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eRAM

encyclopedia of Rare Disease Annotation for Precision Medicine



   pycnodysostosis
  

Disease ID 146
Disease pycnodysostosis
Definition
Rare autosomal recessive syndrome characterized by delayed closing of CRANIAL SUTURES, short stature, ACRO-OSTEOLYSIS of distal phalanges, dental and MAXILLOFACIAL ABNORMALITIES and an increase in bone density that results in frequent BONE FRACTURES. It is associated with BONE RESORPTION defect due to mutations in the lysosomal cysteine protease CATHEPSIN K.
Synonym
maroteaux-lamy pyknodysostosis syndrome
maroteaux-lamy syndrome 2
maroteaux-lamy syndrome ii
pknd
pycd
pycnodysostoses
pycnodysostosis (disorder)
pycnodysostosis [disease/finding]
pyknodysostoses
pyknodysostosis
pyknodysostosis (disorder)
stanesco's dysostosis syndrome
Orphanet
OMIM
DOID
UMLS
C0238402
MeSH
SNOMED-CT
Comorbidity
UMLS | Disease | Sentences' Count(Total Sentences:7)
C0029443  |  osteomyelitis  |  2
C0008928  |  cleidocranial dysplasia  |  1
C0037315  |  sleep apnea  |  1
C0010278  |  craniosynostosis  |  1
C0041296  |  tuberculosis  |  1
C0032827  |  k deficiency  |  1
C0028754  |  obesity  |  1
Curated Gene
Entrez_id | Symbol | Resource(Total Genes:1)
1513  |  CTSK  |  CLINVAR;CTD_human;ORPHANET;UNIPROT
Inferring Gene(Waiting for update.)
Text Mined Gene
Entrez_id | Symbol | Score | Resource(Total Genes:15)
249  |  ALPL  |  1.726  |  DISEASES
632  |  BGLAP  |  1.15  |  DISEASES
796  |  CALCA  |  1.612  |  DISEASES
799  |  CALCR  |  1.776  |  DISEASES
1186  |  CLCN7  |  3.73  |  DISEASES
1435  |  CSF1  |  1.031  |  DISEASES
1520  |  CTSS  |  3.21  |  DISEASES
1893  |  ECM1  |  2.232  |  DISEASES
128178  |  EDARADD  |  2.94  |  DISEASES
3570  |  IL6R  |  1.554  |  DISEASES
4170  |  MCL1  |  1.55  |  DISEASES
58484  |  NLRC4  |  1.83  |  DISEASES
5251  |  PHEX  |  1.01  |  DISEASES
5744  |  PTHLH  |  1.624  |  DISEASES
6696  |  SPP1  |  1.366  |  DISEASES
Locus
Symbol | Locus(Total Locus:1)
CTSK  |  1q21.3
Disease ID 146
Disease pycnodysostosis
Integrated Phenotype
HPO | Name(Total Integrated Phenotypes:66)
HP:0011800  |  Midface retrusion
HP:0000520  |  Proptosis
HP:0000670  |  Dental caries
HP:0006335  |  Delayed loss of primary teeth
HP:0002653  |  Bone pain
HP:0004474  |  Front fontanelle stays open
HP:0000347  |  Hypoplasia of mandible
HP:0003302  |  Spondylolithesis
HP:0004322  |  Short stature
HP:0100543  |  Cognitive impairment
HP:0009839  |  Osteolytic defects of the outermost finger bone of the hand
HP:0000248  |  Brachycephaly
HP:0000696  |  Delayed eruption of secondary dentition
HP:0000592  |  Blue sclerae
HP:0005930  |  Abnormality of epiphysis morphology
HP:0002645  |  Wormian bones
HP:0002793  |  Abnormal pattern of respiration
HP:0002797  |  Osteolysis
HP:0002644  |  Abnormality of pelvic girdle bone morphology
HP:0001807  |  Ridged nail
HP:0003304  |  Spondylolysis
HP:0001156  |  Brachydactyly syndrome
HP:0004322  |  Stature below 3rd percentile
HP:0002652  |  Skeletal dysplasia
HP:0002007  |  Frontal bossing
HP:0003307  |  Hyperlordosis
HP:0006482  |  Abnormality of dental morphology
HP:0000164  |  Abnormality of the teeth
HP:0000684  |  Delayed eruption of teeth
HP:0000774  |  Narrow chest
HP:0002007  |  Frontal protruberance
HP:0000189  |  Decreased transverse dimension of palate
