |  DISEASES
219844  |  HYLS1  |  2.619  |  DISEASES
80173  |  IFT74  |  3.337  |  DISEASES
8100  |  IFT88  |  3.034  |  DISEASES
56623  |  INPP5E  |  2.781  |  DISEASES
9851  |  KIAA0753  |  2.117  |  DISEASES
11127  |  KIF3A  |  2.09  |  DISEASES
3980  |  LIG3  |  1.136  |  DISEASES
85444  |  LRRCC1  |  4.904  |  DISEASES
54903  |  MKS1  |  6.99  |  DISEASES
51199  |  NIN  |  1.93  |  DISEASES
27031  |  NPHP3  |  3.242  |  DISEASES
261734  |  NPHP4  |  4.524  |  DISEASES
11247  |  NXPH4  |  3.312  |  DISEASES
4952  |  OCRL  |  1.504  |  DISEASES
8481  |  OFD1  |  3.623  |  DISEASES
5158  |  PDE6B  |  1.153  |  DISEASES
51230  |  PHF20  |  2.202  |  DISEASES
5314  |  PKHD1  |  2.205  |  DISEASES
5730  |  PTGDS  |  1.426  |  DISEASES
5991  |  RFX3  |  2.984  |  DISEASES
387  |  RHOA  |  1.278  |  DISEASES
6103  |  RPGR  |  2.238  |  DISEASES
57096  |  RPGRIP1  |  3.779  |  DISEASES
23322  |  RPGRIP1L  |  5.795  |  DISEASES
6303  |  SAT1  |  1.49  |  DISEASES
10806  |  SDCCAG8  |  2.421  |  DISEASES
23345  |  SYNE1  |  1.686  |  DISEASES
23224  |  SYNE2  |  1.782  |  DISEASES
23336  |  SYNM  |  2.701  |  DISEASES
10732  |  TCFL5  |  1.521  |  DISEASES
79600  |  TCTN1  |  4.967  |  DISEASES
200728  |  TMEM17  |  4.545  |  DISEASES
51259  |  TMEM216  |  6.407  |  DISEASES
79583  |  TMEM231  |  5.273  |  DISEASES
65062  |  TMEM237  |  3.767  |  DISEASES
91147  |  TMEM67  |  7.321  |  DISEASES
283232  |  TMEM80  |  4.456  |  DISEASES
83857  |  TMTC1  |  1.724  |  DISEASES
27095  |  TRAPPC3  |  2.797  |  DISEASES
7106  |  TSPAN4  |  2.018  |  DISEASES
79770  |  TXNDC15  |  4.975  |  DISEASES
57728  |  WDR19  |  2.828  |  DISEASES
63929  |  XPNPEP3  |  3.359  |  DISEASES
Locus
Symbol | Locus(Total Locus:13)
TCTN2  |  12q24.31
TMEM231  |  16q23.1
CSPP1  |  8q13.1-q13.2
B9D1  |  17p11.2
B9D2  |  19q13.2
CEP290  |  12q21.32
RPGRIP1  |  14q11.2
TMEM67  |  8q22.1
CC2D2A  |  4p15.32
WDPCP  |  2p15
RPGRIP1L  |  16q12.2
MKS1  |  17q22
TMEM216  |  11q13.1
Disease ID 762
Disease meckel syndrome
Integrated Phenotype
HPO | Name(Total Integrated Phenotypes:45)
HP:0001830  |  Postaxial foot polydactyly
HP:0000028  |  Cryptorchidism
HP:0001746  |  Asplenia
HP:0000037  |  Male pseudohermaphroditism
HP:0006487  |  Bowing of the long bones
HP:0000568  |  Microphthalmia
HP:0100732  |  Pancreatic fibrosis
HP:0000068  |  Urethral atresia
HP:0000647  |  Sclerocornea
HP:0000518  |  Cataract
HP:0001562  |  Oligohydramnios
HP:0001696  |  Situs inversus totalis
HP:0010295  |  Aplasia/Hypoplasia of the tongue
HP:0000347  |  Micrognathia
HP:0007370  |  Aplasia/Hypoplasia of the corpus callosum
HP:0002564  |  Malformation of the heart and great vessels
HP:0000532  |  Chorioretinal abnormality
HP:0008053  |  Aplasia/Hypoplasia of the iris
HP:0000316  |  Hypertelorism
HP:0001162  |  Postaxial hand polydactyly
HP:0000062  |  Ambiguous genitalia
HP:0001737  |  Pancreatic cysts
HP:0002612  |  Congenital hepatic fibrosis
HP:0006706  |  Cystic liver disease
HP:0000175  |  Cleft palate
HP:0000003  |  Multicystic kidney dysplasia
HP:0001177  |  Preaxial hand polydactyly
HP:0000457  |  Depressed nasal ridge
HP:0000221  |  Furrowed tongue
HP:0000293  |  Full cheeks
HP:0000252  |  Microcephaly
HP:0000528  |  Anophthalmia
HP:0000648  |  Optic atrophy
HP:0010459  |  True hermaphroditism
HP:0001305  |  Dandy-Walker malformation
HP:0001883  |  Talipes
HP:0000073  |  Ureteral duplication
HP:0000368  |  Low-set, posteriorly rotated ears
HP:0001747  |  Accessory spleen
HP:0002084  |  Encephalocele
HP:0006870  |  Lobar holoprosencephaly
HP:0000340  |  Sloping forehead
HP:0000238  |  Hydrocephalus
HP:0002323  |  Anencephaly
HP:0000482  |  Microcornea
Text Mined Phenotype
HPO | Name | Sentences' Count(Total Phenotypes:2)
Disease ID 762
Disease meckel syndrome
Manually Symptom(Waiting for update.)
