MCID: RHZ014
MIFTS: 46

Rhizomelic Chondrodysplasia Punctata, Type 2

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

Aliases & Classifications for Rhizomelic Chondrodysplasia Punctata, Type 2

MalaCards integrated aliases for Rhizomelic Chondrodysplasia Punctata, Type 2:

Name: Rhizomelic Chondrodysplasia Punctata, Type 2 54 71 69
Rhizomelic Chondrodysplasia Punctata Type 2 12 50 24 56 29 14
Dihydroxyacetonephosphate Acyltransferase Deficiency 12 50 71 52
Dhapat Deficiency 12 50 24 71
Peroxisomal Dihydroxyacetonephosphate Acyltransferase Deficiency 12 50 71
Rcdp2 12 50 71
Chondrodysplasia Punctata, Rhizomelic, Due to Dihydroxyacetonephosphate Acyltransferase Deficiency 12 71
Glyceronephosphate O-Acyltransferase Deficiency 12 71
Gnpat Deficiency 12 71
Chondrodysplasia Punctata, Rhizomelic, Due to Dihydroxyacetonephosphate 50
Chondrodysplasia Punctata, Rhizomelic, Type 2 13
Type 2 Rhizomelic Chondrodysplasia Punctata 50
Rhizomelic Chondrodysplasia Punctata 2 71
Glyceronephosphate O-Acyltransferase 13
Rcdp 2 24

Characteristics:

OMIM:

54
Inheritance:
autosomal recessive


HPO:

32
rhizomelic chondrodysplasia punctata, type 2:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Rhizomelic Chondrodysplasia Punctata, Type 2

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 (215100) is the most frequent form of RCDP (summary by Wanders and Waterham, 2005). Whereas RCDP1 is a peroxisomal biogenesis disorder (PBD), RCDP2 is classified as a single peroxisome enzyme deficiency (Waterham and Ebberink, 2012). For a discussion of genetic heterogeneity of rhizomelic chondrodysplasia punctata, see 215100. (222765)

MalaCards based summary : Rhizomelic Chondrodysplasia Punctata, Type 2, also known as rhizomelic chondrodysplasia punctata type 2, is related to porphyria cutanea tarda and growth hormone deficiency, isolated, type ia, and has symptoms including failure to thrive, scoliosis and high forehead. An important gene associated with Rhizomelic Chondrodysplasia Punctata, Type 2 is GNPAT (Glyceronephosphate O-Acyltransferase), and among its related pathways/superpathways are Peroxisome and Peroxisomal lipid metabolism. Affiliated tissues include bone and eye, and related phenotypes are behavior/neurological and homeostasis/metabolism

Disease Ontology : 12 A rhizomelic chondrodysplasia punctata that has material basis in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the GNPAT gene on chromosome 1q42.2.

UniProtKB/Swiss-Prot : 71 Rhizomelic chondrodysplasia punctata 2: A form of rhizomelic chondrodysplasia punctata, a disease 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.

Related Diseases for Rhizomelic Chondrodysplasia Punctata, Type 2

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 2 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 29)
id Related Disease Score Top Affiliating Genes
1 porphyria cutanea tarda 29.3 HAMP HFE UROD
2 growth hormone deficiency, isolated, type ia 10.6 PEX5 PEX7
3 leishmaniasis 10.5 GNPAT PEX5
4 metaphyseal dysplasia, braun-tinschert type 10.4 GNPAT PEX5 PEX7
5 pityriasis versicolor 10.4 AGPS GNPAT PEX5
6 rhizomelic chondrodysplasia punctata 10.3
7 congenital disorder of glycosylation, type iig 10.2 CAT PEX5
8 perrault syndrome 1 10.1 CAT PEX5
9 porphyria 10.1
10 familial porphyria cutanea tarda 10.1
11 neonatal ovarian cyst 10.0 CAT PEX5 PEX7
12 glottis neoplasm 10.0 AGPS GNPAT PEX5 PEX7 PHYH
13 bardet-biedl syndrome 5 9.9 AGPS GNPAT PEX5 PEX7 UROD
14 multiple symmetrical lipomatosis 9.9 HFE UROD
15 glycogen storage disease ixa 9.8 HAMP HFE
16 porphyria variegata 9.8 HFE UROD
17 tinf2-related dyskeratosis congenita 9.7 HAMP HFE
18 pfeiffer kapferer syndrome 9.6 CAT PEX5 PEX7 PHEX
19 slate pneumoconiosis 9.6 HFE UROD
20 oocyte maturation defect 2 9.6 CAT GNPAT PEX5 PEX7 PHYH
21 ovarian clear cell malignant adenofibroma 9.5 HAMP HFE PEX5
22 narcolepsy 9.5 HAMP HFE
23 nasu-hakola disease 9.4 HAMP HFE UROD
24 pfeiffer mayer syndrome 9.4 AGPS CAT GNPAT PEX5 PEX7 PHYH
25 episcleritis periodica fugax 9.2 HAMP HFE
26 heimler syndrome 1 9.2 CAT GNPAT PEX5 PEX7 PHEX PHYH
27 tendinosis 9.2 CAT HAMP HFE
28 von willebrand disease, types 2a, 2b, 2m, and 2n 9.0 AGPS FAR1 GNPAT PEX5 PEX5L PEX7
29 peroxisome biogenesis disorder 9b 8.1 AGPS FAR1 GNPAT PEX5 PEX5L PEX7

