MCID: RHZ011
MIFTS: 50

Rhizomelic Chondrodysplasia Punctata, Type 1

Categories: Genetic diseases, Rare diseases, Neuronal diseases, Eye diseases, Bone diseases, Metabolic diseases, Fetal diseases

Aliases & Classifications for Rhizomelic Chondrodysplasia Punctata, Type 1

MalaCards integrated aliases for Rhizomelic Chondrodysplasia Punctata, Type 1:

Name: Rhizomelic Chondrodysplasia Punctata, Type 1 54 71 13 52 69
Rhizomelic Chondrodysplasia Punctata Type 1 12 23 50 24 56 29 14
Rcdp1 12 23 50 71
Peroxisome Biogenesis Disorder 9 12 71
Pbd9 12 71
Chondrodysplasia Punctata, Rhizomelic Form 71
Rhizomelic Chondrodysplasia Punctata 1 71
Chondrodystrophia Calcificans Punctata 71
Chondrodysplasia Punctata, Rhizomelic 69
Rcdp 1 24
Cdpr 71

Characteristics:

OMIM:

54
Inheritance:
autosomal recessive

Miscellaneous:
majority of children die before age 2


HPO:

32
rhizomelic chondrodysplasia punctata, type 1:
Inheritance autosomal recessive inheritance


GeneReviews:

23
Penetrance Penetrance is complete and the same for either sex...

Classifications:



Summaries for Rhizomelic Chondrodysplasia Punctata, Type 1

OMIM : 54
Rhizomelic chondrodysplasia punctata (RCDP) is a peroxisomal disorder characterized by disproportionately short stature primarily affecting the proximal parts of the extremities, a typical facial appearance including a broad nasal bridge, epicanthus, high-arched palate, dysplastic external ears, and micrognathia, congenital contractures, characteristic ocular involvement, dwarfism, and severe mental retardation with spasticity. Biochemically, plasmalogen synthesis and phytanic acid alpha-oxidation are defective. Most patients die in the first decade of life. RCDP1 is the most frequent form of RCDP (summary by Wanders and Waterham, 2005). Individuals with RCDP1, carrying mutations in the PEX7 gene, have cells of peroxisome biogenesis disorder (PBD) complementation group 11 (CG11, equivalent to CGR). For information on the history of PBD complementation groups, see 214100. (215100)

MalaCards based summary : Rhizomelic Chondrodysplasia Punctata, Type 1, also known as rhizomelic chondrodysplasia punctata type 1, is related to rhizomelic chondrodysplasia punctata, type 2 and rhizomelic chondrodysplasia punctata, type 3, and has symptoms including congenital cataract, spasticity and seizures. An important gene associated with Rhizomelic Chondrodysplasia Punctata, Type 1 is PEX7 (Peroxisomal Biogenesis Factor 7), and among its related pathways/superpathways are Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways and Peroxisome. Affiliated tissues include bone and eye, and related phenotypes are growth/size/body region and homeostasis/metabolism

NIH Rare Diseases : 50 rhizomelic chondrodysplasia punctata type 1 (rcdp1) is a condition that impairs the normal development of many parts of the body. the major features of this disorder include skeletal abnormalities, distinctive facial features, intellectual disability, and respiratory problems. the condition is caused by mutations in the pex7 gene. it is inherited in an autosomal recessive pattern. rhizomelic chondrodysplasia punctata type 1 is one of five types of rhizomelic chondrodysplasia punctata. the types have similar features and are distinguished by their genetic cause. last updated: 5/26/2015

UniProtKB/Swiss-Prot : 71 Rhizomelic chondrodysplasia punctata 1: A peroxisome biogenesis disorder. It is characterized by severely disturbed endochondral bone formation, rhizomelic shortening of femur and humerus, vertebral disorders, dwarfism, cataract, cutaneous lesions, facial dysmorphism, and severe mental retardation with spasticity.

Disease Ontology : 12 A rhizomelic chondrodysplasia punctata that has material basis in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the PEX7 gene on chromosome 6q23.3.