Text Mined Symptom(Waiting for update.)
Manually Genotype(Total Text Mining Genotypes:0)
(Waiting for update.)
Text Mining Genotype(Total Genotypes:0)
(Waiting for update.)
All Snps(Total Genotypes:18)
snpId pubmedId geneId geneSymbol diseaseId sourceId sentence score Year geneSymbol_dbSNP CHROMOSOME POS REF ALT
rs199874059NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758210658CT
rs201933838NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758214740CT
rs386834041NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758208560GC,A
rs386834042NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758207083A-
rs386834043NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758206554CATGCCATTGGGACAGCCTCAGGTTTCTG-
rs386834044NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758206501-TGCC
rs386834045NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758206465CT
rs386834046NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS1;LOC1053718411758218620TGGCAGT-
rs386834047NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758216112AG-
rs386834048NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758216088CT
rs386834049NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758214832GA
rs386834050NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758214784GA
rs386834051NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS1;LOC1053718411758219175-CCCGG
rs386834052NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS1;LOC1053718411758219149AG
rs386834053NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758210980CT
rs730880323NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS1;LOC1053718411758219176-CCGGG
rs794727070NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758208585TG
rs797045706NA54903MKS1umls:C3714506CLINVARNA0.327719925NAMKS11758212996GA
GWASdb Annotation(Total Genotypes:0)
(Waiting for update.)
GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)
Mapped by lexical matching(Total Items:20)
HP ID HP Name MP ID MP Name Annotation
HP:0008053Aplasia/Hypoplasia of the irisMP:0011665d-loop transposition of the great arteriescomplete transposition of the great arteries; the d- refers to the dextroposition of the bulboventricular loop (ie, the position of the right ventricle, which is on the right side); in addition, the aorta also tends to be on the right and anterior, and th
HP:0000175Cleft palateMP:0013550abnormal secondary palate morphology
HP:0001162Postaxial hand polydactylyMP:0009743preaxial polydactylyduplication of all or part of the first ray on one or more of the autopods
HP:0006487Bowing of the long bonesMP:0013621decreased internal diameter of femurreduced cross-sectional distance that extends from one lateral edge of the femur long bone marrow cavity, through its center and to the opposite lateral edge of the bone marrow cavity through the mid point of the femur
HP:0000062Ambiguous genitaliaMP:0009202small external male genitaliareduced size of the external masculine genital organs
HP:0000003Multicystic kidney dysplasiaMP:0011376abnormal kidney corticomedullary boundary morphologyany structural anomaly of the region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary
HP:0001177Preaxial hand polydactylyMP:0009744postaxial polydactylyduplication of all or part of any of the rays except the first ray on one or more of the autopods
HP:0000457Depressed nasal ridgeMP:0004872absent nasal septumabsence of the structure that separates the two nasal cavities
HP:0001696Situs inversus totalisMP:0011252situs inversus totalisthe complete right to left reversal (transposition) of the thoracic and abdominal organs, including the heart (dextrocardia)
HP:0001747Accessory spleenMP:0003342accessory spleenthe splenic tissue is divided into equal masses; often related to situs inversus
HP:0000221Furrowed tongueMP:0000764abnormal tongue epithelium morphologyany structural anomaly of the epithelial layer of the tongue
HP:0000648Optic atrophyMP:0012506brain atrophyacquired diminution of the size of the brain associated with wasting as from death and reabsorbtion of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal chan
HP:0000073Ureteral duplicationMP:0012156rostral-caudal axis duplicationpartial or complete duplication of rostral-caudal axis structures
HP:0007370Aplasia/Hypoplasia of the corpus callosumMP:0013283failure of ventral body wall closurefailure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h
HP:0001830Postaxial foot polydactylyMP:0009744postaxial polydactylyduplication of all or part of any of the rays except the first ray on one or more of the autopods
HP:0001737Pancreatic cystsMP:0011682renal glomerulus cystsabnormal membranous sacs in any portion of the renal glomerulus
HP:0100732Pancreatic fibrosisMP:0003985renal fibrosisformation of fibrous tissue in the kidney as a result of repair or a reactive process
HP:0010295Aplasia/Hypoplasia of the tongueMP:0003409decreased width of hypertrophic chondrocyte zonedecreased width of cartilage cell matrix layer
HP:0006706Cystic liver diseaseMP:0003333liver fibrosisinvasion of fibrous connective tissue into the liver, often resulting from inflammation or injury
HP:0002612Congenital hepatic fibrosisMP:0009501abnormal hepatic duct morphologyany structural anomaly of the two canals (left and right) that collect and drain bile from the left and right half of the liver from the biliary ductules and join external to the liver to form the common hepatic duct
Mapped by homologous gene(Total Items:44)
HP ID HP Name MP ID MP Name Annotation
HP:0001883TalipesMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000528AnophthalmiaMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0002323AnencephalyMP:0013349small Rathke's pouchreduced size of the pouch of ectoderm which grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland
HP:0000221Furrowed tongueMP:0014171increased fatty acid oxidationincreased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr
HP:0001830Postaxial foot polydactylyMP:0013901absent female preputial glandabsence of the paired, lobulated, modified sebaceous glands located on the side of the clitoris in female rodents; in contrast to the preputial glands in male rodents, clitoral glands are a minor source of olfactory stimuli contributing to sexual attracti
HP:0001177Preaxial hand polydactylyMP:0020039increased bone ossificationincrease in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance
HP:0001162Postaxial hand polydactylyMP:0014117increased pancreatic beta cell apoptosisincrease in the number of pancreatic beta cells undergoing programmed cell death
HP:0000238HydrocephalusMP:0020080increased bone mineralizationincrease in the rate at which minerals are deposited into bone
HP:0000347MicrognathiaMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0000062Ambiguous genitaliaMP:0014198absent pituitary infundibular stalkabsence of the apical portion of the tubular structure extending from the hypothalamus to the posterior lobe of the pituitary gland
HP:0001696Situs inversus totalisMP:0014185cerebellum atrophyacquired diminution of the size of the cerebellum associated with wasting as from death and reabsorption of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal
HP:0001746AspleniaMP:0020220decreased tear productiondecreased production of the amount of fluid produced in the eye
HP:0000316HypertelorismMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0000003Multicystic kidney dysplasiaMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000482MicrocorneaMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000340Sloping foreheadMP:0020040decreased bone ossificationdecrease in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance
HP:0100732Pancreatic fibrosisMP:0013502decreased fibroblast apoptosisreduction in the timing or the number of fibroblast cells undergoing programmed cell death
HP:0000518CataractMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0008053Aplasia/Hypoplasia of the irisMP:0014164abnormal ciliary process morphology any structural anomaly of any of the pigmented processes that radiate from the ciliary muscle and give attachments to ligaments supporting the lens of the eye; these processes increase in thickness as they advance from the orbiculus ciliaris to the exter
HP:0001747Accessory spleenMP:0013349small Rathke's pouchreduced size of the pouch of ectoderm which grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland
HP:0000028CryptorchidismMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0007370Aplasia/Hypoplasia of the corpus callosumMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0002084EncephaloceleMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0001305Dandy-Walker malformationMP:0013785abnormal mammary gland bud morphologyany structural anomaly of the morphologically distinct bulb of epithelial cells formed once each mammary placode expands and invaginates into the underlying mesenchyme; in mouse embryos at E12.5, each epithelial bud with its contiguous mesenchyme is eleva
HP:0010459True hermaphroditismMP:0014198absent pituitary infundibular stalkabsence of the apical portion of the tubular structure extending from the hypothalamus to the posterior lobe of the pituitary gland
HP:0006706Cystic liver diseaseMP:0013349small Rathke's pouchreduced size of the pouch of ectoderm which grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland
HP:0006487Bowing of the long bonesMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000457Depressed nasal ridgeMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000532Chorioretinal abnormalityMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000568MicrophthalmiaMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0000175Cleft palateMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0001562OligohydramniosMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0010295Aplasia/Hypoplasia of the tongueMP:0013906absent embryonic telencephalonabsence of the paired diverticula of the embryonic telencephalon, from which the forebrain develops
HP:0001737Pancreatic cystsMP:0013293embryonic lethality prior to tooth bud stagedeath prior to the appearance of tooth buds (Mus: E12-E12.5)
HP:0000647SclerocorneaMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0000073Ureteral duplicationMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000368Low-set, posteriorly rotated earsMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0002612Congenital hepatic fibrosisMP:0013504increased embryonic tissue cell apoptosisincrease in the timing or the number of cells in embryonic tissue undergoing programmed cell death
HP:0000293Full cheeksMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0000252MicrocephalyMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0000068Urethral atresiaMP:0012739abnormal anterior primitive streak morphologyany structural anomaly of the anterior region of the vertebrate primitive streak which gives rise to the axial and paraxial mesoderm, the definitive endoderm, the primitive groove, and the primitive node
HP:0000648Optic atrophyMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0000037Male pseudohermaphroditismMP:0013745abnormal eyelid margin morphologyany structural anomaly of the confluence of the mucosal surface of the conjunctiva, the edge of the orbicularis, and the cutaneous epithelium
HP:0006870Lobar holoprosencephalyMP:0014051abnormal maxillary-premaxillary suture morphologyany structural anomaly of the line of union of the two portions of the maxilla (pre- and postmaxilla)
Disease ID 762
Disease meckel syndrome
Case(Waiting for update.)