Graphical network of the top 20 diseases related to Rhizomelic Chondrodysplasia Punctata, Type 2:



Diseases related to Rhizomelic Chondrodysplasia Punctata, Type 2

Symptoms & Phenotypes for Rhizomelic Chondrodysplasia Punctata, Type 2

Symptoms via clinical synopsis from OMIM:

54

Growth- Other:
failure to thrive

Skeletal- Spine:
scoliosis
irregular vertebral endplates

Head And Neck- Nose:
anteverted nostrils
broad nasal bridge
low nasal bridge

Head And Neck- Head:
microcephaly
large fontanelles

Skeletal- Limbs:
rhizomelic shortening
short humeri
short femora

Skeletal:
contractures
osteopenia
calcific stippling

Laboratory- Abnormalities:
decreased plasmalogens
normal phytanic acid
decreased dihydroxyacetonephosphate acyltransferase (dhap-at) activity

Head And Neck- Mouth:
high-arched palate

Neurologic- Central Nervous System:
hypotonia
mental retardation

Head And Neck- Face:
high forehead
micrognathia

Growth- Height:
short stature, disproportionate

Head And Neck- Eyes:
cataract

Skeletal- Pelvis:
stippled calcification proximal humeral epiphyses


Clinical features from OMIM:

222765

Human phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 2:

32 (show all 21)
id Description HPO Frequency HPO Source Accession
1 failure to thrive 32 HP:0001508
2 scoliosis 32 HP:0002650
3 high forehead 32 HP:0000348
4 microcephaly 32 HP:0000252
5 micrognathia 32 HP:0000347
6 depressed nasal bridge 32 HP:0005280
7 large fontanelles 32 HP:0000239
8 anteverted nares 32 HP:0000463
9 intellectual disability 32 HP:0001249
10 cataract 32 HP:0000518
11 wide nasal bridge 32 HP:0000431
12 osteopenia 32 HP:0000938
13 high palate 32 HP:0000218
14 calcific stippling 32 HP:0002832
15 irregular vertebral endplates 32 HP:0003301
16 stippled calcification proximal humeral epiphyses 32 HP:0008838
17 rhizomelia 32 HP:0008905
18 muscular hypotonia 32 HP:0001252
19 short humerus 32 HP:0005792
20 flexion contracture 32 HP:0001371
21 abnormality of pelvic girdle bone morphology 32 HP:0002644

MGI Mouse Phenotypes related to Rhizomelic Chondrodysplasia Punctata, Type 2:

44
id Description MGI Source Accession Score Top Affiliating Genes
1 behavior/neurological MP:0005386 10.1 C3 CTSC HFE NTS PEX5 PEX5L
2 homeostasis/metabolism MP:0005376 10.07 AGPS C3 CAT CTSC GNPAT HFE
3 cellular MP:0005384 10.02 C3 CAT CTSC PEX7 GNPAT PHEX
4 growth/size/body region MP:0005378 10.02 PLP1 C3 CTSC GNPAT HFE NTS
5 nervous system MP:0003631 9.7 CTSC GNPAT HFE NTS PEX5 PEX5L
6 liver/biliary system MP:0005370 9.63 C3 HFE PEX5 PEX7 PHYH UROD
7 reproductive system MP:0005389 9.17 AGPS C3 GNPAT PEX5 PEX7 PHYH

Drugs & Therapeutics for Rhizomelic Chondrodysplasia Punctata, Type 2

Search Clinical Trials , NIH Clinical Center for Rhizomelic Chondrodysplasia Punctata, Type 2

Genetic Tests for Rhizomelic Chondrodysplasia Punctata, Type 2

Genetic tests related to Rhizomelic Chondrodysplasia Punctata, Type 2:

id Genetic test Affiliating Genes
1 Rhizomelic Chondrodysplasia Punctata Type 2 29 24 GNPAT

Anatomical Context for Rhizomelic Chondrodysplasia Punctata, Type 2

MalaCards organs/tissues related to Rhizomelic Chondrodysplasia Punctata, Type 2:

39
Bone, Eye

Publications for Rhizomelic Chondrodysplasia Punctata, Type 2

Articles related to Rhizomelic Chondrodysplasia Punctata, Type 2:

id Title Authors Year
1
Abnormal myelin formation in rhizomelic chondrodysplasia punctata type 2 (DHAPAT-deficiency). ( 10972423 )
2000
2
Acyl-CoA:dihydroxyacetonephosphate acyltransferase: cloning of the human cDNA and resolution of the molecular basis in rhizomelic chondrodysplasia punctata type 2. ( 9536089 )
1998

Variations for Rhizomelic Chondrodysplasia Punctata, Type 2

UniProtKB/Swiss-Prot genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 2:

71
id Symbol AA change Variation ID SNP ID
1 GNPAT p.Arg211Cys VAR_006357 rs121434440
2 GNPAT p.Arg211His VAR_006358 rs121434439
3 GNPAT p.Asp519Gly VAR_025897 rs11558492

ClinVar genetic disease variations for Rhizomelic Chondrodysplasia Punctata, Type 2:

6
id Gene Variation Type Significance SNP ID Assembly Location
1 GNPAT NM_014236.3(GNPAT): c.632G> A (p.Arg211His) single nucleotide variant Pathogenic rs121434439 GRCh37 Chromosome 1, 231401102: 231401102
2 GNPAT NM_014236.3(GNPAT): c.631C> T (p.Arg211Cys) single nucleotide variant Pathogenic rs121434440 GRCh37 Chromosome 1, 231401101: 231401101
3 GNPAT GNPAT, 2-BP INS, 848TT insertion Pathogenic
4 GNPAT GNPAT, 1-BP DEL, NT780 deletion Pathogenic
5 GNPAT GNPAT, 1-BP DEL, NT1575 deletion Pathogenic
6 GNPAT GNPAT, IVS9AS, T-G, -3 single nucleotide variant Pathogenic
7 GNPAT GNPAT, 2-BP DEL, 1429AT deletion Pathogenic
8 GNPAT GNPAT, IVS14DS, G-A, +5 single nucleotide variant Pathogenic

Expression for Rhizomelic Chondrodysplasia Punctata, Type 2

Search GEO for disease gene expression data for Rhizomelic Chondrodysplasia Punctata, Type 2.

Pathways for Rhizomelic Chondrodysplasia Punctata, Type 2

Pathways related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

id Super pathways Score Top Affiliating Genes
1 11.14 AGPS CAT FAR1 GNPAT PEX5 PEX5L
2
Show member pathways
10.86 AGPS GNPAT PHYH
3
Show member pathways
10.62 AGPS GNPAT
4 10 HAMP HFE

GO Terms for Rhizomelic Chondrodysplasia Punctata, Type 2

Cellular components related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 peroxisomal membrane GO:0005778 9.63 AGPS CAT FAR1 GNPAT PEX5 PEX5L
2 peroxisome GO:0005777 9.5 AGPS CAT FAR1 GNPAT PEX5 PEX7
3 peroxisomal matrix GO:0005782 9.1 AGPS CAT FAR1 GNPAT PEX7 PHYH

Biological processes related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

(show all 13)
id Name GO ID Score Top Affiliating Genes
1 aging GO:0007568 9.67 CAT CTSC HAMP
2 acute-phase response GO:0006953 9.52 HAMP HFE
3 liver regeneration GO:0097421 9.51 HAMP HFE
4 peroxisome organization GO:0007031 9.48 PEX5 PEX7
5 response to iron ion GO:0010039 9.46 HAMP HFE
6 response to vitamin A GO:0033189 9.43 CAT HAMP
7 response to fatty acid GO:0070542 9.4 CAT GNPAT
8 cellular lipid metabolic process GO:0044255 9.37 GNPAT PEX5
9 multicellular organismal iron ion homeostasis GO:0060586 9.32 HAMP HFE
10 protein import into peroxisome matrix GO:0016558 9.26 PEX5 PEX7
11 protein import into peroxisome matrix, docking GO:0016560 9.16 PEX5 PEX5L
12 response to iron ion starvation GO:1990641 8.96 HAMP HFE
13 ether lipid biosynthetic process GO:0008611 8.92 AGPS FAR1 GNPAT PEX7

Molecular functions related to Rhizomelic Chondrodysplasia Punctata, Type 2 according to GeneCards Suite gene sharing:

id Name GO ID Score Top Affiliating Genes
1 receptor binding GO:0005102 9.56 C3 CAT GNPAT HFE
2 small GTPase binding GO:0031267 9.16 PEX5 PEX5L
3 peroxisome targeting sequence binding GO:0000268 8.96 PEX5 PEX5L
4 peroxisome matrix targeting signal-1 binding GO:0005052 8.62 PEX5 PEX5L

Sources for Rhizomelic Chondrodysplasia Punctata, Type 2

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 MedGen
42 MeSH
43 MESH via Orphanet
44 MGI
46 NCI
47 NCIt
48 NDF-RT
51 NINDS
52 Novoseek
54 OMIM
55 OMIM via Orphanet
59 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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