GeneReviews: NBK1270

Related Diseases for Rhizomelic Chondrodysplasia Punctata, Type 1

Diseases in the Rhizomelic Chondrodysplasia Punctata family:

Rhizomelic Chondrodysplasia Punctata, Type 2 Rhizomelic Chondrodysplasia Punctata, Type 3
Rhizomelic Chondrodysplasia Punctata, Type 1 Rhizomelic Chondrodysplasia Punctata, Type 5
Rhizomelic Chondrodysplasia Punctata Spectrum

Diseases related to Rhizomelic Chondrodysplasia Punctata, Type 1 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 24)
id Related Disease Score Top Affiliating Genes
1 rhizomelic chondrodysplasia punctata, type 2 27.5 AGPS FAR1 GNPAT PEX5 PEX5L PEX7
2 rhizomelic chondrodysplasia punctata, type 3 10.9
3 rhizomelic chondrodysplasia punctata 10.6
4 growth hormone deficiency, isolated, type ia 10.3 PEX5 PEX7
5 fgb-related congenital afibrinogenemia 10.2 HSD17B4 SCP2
6 neonatal respiratory failure 10.1
7 respiratory failure 10.1
8 metaphyseal dysplasia, braun-tinschert type 10.0 GNPAT PEX5 PEX7
9 bile acid synthesis defect, congenital, 4 10.0 ACOX1 HSD17B4 PHYH SCP2
10 heterotaxy, visceral, 4, autosomal 10.0 IL6R RBFOX2
11 congenital disorder of glycosylation, type iig 10.0 ACOX1 HSD17B4 PEX5 SCP2
12 primary autosomal recessive microcephalies and seckel syndrome spectrum disorders 9.9 PEX12 PEX2 PEX5
13 perrault syndrome 1 9.8 ACOX1 HADHB HSD17B4 PEX5 SCP2
14 leishmaniasis 9.5 GNPAT HADHB HSD17B4 PEX12 PEX2 PEX5
15 pityriasis versicolor 9.5 AGPS GNPAT PEX12 PEX2 PEX5
16 neonatal ovarian cyst 9.5 ACOX1 PEX12 PEX2 PEX5 PEX7 SCP2
17 glottis neoplasm 9.5 AGPS GNPAT HADHB PEX5 PEX7 PHYH
18 pfeiffer kapferer syndrome 9.4 HSD17B4 PEX12 PEX2 PEX5 PEX7 PHEX
19 bardet-biedl syndrome 5 9.4 AGPS GNPAT PEX5 PEX7 UROD
20 oocyte maturation defect 2 9.4 GNPAT PEX2 PEX5 PEX7 PHYH SCP2
21 pfeiffer mayer syndrome 9.0 AGPS GNPAT HADHB HSD17B4 PEX2 PEX5
22 von willebrand disease, types 2a, 2b, 2m, and 2n 9.0 AGPS FAR1 GNPAT PEX5 PEX5L PEX7
23 heimler syndrome 1 8.8 GNPAT HSD17B4 PEX12 PEX2 PEX5 PEX7
24 peroxisome biogenesis disorder 9b 4.1 ACOX1 AGPS DOK7 FAR1 GNPAT HADHB

Graphical network of the top 20 diseases related to Rhizomelic Chondrodysplasia Punctata, Type 1:



Diseases related to Rhizomelic Chondrodysplasia Punctata, Type 1

Symptoms & Phenotypes for Rhizomelic Chondrodysplasia Punctata, Type 1

Symptoms via clinical synopsis from OMIM:

54

Skeletal- Limbs:
joint contractures
symmetrical rhizomelic limb shortening
metaphyseal splaying
epiphyseal calcification

Head And Neck- Head:
microcephaly

Skin Nails & Hair- Hair:
alopecia

Skeletal- Spine:
kyphoscoliosis
coronal cleft of vertebrae

Skin Nails & Hair- Skin:
ichthyosis

Head And Neck- Ears:
sensorineural deafness

Growth- Height:
dwarfism

Skeletal:
calcific stippling of infantile cartilaginous skeleton
disappearance of stippling in first year of life

Neurologic- Central Nervous System:
mental retardation
spasticity
seizures
cortical atrophy
severe delay in myelination