HP:0001903  |  Anemia
HP:0000271  |  Abnormality of the face
HP:0000924  |  Abnormality of the skeletal system
HP:0000889  |  Abnormality of the clavicle
HP:0001831  |  Short toe
HP:0000925  |  Abnormality of the vertebral column
HP:0002754  |  Osteomyelitis
HP:0000269  |  Protruding occiput
HP:0011001  |  Increased bone mineral density
HP:0002688  |  Absent frontal sinuses
HP:0001807  |  Grooved nails
HP:0001156  |  Brachydactyly
HP:0002650  |  Scoliosis
HP:0000951  |  Abnormality of the skin
HP:0002757  |  Recurrent fractures
HP:0003468  |  Abnormality of the vertebrae
HP:0002808  |  Kyphosis
HP:0000272  |  Malar flattening
HP:0002240  |  Hepatomegaly
HP:0000680  |  Late eruption of primary teeth
HP:0001231  |  Abnormality of the fingernails
HP:0001597  |  Abnormality of the nail
HP:0001744  |  Splenomegaly
HP:0000448  |  Big nose
HP:0002644  |  Abnormal shape of pelvic girdle bone
HP:0009106  |  Abnormal pelvis bone ossification
HP:0000348  |  High forehead
HP:0002645  |  Extra bones within cranial sutures
HP:0000765  |  Abnormality of the thorax
HP:0004474  |  Persistent open anterior fontanelle
HP:0000189  |  Narrow palate
HP:0000238  |  Hydrocephalus
HP:0000668  |  Failure of development of between one and six teeth
HP:0009882  |  Short distal phalanx of finger
Text Mined Phenotype
HPO | Name | Sentences' Count(Total Phenotypes:8)
Disease ID 146
Disease pycnodysostosis
Manually Symptom
UMLS  | Name(Total Manually Symptoms:6)
C1390474  |  bone fragility
C0410656  |  isthmic spondylolisthesis
C0238074  |  cor pulmonale
C0038018  |  spondylolysis
C0032827  |  k deficiency
C0003864  |  arthritis
Text Mined Symptom
UMLS | Name | Sentences' Count(Total Symptoms:1)
C0032827  |  k deficiency  |  1
Manually Genotype(Total Manually Genotypes:2)
Gene Mutation DOI Article Title
CTSKc.26T>C / c.27T>C, p.L9P / p.L9Pdoi:10.1038/gim.2015.129Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing
CTSKc.26T>C / c.508T>A, p.L9P / p.C170Sdoi:10.1038/gim.2015.129Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing
Text Mining Genotype(Total Genotypes:0)
(Waiting for update.)
All Snps(Total Genotypes:9)
snpId pubmedId geneId geneSymbol diseaseId sourceId sentence score Year geneSymbol_dbSNP CHROMOSOME POS REF ALT
rs29001685NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150796863AG
rs29001685108786631513CTSKumls:C0238402UNIPROTCathepsin K gene mutations and 1q21 haplotypes in at patients with pycnodysostosis in an outbred population.0.5678718142000CTSK1150796863AG
rs74315301NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150796799TC
rs74315302NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150804203CG
rs74315303NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150799607GT,A
rs74315304NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150799228GA
rs7431530495293531513CTSKumls:C0238402BeFreeMolecular analysis of a patient affected by the autosomal recessive skeletal dysplasia, pycnodysostosis (cathepsin K deficiency; MIM 265800), revealed homozygosity for a novel missense mutation (A277V).0.5678718141998CTSK1150799228GA
rs74315305NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150806109CT
rs74315306NA1513CTSKumls:C0238402CLINVARNA0.567871814NACTSK1150806191TA
GWASdb Annotation(Total Genotypes:0)
(Waiting for update.)
GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)
Mapped by lexical matching(Total Items:31)
HP ID HP Name MP ID MP Name Annotation
HP:0000670Carious teethMP:0004033supernumerary teethoccurrence of more than the usual number of teeth
HP:0002645Wormian bonesMP:0008915fused carpal bonesanomaly of the nine nodular bones of the joint between the forelimb bones and the front paws/hands resulting in some or all the bones being joined together
HP:0005930Abnormality of epiphysis morphologyMP: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:0003468Abnormality of the vertebraeMP:0009657failure of chorioallantoic fusionfailure to initiate and/or complete the formation of a highly vascularized extra-embryonic fetal membrane by fusion of the chorion and allantois
HP:0000774Narrow chestMP:0004134abnormal chest morphologyany structural anomaly of the part of the body between the neck and the abdomen
HP:0000924Abnormality of the skeletal systemMP: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:0009106Abnormal pelvis bone ossificationMP:0003055abnormal long bone epiphyseal plate morphologyany structural anomaly of the cartilaginous center of ossification located at one or both ends of bones between the epiphysis (end) and the diaphysis (shaft) of long bones; longitudinal growth of the bone occurs at the plate during development in children
HP:0006335Persistence of primary teethMP: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:0002644Abnormality of pelvic girdle bone morphologyMP:0013620increased internal diameter of femurincreased 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:0000696Delayed eruption of permanent teethMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0004474Persistent open anterior fontanelleMP:0001302eyelids open at birthopen eyes instead of closed at perinatal stage; failure of the upper and lower thin folds of skin and muscle that cover the exposed portion of the eye to fuse completely together during development and an individual is born with the eye(s) uncovered leadi
HP:0000925Abnormality of the vertebral columnMP:0009005abnormal sesamoid bone of gastrocnemius morphologyany structural anomaly of the small sesamoid bones situated behind the condyles of the femur
HP:0000951Abnormality of the skinMP:0013620increased internal diameter of femurincreased 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:0006482Abnormality of dental morphologyMP:0012069abnormal horizontal basal cell of olfactory epithelium morphologyany structural anomaly of the flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells, that lie in contact with the bas
HP:0000189Narrow palateMP:0009653abnormal palate developmentabnormal formation of the roof of the mouth in vertebrates formed anteriorly by a bony projection of the upper jaw (hard palate) and posteriorly by the fold of connective tissue (soft palate)
HP:0011800Hypoplasia of midfaceMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0001597Abnormality of the nailMP:0011205excessive folding of visceral yolk sacthe appearance of wrinkles or folds on the surface of the visceral yolk sac
HP:0002757Recurrent fracturesMP:0004675rib fracturesa crack or break in the bones forming the bony wall of the chest
HP:0001807Ridged nailMP:0012405abnormal nail matrix morphologyany structural anomaly of the nail-forming area of the nail bed comprised of a germinal matrix, responsible for most of the nail production, and the sterile matrix, a secondary site of nail production which is tightly adherent to the nail plate
HP:0001231Abnormality of the fingernailsMP:0012069abnormal horizontal basal cell of olfactory epithelium morphologyany structural anomaly of the flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells, that lie in contact with the bas
HP:0000765Abnormality of the thoraxMP:0013620increased internal diameter of femurincreased 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:0000680Delayed eruption of primary teethMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0011001Increased bone mineral densityMP:0013630increased bone trabecular spacingincrease in the amount of space between trabeculae in cancellous bone
HP:0000684Delayed eruption of teethMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0009882Short distal phalanx of fingerMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0002793Abnormal pattern of respirationMP:0010954abnormal cellular respirationanomaly in the enzymatic release of energy from organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration)
HP:0000448Prominent noseMP:0002233abnormal nose morphologyany structural anomaly of the organ that is specialized for smell and is part of the respiratory system
HP:0000164Abnormality of the teethMP:0010382abnormal dosage compensation, by inactivation of X chromosomeanomaly in the process of compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex
HP:0000889Abnormality of the clavicleMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0000271Abnormality of the faceMP:0009889persistence of medial edge epithelium during palatal shelf fusionpalatal shelves meet at the midline during development but do not adhere along the medial edge epithelia, and fail to form the midline epithelial seam
HP:0009839Osteolytic defects of the distal phalanges of the handMP:0009536abnormal interstitial cell of Cajal morphologyany structural anomaly in the type of cell found in the gastrointestinal tract and serving as a pacemaker that triggers gut contraction; ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which
Mapped by homologous gene(Total Items:58)
HP ID HP Name MP ID MP Name Annotation
HP:0002650ScoliosisMP:0020309increased creatine kinase activityincreased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
HP:0002754OsteomyelitisMP:0020080increased bone mineralizationincrease in the rate at which minerals are deposited into bone