Head And Neck- Face:
micrognathia
frontal bossing
flat face

Head And Neck- Mouth:
cleft palate

Head And Neck- Eyes:
congenital cataracts
upward slanting palpebral fissures

Respiratory- Lung:
respiratory insufficiency

Head And Neck- Nose:
low nasal bridge

Growth- Other:
severe failure to thrive

Laboratory- Abnormalities:
plasmalogen deficiency
acyl-coa:dihydroxyacetonephosphate acyltransferase deficiency
elevated plasma phytanic acid
unprocessed 3-oxoacyl coa thiolase


Clinical features from OMIM:

215100

Human phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 1:

32 (show all 28)
id Description HPO Frequency HPO Source Accession
1 congenital cataract 32 HP:0000519
2 spasticity 32 HP:0001257
3 seizures 32 HP:0001250
4 microcephaly 32 HP:0000252
5 micrognathia 32 HP:0000347
6 depressed nasal bridge 32 HP:0005280
7 alopecia 32 HP:0001596
8 cleft palate 32 HP:0000175
9 kyphoscoliosis 32 HP:0002751
10 frontal bossing 32 HP:0002007
11 intellectual disability 32 HP:0001249
12 cerebral cortical atrophy 32 HP:0002120
13 ichthyosis 32 HP:0008064
14 respiratory insufficiency 32 HP:0002093
15 flat face 32 HP:0012368
16 rhizomelia 32 HP:0008905
17 sensorineural hearing impairment 32 HP:0000407
18 malar flattening 32 HP:0000272
19 severe failure to thrive 32 HP:0001525
20 calcific stippling of infantile cartilaginous skeleton 32 HP:0005841
21 coronal cleft vertebrae 32 HP:0003417
22 epiphyseal stippling 32 HP:0010655
23 flexion contracture 32 HP:0001371
24 abnormality of metabolism/homeostasis 32 HP:0001939
25 upslanted palpebral fissure 32 HP:0000582
26 severe short stature 32 HP:0003510
27 flared metaphysis 32 HP:0003015
28 delayed cns myelination 32 HP:0002188

UMLS symptoms related to Rhizomelic Chondrodysplasia Punctata, Type 1:


muscle spasticity, seizures

MGI Mouse Phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 1:

44
id Description MGI Source Accession Score Top Affiliating Genes
1 growth/size/body region MP:0005378 10.25 RBFOX2 SCP2 ACOX1 DOK7 GNPAT HADHB
2 homeostasis/metabolism MP:0005376 10.24 ACOX1 AGPS GNPAT HADHB HSD17B4 IL1A
3 behavior/neurological MP:0005386 10.23 DOK7 HSD17B4 IL6R PEX2 PEX5 PEX5L
4 endocrine/exocrine gland MP:0005379 10.03 PEX2 PEX5 PEX7 ACOX1 AGPS GNPAT
5 immune system MP:0005387 10.02 ACOX1 HSD17B4 IL1A IL6R PEX5 PEX7
6 mortality/aging MP:0010768 9.97 PEX5 PEX7 PHEX PLP1 RBFOX2 UROD
7 liver/biliary system MP:0005370 9.96 SCP2 UROD ACOX1 HADHB HSD17B4 IL6R
8 nervous system MP:0003631 9.73 DOK7 GNPAT HSD17B4 IL6R PEX2 PEX5
9 reproductive system MP:0005389 9.23 ACOX1 AGPS GNPAT HSD17B4 PEX5 PEX7

Drugs & Therapeutics for Rhizomelic Chondrodysplasia Punctata, Type 1

Search Clinical Trials , NIH Clinical Center for Rhizomelic Chondrodysplasia Punctata, Type 1

Genetic Tests for Rhizomelic Chondrodysplasia Punctata, Type 1

Genetic tests related to Rhizomelic Chondrodysplasia Punctata, Type 1:

id Genetic test Affiliating Genes
1 Rhizomelic Chondrodysplasia Punctata Type 1 29 24 PEX7

Anatomical Context for Rhizomelic Chondrodysplasia Punctata, Type 1

MalaCards organs/tissues related to Rhizomelic Chondrodysplasia Punctata, Type 1:

39
Bone, Eye

Publications for Rhizomelic Chondrodysplasia Punctata, Type 1

Articles related to Rhizomelic Chondrodysplasia Punctata, Type 1:

id Title Authors Year
1
Rhizomelic Chondrodysplasia Punctata Type 1 Caused by a Novel Mutation in the PEX7 Gene. ( 25800479 )
2015
2
Whole Exome Sequencing Reveals Compound Heterozygosity for Ethnically Distinct PEX7 Mutations Responsible for Rhizomelic Chondrodysplasia Punctata, Type 1. ( 26587300 )
2015
3
Identification of a novel missense mutation of PEX7 gene in an Iranian patient with rhizomelic chondrodysplasia punctata type 1. ( 23357221 )
2013
4
Rhizomelic chondrodysplasia punctata type 1 and fulminant neonatal respiratory failure, a case report and discussion of pathophysiology. ( 22052861 )
2011
5
Rhizomelic chondrodysplasia punctata type 1: report of mutations in 3 children from India. ( 20145307 )
2010
6
Second trimester prenatal diagnosis of rhizomelic chondrodysplasia punctata type 1 on ultrasound findings. ( 20014169 )
2010
7
Mutational spectrum in the PEX7 gene and functional analysis of mutant alleles in 78 patients with rhizomelic chondrodysplasia punctata type 1. ( 11781871 )
2002
8
Rhizomelic Chondrodysplasia Punctata Type 1 ( 20301447 )
1993

Variations for Rhizomelic Chondrodysplasia Punctata, Type 1

UniProtKB/Swiss-Prot genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 1:

71
id Symbol AA change Variation ID SNP ID
1 PEX7 p.Ala218Val VAR_007726 rs121909151

ClinVar genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 1:

6 (show all 33)
id Gene Variation Type Significance SNP ID Assembly Location
1 PEX7 NM_000288.3(PEX7): c.875T> A (p.Leu292Ter) single nucleotide variant Pathogenic/Likely pathogenic rs1805137 GRCh37 Chromosome 6, 137219351: 137219351
2 PEX7 NM_000288.3(PEX7): c.653C> T (p.Ala218Val) single nucleotide variant Pathogenic rs121909151 GRCh37 Chromosome 6, 137191047: 137191047
3 PEX7 NM_000288.3(PEX7): c.649G> A (p.Gly217Arg) single nucleotide variant Pathogenic rs121909152 GRCh37 Chromosome 6, 137191043: 137191043
4 PEX7 NM_000288.3(PEX7): c.694C> T (p.Arg232Ter) single nucleotide variant Pathogenic/Likely pathogenic rs121909153 GRCh37 Chromosome 6, 137191088: 137191088
5 PEX7 NM_000288.3(PEX7): c.45_52dupGGGACGCC (p.His18Argfs) duplication Pathogenic rs199470486 GRCh37 Chromosome 6, 137143848: 137143855
6 PEX7 NM_000288.3(PEX7): c.903+1G> C single nucleotide variant Pathogenic rs148591292 GRCh37 Chromosome 6, 137219380: 137219380
7 PEX7 NM_000288.3(PEX7): c.345T> G (p.Tyr115Ter) single nucleotide variant Pathogenic/Likely pathogenic rs121909154 GRCh37 Chromosome 6, 137166758: 137166758
8 PEX7 NM_000288.3(PEX7): c.120C> G (p.Tyr40Ter) single nucleotide variant Pathogenic/Likely pathogenic rs61753238 GRCh37 Chromosome 6, 137143923: 137143923
9 PEX7 NM_000288.3(PEX7): c.40A> C (p.Thr14Pro) single nucleotide variant Pathogenic rs61753233 GRCh37 Chromosome 6, 137143843: 137143843
10 PEX7 NM_000288.3(PEX7): c.854A> G (p.His285Arg) single nucleotide variant Pathogenic rs62653611 GRCh37 Chromosome 6, 137219330: 137219330
11 PEX7 NM_000288.3(PEX7): c.74C> T (p.Ser25Phe) single nucleotide variant Likely pathogenic rs61753236 GRCh37 Chromosome 6, 137143877: 137143877
12 PEX7 NM_000288.3(PEX7): c.188+1G> C single nucleotide variant Pathogenic rs267608254 GRCh37 Chromosome 6, 137146410: 137146410
13 PEX7 NM_000288.3(PEX7): c.400G> A (p.Asp134Asn) single nucleotide variant Likely pathogenic rs764346452 GRCh37 Chromosome 6, 137166813: 137166813
14 PEX7 NM_000288.3(PEX7): c.618G> A (p.Trp206Ter) single nucleotide variant Likely pathogenic rs61753245 GRCh37 Chromosome 6, 137187856: 137187856
15 PEX7 NM_000288.3(PEX7): c.183delT (p.Phe61Leufs) deletion Likely pathogenic rs1085307085 GRCh38 Chromosome 6, 136825266: 136825266
16 PEX7 NM_000288.3(PEX7): c.13_19dupTGCGGTG (p.Gly7Valfs) duplication Pathogenic/Likely pathogenic rs62636519 GRCh38 Chromosome 6, 136822678: 136822684
17 PEX7 NM_000288.3(PEX7): c.31_56del26 (p.Met11Leufs) deletion Likely pathogenic rs1057516961 GRCh38 Chromosome 6, 136822696: 136822721
18 PEX7 NM_000288.3(PEX7): c.60C> G (p.Tyr20Ter) single nucleotide variant Likely pathogenic rs1057516882 GRCh37 Chromosome 6, 137143863: 137143863
19 PEX7 NM_000288.3(PEX7): c.81C> G (p.Tyr27Ter) single nucleotide variant Likely pathogenic rs1057516737 GRCh37 Chromosome 6, 137143884: 137143884
20 PEX7 NM_000288.3(PEX7): c.130+1G> C single nucleotide variant Likely pathogenic rs267608253 GRCh37 Chromosome 6, 137143934: 137143934
21 PEX7 NM_000288.3(PEX7): c.277C> T (p.Gln93Ter) single nucleotide variant Likely pathogenic rs763514968 GRCh38 Chromosome 6, 136826407: 136826407
22 PEX7 NM_000288.3(PEX7): c.334C> T (p.Gln112Ter) single nucleotide variant Likely pathogenic rs62653604 GRCh37 Chromosome 6, 137147602: 137147602
23 PEX7 NM_000288.3(PEX7): c.339+2T> C single nucleotide variant Likely pathogenic rs1057517059 GRCh38 Chromosome 6, 136826471: 136826471
24 PEX7 NM_000288.3(PEX7): c.508delT (p.Cys170Valfs) deletion Likely pathogenic rs1057516827 GRCh37 Chromosome 6, 137167301: 137167301
25 PEX7 NM_000288.3(PEX7): c.527-2A> G single nucleotide variant Likely pathogenic rs1057517339 GRCh38 Chromosome 6, 136866625: 136866625
26 PEX7 NM_000288.3(PEX7): c.545dupT (p.Trp183Metfs) duplication Likely pathogenic rs1057516574 GRCh38 Chromosome 6, 136866645: 136866645
27 PEX7 NM_000288.3(PEX7): c.633+1G> A single nucleotide variant Likely pathogenic rs1057516989 GRCh38 Chromosome 6, 136866734: 136866734
28 PEX7 NM_000288.3(PEX7): c.736_747+17del29 deletion Likely pathogenic rs1057517257 GRCh38 Chromosome 6, 136869992: 136870020
29 PEX7 NM_000288.3(PEX7): c.748-2A> G single nucleotide variant Likely pathogenic rs778862698 GRCh38 Chromosome 6, 136872196: 136872196
30 PEX7 NM_000288.3(PEX7): c.774_784delGGCCTCTTGCT (p.Ala259Valfs) deletion Likely pathogenic rs1057516824 GRCh38 Chromosome 6, 136872224: 136872234
31 PEX7 NM_000288.3(PEX7): c.357G> A (p.Trp119Ter) single nucleotide variant Pathogenic GRCh38 Chromosome 6, 136845632: 136845632
32 PEX7 NM_000288.3(PEX7): c.538delC (p.Leu180Terfs) deletion Pathogenic GRCh38 Chromosome 6, 136866638: 136866638
33 PEX7 NM_000288.3(PEX7): c.641T> C (p.Leu214Pro) single nucleotide variant Likely pathogenic GRCh38 Chromosome 6, 136869897: 136869897

Expression for Rhizomelic Chondrodysplasia Punctata, Type 1

Search GEO for disease gene expression data for Rhizomelic Chondrodysplasia Punctata, Type 1.