HP:0002645Wormian bonesMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0002653Bone painMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0005930Abnormality of epiphysis morphologyMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000164Abnormality of the teethMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000774Narrow chestMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0003307HyperlordosisMP:0020309increased creatine kinase activityincreased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
HP:0000680Delayed eruption of primary teethMP: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:0006335Persistence of primary teethMP:0020080increased bone mineralizationincrease in the rate at which minerals are deposited into bone
HP:0000592Blue scleraeMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0004322Short statureMP: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:0002240HepatomegalyMP:0020329decreased capillary densityreduction in the number of capillaries in a given cross-sectional area of a tissue
HP:0003302SpondylolisthesisMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0000347MicrognathiaMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0001903AnemiaMP:0020316decreased vascular endothelial cell proliferationdecrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0003304SpondylolysisMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000925Abnormality of the vertebral columnMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0001744SplenomegalyMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000238HydrocephalusMP:0020080increased bone mineralizationincrease in the rate at which minerals are deposited into bone
HP:0100543Cognitive impairmentMP:0020316decreased vascular endothelial cell proliferationdecrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0002797OsteolysisMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000889Abnormality of the clavicleMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000271Abnormality of the faceMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0000269Prominent occiputMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0009882Short distal phalanx of fingerMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000189Narrow palateMP: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:0001231Abnormality of the fingernailsMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000696Delayed eruption of permanent teethMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0000248BrachycephalyMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000765Abnormality of the thoraxMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0001156Brachydactyly syndromeMP:0020157abnormal behavioral response to alcoholany anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior
HP:0000670Carious teethMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0002757Recurrent fracturesMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0001597Abnormality of the nailMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000348High foreheadMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0009106Abnormal pelvis bone ossificationMP:0013178tail necrosismorphological changes resulting from pathological death of tail tissue; usually due to irreversible damage
HP:0000520ProptosisMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0004474Persistent open anterior fontanelleMP:0020010decreased bone mineral density of femurreduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh
HP:0002793Abnormal pattern of respirationMP:0013572abnormal parathyroid gland chief cell morphologyany structural anomaly of an epithelial cell that are collectively arranged in wide, irregular interconnecting columns in the parathyroid gland, that is responsible for the synthesis and secretion of parathyroid hormone (PTH)
HP:0011001Increased bone mineral densityMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0003468Abnormality of the vertebraeMP: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:0001831Short toeMP: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:0000924Abnormality of the skeletal systemMP:0014071increased cardiac muscle glycogen levelgreater than the normal concentration of a readily converted carbohydrate reserve in heart muscle
HP:0002652Skeletal dysplasiaMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000684Delayed eruption of teethMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0001807Ridged nailMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000272Malar flatteningMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0011800Hypoplasia of midfaceMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0009839Osteolytic defects of the distal phalanges of the handMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0002644Abnormality of pelvic girdle bone morphologyMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0002808KyphosisMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000448Prominent noseMP:0020157abnormal behavioral response to alcoholany anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior
HP:0000668HypodontiaMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0002007Frontal bossingMP: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:0000951Abnormality of the skinMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0006482Abnormality of dental morphologyMP:0014176abnormal cilary zonule morphologyany structural anomaly of the circumferential suspensory ligaments that anchor the lens to the ciliary process and are made of bundles of fibrillin microfibrils, an elaborate system of fibers that spans the gap between the lens and the adjacent nonpigment
HP:0002688Absent frontal sinusesMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
Disease ID 146
Disease pycnodysostosis
Case(Waiting for update.)