Pathways for Rhizomelic Chondrodysplasia Punctata, Type 1

GO Terms for Rhizomelic Chondrodysplasia Punctata, Type 1

Cellular components related to Rhizomelic Chondrodysplasia Punctata, Type 1 according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 mitochondrion GO:0005739 9.92 ACOX1 AGPS GNPAT HADHB HSD17B4 PEX5
2 peroxisome GO:0005777 9.9 ACOX1 AGPS FAR1 GNPAT HSD17B4 PEX12
3 peroxisomal membrane GO:0005778 9.61 ACOX1 AGPS FAR1 GNPAT HSD17B4 PEX12
4 integral component of peroxisomal membrane GO:0005779 9.43 FAR1 PEX12 PEX2
5 peroxisomal matrix GO:0005782 9.23 ACOX1 AGPS FAR1 GNPAT HSD17B4 PEX7
6 membrane GO:0016020 10.24 ACOX1 AGPS DOK7 FAR1 GNPAT HADHB

Biological processes related to Rhizomelic Chondrodysplasia Punctata, Type 1 according to GeneCards Suite gene sharing:

(show all 13)
id Name GO ID Score Top Affiliating Genes
1 lipid metabolic process GO:0006629 9.89 ACOX1 AGPS FAR1 HADHB HSD17B4
2 fatty acid metabolic process GO:0006631 9.76 ACOX1 HADHB HSD17B4 PHYH
3 fatty acid beta-oxidation using acyl-CoA oxidase GO:0033540 9.58 ACOX1 HSD17B4 SCP2
4 protein import into peroxisome matrix GO:0016558 9.56 PEX12 PEX2 PEX5 PEX7
5 peroxisome organization GO:0007031 9.55 PEX12 PEX2 PEX5 PEX7 SCP2
6 alpha-linolenic acid metabolic process GO:0036109 9.54 ACOX1 HSD17B4 SCP2
7 bile acid biosynthetic process GO:0006699 9.52 HSD17B4 SCP2
8 cellular lipid metabolic process GO:0044255 9.51 GNPAT PEX5
9 very long-chain fatty acid metabolic process GO:0000038 9.5 ACOX1 HSD17B4 PEX2
10 protein targeting to peroxisome GO:0006625 9.48 PEX12 PEX7
11 protein import into peroxisome matrix, docking GO:0016560 9.43 PEX5 PEX5L
12 ether lipid biosynthetic process GO:0008611 9.26 AGPS FAR1 GNPAT PEX7
13 fatty acid beta-oxidation GO:0006635 9.1 ACOX1 HADHB HSD17B4 PEX2 PEX5 PEX7

Molecular functions related to Rhizomelic Chondrodysplasia Punctata, Type 1 according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 oxidoreductase activity GO:0016491 9.65 ACOX1 AGPS FAR1 HSD17B4 PHYH
2 small GTPase binding GO:0031267 9.4 PEX5 PEX5L
3 transferase activity, transferring acyl groups other than amino-acyl groups GO:0016747 9.37 HADHB SCP2
4 FAD binding GO:0071949 9.32 ACOX1 AGPS
5 3-hydroxyacyl-CoA dehydrogenase activity GO:0003857 9.16 HADHB HSD17B4
6 peroxisome targeting sequence binding GO:0000268 8.96 PEX5 PEX5L
7 peroxisome matrix targeting signal-1 binding GO:0005052 8.62 PEX5 PEX5L

Sources for Rhizomelic Chondrodysplasia Punctata, Type 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
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33 ICD10
34 ICD10 via Orphanet
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36 IUPHAR
37 KEGG
38 LifeMap
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42 MeSH
43 MESH via Orphanet
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55 OMIM via Orphanet
59 PubMed
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65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
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